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  1. Book ; Online: DISCO

    Qin, Minghai / Sun, Chao / Hofmann, Jaco / Vucinic, Dejan

    Distributed Inference with Sparse Communications

    2023  

    Abstract: Deep neural networks (DNNs) have great potential to solve many real-world problems, but they usually require an extensive amount of computation and memory. It is of great difficulty to deploy a large DNN model to a single resource-limited device with ... ...

    Abstract Deep neural networks (DNNs) have great potential to solve many real-world problems, but they usually require an extensive amount of computation and memory. It is of great difficulty to deploy a large DNN model to a single resource-limited device with small memory capacity. Distributed computing is a common approach to reduce single-node memory consumption and to accelerate the inference of DNN models. In this paper, we explore the "within-layer model parallelism", which distributes the inference of each layer into multiple nodes. In this way, the memory requirement can be distributed to many nodes, making it possible to use several edge devices to infer a large DNN model. Due to the dependency within each layer, data communications between nodes during this parallel inference can be a bottleneck when the communication bandwidth is limited. We propose a framework to train DNN models for Distributed Inference with Sparse Communications (DISCO). We convert the problem of selecting which subset of data to transmit between nodes into a model optimization problem, and derive models with both computation and communication reduction when each layer is inferred on multiple nodes. We show the benefit of the DISCO framework on a variety of CV tasks such as image classification, object detection, semantic segmentation, and image super resolution. The corresponding models include important DNN building blocks such as convolutions and transformers. For example, each layer of a ResNet-50 model can be distributively inferred across two nodes with five times less data communications, almost half overall computations and half memory requirement for a single node, and achieve comparable accuracy to the original ResNet-50 model. This also results in 4.7 times overall inference speedup.
    Keywords Computer Science - Computer Vision and Pattern Recognition
    Subject code 006
    Publishing date 2023-02-22
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Ovalbumin interaction with polystyrene and polyethylene terephthalate microplastics alters its structural properties.

    Gligorijevic, Nikola / Lujic, Tamara / Mutic, Tamara / Vasovic, Tamara / de Guzman, Maria Krishna / Acimovic, Jelena / Stanic-Vucinic, Dragana / Cirkovic Velickovic, Tanja

    International journal of biological macromolecules

    2024  Volume 267, Issue Pt 2, Page(s) 131564

    Abstract: Contaminating microplastics can interact with food proteins in the food matrix and during digestion. This study investigated adsorption of chicken egg protein ovalbumin to polystyrene (PS, 110 and 260 μm) and polyethylene terephthalate (PET, 140 μm) MPs ... ...

    Abstract Contaminating microplastics can interact with food proteins in the food matrix and during digestion. This study investigated adsorption of chicken egg protein ovalbumin to polystyrene (PS, 110 and 260 μm) and polyethylene terephthalate (PET, 140 μm) MPs in acidic and neutral conditions and alterations in ovalbumin structure. Ovalbumin adsorption affinity depended on MPs size (smaller > larger), type (PS > PET) and pH (pH 3 > pH 7). In bulk solution, MPs does not change ovalbumin secondary structure significantly, but induces loosening (at pH 3) and tightening (at pH 7) of tertiary structure. Formed soft corona exclusively consists of full length non-native ovalbumin, while in hard corona also shorter ovalbumin fragments were found. At pH 7 soft corona ovalbumin has rearranged but still preserved level of ordered secondary structure, resulting in preserved thermostability and proteolytic stability, but decreased ability to form fibrils upon heating. Secondary structure changes in soft corona resemble changes in native ovalbumin induced by heat treatment (80 °C). Ovalbumin is abundantly present in corona around microplastics also in the presence of other egg white proteins. These results imply that microplastics contaminating food may bind and change structure and functional properties of the main egg white protein.
    Language English
    Publishing date 2024-04-16
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2024.131564
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Transcranial brain parenchyma sonography in patients with juvenile myoclonic epilepsy.

