Search results for: gene expression datasets

Authors: Seyyedeh Faezeh Hassani Ziabari, Sadegh Eskandari, Maziar Salahi

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Infinite Feature Selection (IFS) algorithm is an efficient feature selection algorithm that selects a subset of features of all sizes (including infinity). In this paper, we present an improved version of it, called clustering IFS (CIFS), by clustering the dataset in advance. To do so, first, we apply the K-means algorithm to cluster the dataset, then we apply IFS. In the CIFS method, the spatial and temporal complexities are reduced compared to the IFS method. Experimental results on 6 datasets show the superiority of CIFS compared to IFS in terms of accuracy, running time, and memory consumption.

Keywords: feature selection, infinite feature selection, clustering, graph

Procedia PDF Downloads 123

Authors: Larissa M. Vargas, Julia M. Sacchi, Renata O. Pereira, Lucas S. Asano, Iara C. Araújo, Patricia Fiorino, Vera Farah

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The aim of this study was to evaluate the occurrence of subclinical organ injuries induced by high-fat diet. Male wistar rats (n=5/group) were divided in control diet group (CD), commercial rat chow, and hyperlipidic diet (30% lipids) group (HD) administrated during 8 weeks, starting after weaning. All the procedures followed the rules of the Committee of Research and Ethics of the Mackenzie University (CEUA Nº 077/03/2011). At the end of protocol the animals were euthanized by anesthesia overload and the left kidney was removed. Intrarenal lipid deposition was evaluated by histological analyses with oilred. Kidney slices were stained with picrosirius red to evaluate the area of the Bowman's capsule (AB) and space (SB), and glomerular tuft area (GT). The renal expression of sterol regulatory element–binding protein (SREBP-2) was performed by Western Blotting. Creatinine concentration (serum and urine) and lipid profile were determined by colorimetric kit (Labtest). At the end of the protocol there was no differences in body weight between the groups, however the HD showed a marked increase in lipid deposits, glomeruli and tubules, and biochemical analysis for cholesterol and triglycerides. Moreover, in the kidney, the high-fat diet induced a reduction in the AB (13%), GT (18%) and SB (17%) associated with a reduction in glomerular filtration rate (creatinine clearance). The renal SRBP2 expression was increased in HD group. These data suggests that consumption of high-fat diet starting in childhood is associated with subclinical renal damage and function.

Keywords: high-fat diet, kidney, intrarenal lipid deposition, SRBP2

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Authors: Juan Huang, Nanqu Huang, Jingshan Shi, Yu Qiu

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Objectives: There are pathophysiological connections between type 2 diabetes mellitus (T2DM) and Alzheimer's disease (AD), and research on drugs with hypoglycemic and beta-amyloid (Aβ)-clearing effects have great therapeutic potential for AD. Dendrobium nobile Lindl. Alkaloids (DNLA) as one of the active compounds of Dendrobium nobile Lindl. In this study, we attempted to verify the hypoglycemic effect and investigate the effects of DNLA on the amyloid precursor protein (APP) metabolic pathway of the hippocampus in db/db mice. Methods: 4-weeks-old male C57BL/KsJ mice were the control group. And the same age and sexuality db/db mice were: model, DNLA-L (20 mg/kg), DNLA-M (40 mg/kg), and DNLA-H (80 mg/kg). After, mice were treated with different concentrations of DNLA for 17 weeks. The fasting blood glucose (FBG) was detected by glucose oxidase assay every week from the 4th to last week. The protein expression of β-amyloid 1-42 (Aβ1-42), β-site amyloid precursor protein-cleaving enzyme 1 (BACE1), and APP were examined by Western blotting. Results: The concentration of FBG and the protein expression of Aβ1-42, BACE1, and APP were increased in the hippocampus of the model group. Moreover, DNLA not only significantly decreased the concentration of FBG but also reduced the protein expressions of Aβ1-42, BACE1 and APP in the hippocampus of db/db mice in a dose-dependent manner. Conclusions: DNLA can decrease the protein expressions of Aβ1-42 in the hippocampus of db/db mice, and the mechanism may be involved in the APP metabolic pathway.

Keywords: Alzheimer's disease, type 2 diabetes mellitus, β-site amyloid precursor protein-cleaving enzyme 1, traditional Chinese medicines, beta-amyloid

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Authors: Ritesh Kumar, Rajendra Pamula

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In this paper, we present our contribution for book recommendation. In our experiment, we combine the results of Sequential Dependence Model (SDM) and exploitation of book information such as reviews, tags and ratings. This social information is assigned by users. For this, we used CLEF-2016 Social Book Search Track Suggestion task. Finally, our proposed method extensively evaluated on CLEF -2015 Social Book Search datasets, and has better performance (nDCG@10) compared to other state-of-the-art systems. Recently we got the good performance in CLEF-2016.

Keywords: sequential dependence model, social information, social book search, query expansion

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Authors: Shivani Tiwari, Prathibha Karanth, B. Rajashekhar

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Impairments of syntactic morphology are often considered central in children with Specific Language Impairment (SLI). In English and related languages, deficits of tense-related grammatical morphology could serve as a clinical marker of SLI. Yet, cross-linguistic studies on SLI in the recent past suggest that the nature and severity of morphosyntactic deficits in children with SLI varies with the language being investigated. Therefore, in the present study we investigated the morphosyntactic deficits in a group of children with SLI who speak Kannada, a morphologically complex Dravidian language spoken in Indian subcontinent. A group of 15 children with SLI participated in this study. Two more groups of typical developing children (15 each) matched for language and age to children with SLI, were included as control participants. All participants were assessed for morphosyntactic comprehension and expression using standardized language test and a spontaneous speech task. Results of the study showed that children with SLI differed significantly from age-matched but not language-matched control group, on tasks of both comprehension and expression of morphosyntax. This finding is, however, in contrast with the reports of English-speaking children with SLI who are reported to be poorer than younger MLU-matched children on tasks of morphosyntax. The observed difference in impairments of morphosyntax in Kannada-speaking children with SLI from English-speaking children with SLI is explained based on the morphological richness theory. The theory predicts that children with SLI perform relatively better in morphologically rich language due to occurrence of their frequent and consistent features that mark the morphological markers. The authors, therefore, conclude that language-specific features do influence manifestation of the disorder in children with SLI.

Keywords: specific language impairment, morphosyntax, Kannada, manifestation

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Authors: Ganesh K. Maurya, Reema Chaudhary, Neha Pandey, Hari S. Misra

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PprA, a pleiotropic protein participating in radioresistance, has been reported for its roles in DNA replication initiation, genome segregation, cell division and DNA repair in polyextremophile Deinococcus radiodurans. Interestingly, expression of deinococcal PprA in E. coli suppresses its growth by reducing the number of colony forming units and provides better resistance against γ-radiation than control. We employed different biochemical and cell biology studies using PprA and its DNA binding/polymerization mutants (K133E & W183R) in E. coli. Cells expressing wild type PprA or its K133E mutant showed reduction in the amount of genomic DNA as well as chromosome copy number in comparison to W183R mutant of PprA and control cells, which suggests the role of PprA protein in regulation of DNA replication initiation in E. coli. Further, E. coli cells expressing PprA or its mutants exhibited different impact on cell morphology than control. Expression of PprA or K133E mutant displayed a significant increase in cell length upto 5 folds while W183R mutant showed cell length similar to uninduced control cells. We checked the interaction of deinococcal PprA and its mutants with E. coli DnaA using Bacterial two-hybrid system and co-immunoprecipitation. We observed a functional interaction of EcDnaA with PprA and K133E mutant but not with W183R mutant of PprA. Further, PprA or K133E mutant has suppressed the ATPase activity of EcDnaA but W183R mutant of PprA failed to do so. These observations suggested that PprA protein regulates DNA replication initiation and cell morphology of surrogate E. coli.

Keywords: DNA replication, radioresistance, protein-protein interaction, cell morphology, ATPase activity

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Authors: Elif Gencturk, Ekin Yurdakul, Ahmet Y. Celik, Senol Mutlu, Kutlu O. Ulgen