    Djordjević, Ivana / Djordjević, Stefan / Kosać, Ana / Vučinić, Dragana / Ivanović Radović, Nelica / Ždraljević, Mirjana / Mijajlović, Milija

    Acta neurologica Belgica

    2024  

    Abstract: Introduction: There are rising evidences that subcortical structures, including the basal ganglia, are affected in patients with epilepsy. These structures are thought to influence the modulation and phenotypic expression of epileptic seizures. Our ... ...

    Abstract Introduction: There are rising evidences that subcortical structures, including the basal ganglia, are affected in patients with epilepsy. These structures are thought to influence the modulation and phenotypic expression of epileptic seizures. Our study aimed to evaluate the presence of structural abnormalities in subcortical structures in patients with juvenile myoclonic epilepsy (JME).
    Methods: This cross-sectional study included 51 patients who were diagnosed with JME and who were monitored on an outpatient basis at the Clinic for Neurology and Psychiatry for Children and Youth in Belgrade from January 1985 to October 2017. All patients underwent transcranial parenchymal sonography (TCS) from October 2015 to October 2017. Relation of clinical parameters (seizure control andcognitive functioning,) with TCS results was assessed.
    Results: Hyperechogenicity of the substantia nigra (SN) was detected in 37.2% of JME subjects and it was significantly more common in patients with JME than in the control group. The marked echogenicity of the red nucleus (RN) was detected in 17.6% of cases, while 11.8% of subjects had hyperechogenic RN. The presence of hyperechogenic RN (both right and left) was significantly more frequent in the group of patients with JME compared to the control group. The third ventricle diameter was larger in patients with JME than in controls.
    Conclusion: Structural changes of certain subcortical structures, primarily SN and RN, detected in JME patients indicate additional non-lesional abnormalities of the basal ganglia and midbrain structures in these patients.
    Language English
    Publishing date 2024-04-21
    Publishing country Italy
    Document type Journal Article
    ZDB-ID 127315-2
    ISSN 2240-2993 ; 0300-9009
    ISSN (online) 2240-2993
    ISSN 0300-9009
    DOI 10.1007/s13760-024-02561-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Ultrasensitive Quantification of Crustacean Tropomyosin by Immuno-PCR.

    Radomirović, Mirjana / Gligorijević, Nikola / Stanić-Vučinić, Dragana / Rajković, Andreja / Ćirković Veličković, Tanja

    International journal of molecular sciences

    2023  Volume 24, Issue 20

    Abstract: Tropomyosin is the major and predominant allergen among shellfish. This study developed an ultrasensitive immuno-PCR method for the quantification of crustacean tropomyosin in foods. The method couples sandwich ELISA with the real-time PCR (rtPCR) ... ...

    Abstract Tropomyosin is the major and predominant allergen among shellfish. This study developed an ultrasensitive immuno-PCR method for the quantification of crustacean tropomyosin in foods. The method couples sandwich ELISA with the real-time PCR (rtPCR) amplification of marker DNAs. Monoclonal anti-TPM antibody was the capture antibody, polyclonal rabbit anti-shrimp tropomyosin antibody was the detection antibody, while natural shrimp tropomyosin served as the standard. A double-stranded amino-DNA was covalently conjugated to a secondary anti-rabbit antibody and subsequently amplified and quantified via rtPCR. The quantification sensitivity of immuno-PCR was 20-fold higher than analogous ELISA, with LOQ 19.8 pg/mL. The developed immuno-PCR method is highly specific for the detection of crustacean tropomyosin and is highly precise in a broad concentration range. Tropomyosin recovery in the spiked vegetable soup was 87.7-115.6%. Crustacean tropomyosin was also quantified in commercial food products. The reported immuno-PCR assay is the most sensitive method for the quantification of crustacean tropomyosin and is the first immuno-PCR-based assay for the quantification of food allergen and food protein in general. The described method could be easily adapted for the specific and ultrasensitive immuno-PCR-based detection of traces of any food allergen that is currently being quantified with ELISA, which is of critical importance for people with food allergies.
    MeSH term(s) Humans ; Animals ; Rabbits ; Tropomyosin/genetics ; Crustacea ; Shellfish ; Seafood/analysis ; Allergens ; Food Hypersensitivity/diagnosis
    Chemical Substances Tropomyosin ; Allergens
    Language English
    Publishing date 2023-10-21
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms242015410
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Prostate Cancer Scoring Index for Risk of Progression of Radioresistant Disease.