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Yeast cells are generally used as a model system of eukaryotes due to their complex genetic structure, rapid growth ability in optimum conditions, easy replication and well-defined genetic system properties. Thus, yeast cells increased the knowledge of the principal pathways in humans. During fermentation, carbohydrates (hexoses and pentoses) degrade into some toxic by-products such as 5-hydroxymethylfurfural (5-HMF or HMF) and furfural. HMF influences the ethanol yield, and ethanol productivity; it interferes with microbial growth and is considered as a potent inhibitor of bioethanol production. In this study, yeast single cell behavior under HMF application was monitored by using a continuous flow single phase microfluidic platform. Microfluidic device in operation is fabricated by hot embossing and thermo-compression techniques from cyclo-olefin polymer (COP). COP is biocompatible, transparent and rigid material and it is suitable for observing fluorescence of cells considering its low auto-fluorescence characteristic. The response of yeast cells was recorded through Red Fluorescent Protein (RFP) tagged Nop56 gene product, which is an essential evolutionary-conserved nucleolar protein, and also a member of the box C/D snoRNP complexes. With the application of HMF, yeast cell proliferation continued but HMF slowed down the cell growth, and after HMF treatment the cell proliferation stopped. By the addition of fresh nutrient medium, the yeast cells recovered after 6 hours of HMF exposure. Thus, HMF application suppresses normal functioning of cell cycle but it does not cause cells to die. The monitoring of Nop56 expression phases of the individual cells shed light on the protein and ribosome synthesis cycles along with their link to growth. Further computational study revealed that the mechanisms underlying the inhibitory or inductive effects of HMF on growth are enriched in functional categories of protein degradation, protein processing, DNA repair and multidrug resistance. The present microfluidic device can successfully be used for studying the effects of inhibitory agents on growth by single cell tracking, thus capturing cell to cell variations. By metabolic engineering techniques, engineered strains can be developed, and the metabolic network of the microorganism can thus be manipulated such that chemical overproduction of target metabolite is achieved along with the maximum growth/biomass yield.  

Keywords: COP, HMF, ribosome biogenesis, thermoplastic microbioreactor, yeast

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Authors: Yali Zheng, Peipei Luo, Shinan Chen, Jiasheng Hao, Hong Cheng

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Most of traditional visual indoor navigation algorithms and methods only consider the localization in ordinary daytime, while we focus on the indoor re-localization in low light in the paper. As RGB images are degraded in low light, less discriminative infrared and depth image pairs are taken, as the input, by RGB-D cameras, the most similar candidates, as the output, are searched from databases which is built in the bag-of-word framework. Epipolar constraints can be used to relocalize the query infrared and depth image sequence. We evaluate our method in two datasets captured by Kinect2. The results demonstrate very promising re-localization results for indoor navigation system in low light environments.

Keywords: indoor navigation, low light, RGB-D camera, vision based

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Authors: Shifu Hu, Qiong Yu, Wei Xia, Changhong Zhu

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Background: P38α MAPK, which is a member of the canonical MAPK family, is activated in response to various extracellular stresses and plays a role in multiple cellular processes. It is well known that p38α MAPK play vital roles in oocyte maturation, but the localization and functional roles of p38α MAPK during the meiotic maturation of rat oocytes remain unknown. Study Design: In this study, western-blot and immunofluorescent staining were used to investigate the expression and subcellular localization of p38α MAPK during the meiotic maturation of rat oocytes. SB203580, a specific inhibitor of p38α MAPK, was used to study the roles of p38α MAPK in the meiotic cell cycle of rat oocytes. Results: The results found that p38α MAPK phosphorylation (p-p38α MAPK, indicative of p38α MAPK activation) was low at the germinal vesicle (GV) stage, increased 3 h after germinal vesicle breakdown (GVBD), and maintained its maximum at MI (metaphase I) or M II (metaphase II). The p-p38α MAPK mainly accumulated in the germinal vesicle and had no obvious expression in the nucleus. From GVBD to M II, p-p38α MAPK was distributed in the cytoplasm around either the chromosomes or the spindle. We used SB203580, an inhibitor of p38α MAPK, to investigate the possible functional role of p38α MAPK during rat oocyte meiotic maturation. Treatment of GV stage oocytes with 20 μM SB203580 blocked p-p38α MAPK activity, and the spindles appeared abnormal. Additionally, the rate of GVBD after 3h of culture with 20 μM SB203580 (58.8%) was significantly inhibited compared with the control (82.5%, p < 0.05), and the polar body extrusion rate after 12 h of culture with SB203580 was also significantly decreased compared with the control (40.1 vs. 73.3%, p < 0.05). Conclusions: These data indicate that p38α MAPK may play a vital role in rat oocyte meiotic maturation.

Keywords: meiotic maturation, oocyte, p38α MAPK, spindle

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Authors: Ganesh K. Maurya, Reema Chaudhary, Neha Pandey, Hari S. Misra

Abstract:

PprA, a pleiotropic protein participating in radioresistance, has been reported for its roles in DNA replication initiation, genome segregation, cell division and DNA repair in polyextremophile Deinococcus radiodurans. Interestingly, expression of deinococcal PprA in E. coli suppresses its growth by reducing the number of colony forming units and provide better resistance against γ-radiation than control. We employed different biochemical and cell biology studies using PprA and its DNA binding/polymerization mutants (K133E & W183R) in E. coli. Cells expressing wild type PprA or its K133E mutant showed reduction in the amount of genomic DNA as well as chromosome copy number in comparison to W183R mutant of PprA and control cells, which suggests the role of PprA protein in regulation of DNA replication initiation in E. coli. Further, E. coli cells expressing PprA or its mutants exhibited different impact on cell morphology than control. Expression of PprA or K133E mutant displayed a significant increase in cell length upto 5 folds while W183R mutant showed cell length similar to uninduced control cells. We checked the interaction of deinococcal PprA and its mutants with E. coli DnaA using Bacterial two-hybrid system and co-immunoprecipitation. We observed a functional interaction of EcDnaA with PprA and K133E mutant but not with W183R mutant of PprA. Further, PprA or K133E mutant has suppressed the ATPase activity of EcDnaA but W183R mutant of PprA failed to do so. These observations suggested that PprA protein regulates DNA replication initiation and cell morphology of surrogate E. coli.

Keywords: DNA replication, radioresistance, protein-protein interaction, cell morphology, ATPase activity

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Authors: Ainur Sharip, Jose E. Perez, Nouf Alsharif, Aldo I. M. Bandeas, Enzo D. Fabrizio, Timothy Ravasi, Jasmeen S. Merzaban, Jürgen Kosel

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Bone marrow-derived human mesenchymal stem cells (MSCs) are attractive candidates for tissue engineering and regenerative medicine, due to their ability to differentiate into osteoblasts, chondrocytes or adipocytes. Differentiation is influenced by biochemical and biophysical stimuli provided by the microenvironment of the cell. Thus, altering the mechanical characteristics of a cell culture scaffold can directly influence a cell’s microenvironment and lead to stem cell differentiation. Mesenchymal stem cells were cultured on densely packed, vertically aligned magnetic iron nanowires (NWs) and the effect of NWs on the cell cytoskeleton rearrangement and differentiation were studied. An electrochemical deposition method was employed to fabricate NWs into nanoporous alumina templates, followed by a partial release to reveal the NW array. This created a cell growth substrate with free-standing NWs. The Fe NWs possessed a length of 2-3 µm, with each NW having a diameter of 33 nm on average. Mechanical stimuli generated by the physical movement of these iron NWs, in response to a magnetic field, can stimulate osteogenic differentiation. Induction of osteogenesis was estimated using an osteogenic marker, osteopontin, and a reduction of stem cell markers, CD73 and CD105. MSCs were grown on the NWs, and fluorescent microscopy was employed to monitor the expression of markers. A magnetic field with an intensity of 250 mT and a frequency of 0.1 Hz was applied for 12 hours/day over a period of one week and two weeks. The magnetically activated substrate enhanced the osteogenic differentiation of the MSCs compared to the culture conditions without magnetic field. Quantification of the osteopontin signal revealed approximately a seven-fold increase in the expression of this protein after two weeks of culture. Immunostaining staining against CD73 and CD105 revealed the expression of antibodies at the earlier time point (two days) and a considerable reduction after one-week exposure to a magnetic field. Overall, these results demonstrate the application of a magnetic NW substrate in stimulating the osteogenic differentiation of MSCs. This method significantly decreases the time needed to induce osteogenic differentiation compared to commercial biochemical methods, such as osteogenic differentiation kits, that usually require more than two weeks. Contact-free stimulation of MSC differentiation using a magnetic field has potential uses in tissue engineering, regenerative medicine, and bone formation therapies.