    Tesar, Eleonora Cini / Mikolasevic, Ivana / Skocilic, Iva / Redjovic, Arnela / Vucinic, Damir / Marusic, Jasna / Djordjevic, Gordana

    Journal of personalized medicine

    2023  Volume 13, Issue 5

    Abstract: Prostate cancer (Pca) is among the most common malignant diseases in men and the fourth leading cause of death worldwide. Surgery and radical radiotherapy (RT) remain the gold standard for the treatment of localized or locally advanced prostate cancer. ... ...

    Abstract Prostate cancer (Pca) is among the most common malignant diseases in men and the fourth leading cause of death worldwide. Surgery and radical radiotherapy (RT) remain the gold standard for the treatment of localized or locally advanced prostate cancer. The efficiency of radiotherapy treatment is limited by toxic side effects due to dose escalation. Cancer cells often develop radio-resistant mechanisms that are related to the DNA repair, inhibition of apoptosis or changes in cell cycle. Based on our earlier research on biomarkers that are involved in those cellular mechanisms (p53, bcl-2, NF-kb, Cripto-1 and Ki67 proliferation) and correlation with clinico-pathological parameters (age, PSA value, Gleason score, grade group, prognostic group), we created the numerical index for risk of tumor progression in patients with radioresistant tumors. For each of these parameters, the strength of association with disease progression was statistically assessed, and a specific number of points was assigned proportional to the strength of the correlation. Statistical analysis identified an optimal cut-off score of 22 or more as an indicator of significant risk for progression with a sensitivity of 91.7% and a specificity of 66.7%. The scoring system in the retrospective receiver operating characteristic analysis showed AUC of 0.82. The potential value of this scoring is the possibility of identifying patients with clinically significant radioresistant Pca.
    Language English
    Publishing date 2023-05-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662248-8
    ISSN 2075-4426
    ISSN 2075-4426
    DOI 10.3390/jpm13050870
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Effectiveness and Safety of Immune Checkpoint Inhibitors in Older Cancer Patients.

    Vucinic, Damir / Skocilic, Iva / Golcic, Marin / Dobrila-Dintinjana, Renata / Kolak, Maja / Jerkovic, Ivona / Tesar, Eleonora Cini / Ferari, Ani Mihaljevic / Redjovic, Arnela / Marusic, Jasna / Kolovrat, Doris / Mikolasevic, Ivana

    Journal of personalized medicine

    2024  Volume 14, Issue 3

    Abstract: Background: The development of immunotherapy checkpoint inhibitors (ICIs) has revolutionized cancer care. However, old patients are underrepresented in most clinical trials, although they represent a significant proportion of real-world patients. We ... ...

    Abstract Background: The development of immunotherapy checkpoint inhibitors (ICIs) has revolutionized cancer care. However, old patients are underrepresented in most clinical trials, although they represent a significant proportion of real-world patients. We aimed to evaluate the effectiveness and safety of ICIs in patients older than the age of 70.
    Methods: We performed a retrospective chart review of 145 patients aged 70 or older treated with ICIs for metastatic or unresectable cancer.
    Results: Median progression-free survival (PFS) was 10.4 months (95% CI 8.6-13.7), with no differences between octogenarians and septuagenarians (
    Conclusion: The effectiveness of ICIs in older cancer patients primarily depends on the line of treatment and treatment discontinuation. Octogenarians experienced similar treatment responses, PFS, OS, and adverse effects compared to septuagenarians.
    Language English
    Publishing date 2024-03-01
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662248-8
    ISSN 2075-4426
    ISSN 2075-4426
    DOI 10.3390/jpm14030278
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Pancreatic Carcinoma Metastatic to the Gingiva.