Keywords: cell substrate, magnetic nanowire, mesenchymal stem cell, stem cell differentiation

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Authors: Waraporn Thaimit, Yuwadee Insamran, Natchanok Jansawang

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Focusing on Analytical Thinking and Learning Achievement are the critical component of visual thinking that gives one the ability to solve problems quickly and effectively that allows to complex problems into components, and the result had been achieved or acquired form of the subject students of which resulted in changes within the individual as a result of activity in learning. The aims of this study are to administer on comparisons between students’ analytical thinking abilities and their learning achievements sample size consisted of 80 students who sat at the 12th grade level in 2 classes from Chaturaphak Phiman Ratchadaphisek School, the 40-student experimental group with the Problem-Based Learning (PBL) and 40-student controlling group with the Concept Mapping Instructional (CMI) methods were designed. Research instruments composed with the 5-lesson instructional plans to be assessed with the pretest and posttest techniques on each instructional method. Students’ responses of their analytical thinking abilities were assessed with the Analytical Thinking Tests and students’ learning achievements were tested of the Learning Achievement Tests. Statistically significant differences with the paired t-test and F-test (Two-way MANCOVA) between post- and pre-tests of the whole students in two chemistry classes were found. Associations between student learning outcomes in each instructional method and their analytical thinking abilities to their learning achievements also were found (ρ < .05). The use of two instructional methods for this study is revealed that the students perceive their abilities to be highly learning achievement in chemistry classes with the PBL group ought to higher than the CMI group. Suggestions that analytical thinking ability involves the process of gathering relevant information and identifying key issues related to the learning achievement information.

Keywords: comparisons, students learning achievements, analytical thinking abilities, the problem-based learning method, the concept mapping instructional method, gene and chromosome issue, chemistry classes

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Authors: Mohammad K. Parvez, Ahmed H. Arbab, Mohammed S. Al-Dosari

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Cyperus rotendus rhizomes are used as traditional medicine, including Ayurveda in chronic liver diseases and hepatitis B. We investigated the in vitro hepatoprotective and anti-hepatitis B virus (HBV) potential of Cyperus rotundus rhizome organic and aqueous fractions. Of these, the n-butanol and aqueous fractions showed the most promising, dose-dependent hepatoprotection in DCFH-injured HepG2 cells at 48 h. DCFH-toxicated cells were recovered to about 88% and 96%, upon treatment with n-butanol and aqueous fractions (200 g/ml), respectively compared to DCFH-only treated cells. Further, C. rotundus fractions were tested for anti-HBV activities by measuring the expression levels of viral antigens (HBsAg and HBeAg) in the HepG2.2.15 culture supernatants. At 48 h post-treatment, the ethyl acetate, n-butanol and aqueous fractions showed dose-dependent inhibition wherein at a higher dose (100 g/ml), HBsAg production was reduced to 60.27%, 46.87 and 42.76%, respectively. In a time-course study, HBsAg production was inhibited up to 50% and 40% by ethyl acetate and n-butanol fractions (100 g/ml), respectively on day 5. Three three active fractions were further subjected to time-dependent inhibition of HBeAg expression, an indirect measure of HBV active DNA replication. At day 5 post-treatment, ethyl acetate and n-butanol fractions downregulated HBV replication by 44.14% and 24.70%, respectively. In conclusion, our results showed very promising hepatoprotective and anti-HBV potential of C. rotendus tubers fractions in vitro. Our data could, therefore, provide the basis for the claimed traditional use of C. rotendus for jaundice and hepatitis.

Keywords: anti-hepatitis B, cyperus rotundus, hepatitis B virus, hepatoprotection

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Authors: Huimin Zhao, Xiaoquan Liu, Haochen Liu