    Zubović, Arijan / Belušić-Gobić, Margita / Harmicar, David / Marušić, Jasna / Vučinić, Damir / Zamolo, Gordana

    Clinics and practice

    2021  Volume 11, Issue 1, Page(s) 58–64

    Abstract: Metastatic tumors to the oral cavity are uncommon, representing approximately 1% of all cases of oral malignant lesions even when a metastatic disease is present. The 53-year-old female is presented complaining of abdominal pain, weight loss, and a loose ...

    Abstract Metastatic tumors to the oral cavity are uncommon, representing approximately 1% of all cases of oral malignant lesions even when a metastatic disease is present. The 53-year-old female is presented complaining of abdominal pain, weight loss, and a loose stool recurring not more than three times per day. A computed tomography (CT) scan of the abdomen showed a retroperitoneal mass expanding along the body of the pancreas. Colonoscopy and gastroscopy with a gastric mucosa biopsy showed a normal result. After laparoscopic surgery, the primary site of adenocarcinoma was not confirmed. The patient was referred to the Maxillofacial Surgery Clinic with pain, swelling, and occasional bleeding around the lower right second mollar. Immunohistochemicaly, the tumor cells were positive for Cytokeratin (CK) 19, Cytokeratin (CK) 7, and homebox protein (CDX-2), which are highly sensitive markers of pancreatobiliar cancer. Therefore, the patient was diagnosed with pancreatic carcinoma. This report describes a rare metastasis of malignant pancreatic tumor to the lower right gingiva and highlights the importance of immunohistochemical examination and how it helped identify both the origin and the nature of gingival neoplasm.
    Language English
    Publishing date 2021-01-31
    Publishing country Switzerland
    Document type Case Reports
    ZDB-ID 2605724-4
    ISSN 2039-7283 ; 2039-7275
    ISSN (online) 2039-7283
    ISSN 2039-7275
    DOI 10.3390/clinpract11010010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Book ; Online: LeaFTL

    Sun, Jinghan / Li, Shaobo / Sun, Yunxin / Sun, Chao / Vucinic, Dejan / Huang, Jian

    A Learning-Based Flash Translation Layer for Solid-State Drives

    2022  

    Abstract: In modern solid-state drives (SSDs), the indexing of flash pages is a critical component in their storage controllers. It not only affects the data access performance, but also determines the efficiency of the precious in-device DRAM resource. A variety ... ...

    Abstract In modern solid-state drives (SSDs), the indexing of flash pages is a critical component in their storage controllers. It not only affects the data access performance, but also determines the efficiency of the precious in-device DRAM resource. A variety of address mapping schemes and optimization techniques have been proposed. However, most of them were developed with human-driven heuristics. They cannot automatically capture diverse data access patterns at runtime in SSD controllers, which leaves a large room for improvement. In this paper, we present a learning-based flash translation layer (FTL), named LeaFTL, which learns the address mapping to tolerate dynamic data access patterns via linear regression at runtime. By grouping a large set of mapping entries into a learned segment, it significantly reduces the memory footprint of the address mapping table, which further benefits the data caching in SSD controllers. LeaFTL also employs various optimization techniques, including out-of-band metadata verification to tolerate mispredictions, optimized flash allocation, and dynamic compaction of learned index segments. We implement LeaFTL with an SSD simulator and evaluate it with various storage workloads. LeaFTL saves the memory consumption of the mapping table by 2.9x on average and improves the storage performance by 1.4x on average, in comparison with state-of-the-art FTL schemes.

    Comment: This paper is accepted at the 28th Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS 2023)
    Keywords Computer Science - Operating Systems
    Subject code 004
    Publishing date 2022-12-30
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Characterization of Nanoprecipitated PET Nanoplastics by

    Djapovic, Milica / Apostolovic, Danijela / Postic, Vojislava / Lujic, Tamara / Jovanovic, Vesna / Stanic-Vucinic, Dragana / van Hage, Marianne / Maslak, Veselin / Cirkovic Velickovic, Tanja

    Polymers

    2023  Volume 15, Issue 24

    Abstract: Manufactured nanoplastic particles (NPs) are indispensable for in vitro and in vivo testing and a health risk assessment of this emerging environmental contaminant is needed. The high surface area and inherent hydrophobicity of plastic materials makes ... ...

    Abstract Manufactured nanoplastic particles (NPs) are indispensable for in vitro and in vivo testing and a health risk assessment of this emerging environmental contaminant is needed. The high surface area and inherent hydrophobicity of plastic materials makes the production of NPs devoid of any contaminants very challenging. In this study, we produced nanoprecipitated polyethylene terephthalate (PET) NPs (300 nm hydrodynamic diameter) with an overall yield of 0.76%. The presence of the ionic surfactant sodium dodecyl sulfate (SDS) was characterized by
    Language English
    Publishing date 2023-12-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527146-5
    ISSN 2073-4360 ; 2073-4360
    ISSN (online) 2073-4360
    ISSN 2073-4360
    DOI 10.3390/polym15244703
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Small polystyrene microplastics interfere with the breakdown of milk proteins during static in vitro simulated human gastric digestion.

    Krishna de Guzman, Maria / Stanic-Vucinic, Dragana / Gligorijevic, Nikola / Wimmer, Lukas / Gasparyan, Manvel / Lujic, Tamara / Vasovic, Tamara / Dailey, Lea Ann / Van Haute, Sam / Cirkovic Velickovic, Tanja

    Environmental pollution (Barking, Essex : 1987)

    2023  Volume 335, Page(s) 122282

    Abstract: Human ingestion of microplastics (MPs) is common and inevitable due to the widespread contamination of food items, but implications on the gastric digestion of food proteins are still unknown. In this study, the interactions between pepsin and ... ...

    Abstract Human ingestion of microplastics (MPs) is common and inevitable due to the widespread contamination of food items, but implications on the gastric digestion of food proteins are still unknown. In this study, the interactions between pepsin and polystyrene (PS) MPs were evaluated by investigating enzyme activity and conformation in a simulated human gastric environment in the presence or absence of PS MPs. The impact on food digestion was also assessed by monitoring the kinetics of protein hydrolysis through static in vitro gastric digestion of cow's milk contaminated with PS. The binding of pepsin to PS showed that the surface chemistry of MPs dictates binding affinity. The key contributor to pepsin adsorption seems to be π-π interactions between the aromatic residues and the PS phenyl rings. During quick exposure (10 min) of pepsin to increasing concentrations (222, 2219, 22188 particles/mL) of 10 μm PS (PS10) and 100 μm PS (PS100), total enzymatic activities were not affected remarkably. However, upon prolonged exposure at 1 and 2 h, preferential binding of pepsin to the small, low zeta-potential PS caused structural changes in the protein which led to a significant reduction of its activity. Digestion of cow's milk mixed with PS10 resulted in transient accumulation of larger peptides (10-35 kDa) and reduced bioavailability of short peptides (2-9 kDa) in the gastric phase. This, however, was only observed at extremely high PS10 concentration (0.3 mg/mL or 5.46E+05 particles/mL). The digestion of milk peptides, bound preferentially over pepsin within the hard corona on the PS10 surface, was delayed up to 15 min in comparison to bulk protein digestion. Intact caseins, otherwise rapidly digested, remained bound to PS10 in the hard corona for up to 15 min. This work presents valuable insights regarding the interaction of MPs, food proteins, and pepsin, and their dynamics during gastric digestion.
    MeSH term(s) Humans ; Milk Proteins/metabolism ; Pepsin A/metabolism ; Microplastics ; Polystyrenes ; Plastics ; Peptides/chemistry ; Peptides/metabolism ; Caseins/chemistry ; Caseins/metabolism ; Allergens ; Digestion
    Chemical Substances Milk Proteins ; Pepsin A (EC 3.4.23.1) ; Microplastics ; Polystyrenes ; Plastics ; Peptides ; Caseins ; Allergens
    Language English
    Publishing date 2023-07-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 280652-6
    ISSN 1873-6424 ; 0013-9327 ; 0269-7491
    ISSN (online) 1873-6424
    ISSN 0013-9327 ; 0269-7491
    DOI 10.1016/j.envpol.2023.122282
    Database MEDical Literature Analysis and Retrieval System OnLINE

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