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The major challenge facing Alzheimer's Disease (AD) drug development is how to effectively improve cognitive function in clinical practice. Growing evidence indicates that stimulating hippocampal neurogenesis is a strategy for restoring cognition in animal models of AD. The mitogen-activated protein kinase (MAPK) pathway is a crucial factor in neurogenesis, which is negatively regulated by Dual-specificity phosphatase 16 (DUSP16). Transcriptome analysis of post-mortem brain tissue revealed up-regulation of DUSP16 expression in AD patients. Additionally, DUSP16 was involved in regulating the proliferation and neural differentiation of neural progenitor cells (NPCs). Nevertheless, whether the effect of DUSP16 on ameliorating cognitive disorders by influencing NPCs differentiation in AD mice remains unclear. Our study demonstrates an association between DUSP16 SNPs and clinical progression in individuals with mild cognitive impairment (MCI). Besides, we found that increased DUSP16 expression in both 3×Tg and SAMP8 models of AD led to NPC differentiation impairments. By silencing DUSP16, cognitive benefits, the induction of AHN and synaptic plasticity, were observed in AD mice. Furthermore, we found that DUSP16 is involved in the process of NPC differentiation by regulating c-Jun N-terminal kinase (JNK) phosphorylation. Moreover, the increased DUSP16 may be regulated by the ETS transcription factor (ELK1), which binds to the promoter region of DUSP16. Loss of ELK1 resulted in decreased DUSP16 mRNA and protein levels. Our data uncover a potential regulatory role for DUSP16 in adult hippocampal neurogenesis and provide a possibility to find the target of AD intervention.

Keywords: alzheimer's disease, cognitive function, DUSP16, hippocampal neurogenesis

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Authors: Linette van der Merwe

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It is known that visual artists, performing artists, and literary artists have inspired each other since time immemorial. The enduring, symbiotic relationship between the various art genres is evident where words, colours, lines, and sounds act as metaphors, a physical separation of the transcendental reality of art. Simonides of Keos (c. 556-468 BC) confirmed this, stating that a poem is a talking picture, or, in a more modern expression, a picture is worth a thousand words. It can be seen as an ancient relationship, originating from the epigram (tombstone or artefact inscriptions), the carmen figuratum (figure poem), and the ekphrasis (a description in the form of a poem of a work of art). Visual artists, including Michelangelo, Leonardo da Vinci, and Goethe, wrote poems and songs. Goya, Degas, and Picasso are famous for their works of art and for trying their hands at poetry. Afrikaans writers whose fine art is often published together with their writing, as in the case of Andries Bezuidenhout, Breyten Breytenbach, Sheila Cussons, Hennie Meyer, Carina Stander, and Johan van Wyk, among others, are not a strange phenomenon either. Imitating one art form into another art form is a form of translation, transposition, contemplation, and discovery of artistic impressions, showing parallel interpretations rather than physical comparison. It is especially about the harmony that exists between the different art genres, i.e., a poem that describes a painting or a visual text that portrays a poem that becomes a translation, interpretation, and rediscovery of the verbal text, or rather, from the word text to the image text. Poetry-film, as a form of such a translation of the word text into an image text, can be considered a hybrid, transdisciplinary art form that connects poetry and film. Poetry-film is regarded as an intertwined entity of word, sound, and visual image. It is an attempt to transpose and transform a poem into a new artwork that makes the poem more accessible to people who are not necessarily open to the written word and will, in effect, attract a larger audience to a genre that usually has a limited market. Poetry-film is considered a creative expression of an inverted ekphrastic inspiration, a visual description, interpretation, and expression of a poem. Research also emphasises that animated poetry-film is not widely regarded as a genre of anything and is thus severely under-theorized. This paper will focus on Afrikaans animated poetry-films as a multimodal transposition of a poem text to an animated poetry film, with specific reference to animated poetry-films in Filmverse I (2014) and Filmverse II (2016).

Keywords: poetry film, animated poetry film, poetic metaphor, conceptual metaphor, monomodal metaphor, multimodal metaphor, semiotic metaphor, multimodality, metaphor analysis, target domain, source domain

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Authors: Tesnim Charrad, Kaouther Nouira, Ahmed Ferchichi

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In order to reduce the number of deaths due to heart problems, we propose the use of Hierarchical Temporal Memory Algorithm (HTM) which is a real time anomaly detection algorithm. HTM is a cortical learning algorithm based on neocortex used for anomaly detection. In other words, it is based on a conceptual theory of how the human brain can work. It is powerful in predicting unusual patterns, anomaly detection and classification. In this paper, HTM have been implemented and tested on ECG datasets in order to detect cardiac anomalies. Experiments showed good performance in terms of specificity, sensitivity and execution time.

Keywords: cardiac anomalies, ECG, HTM, real time anomaly detection

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Authors: Amy M. Kwon

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Support vector machine (SVM) is a well-known algorithm in machine learning due to its superior performance, and it also functions well in multiple-instance (MI) problems. Our study proposes a schematic algorithm to select instances based on Hausdorff distance, which can be adapted to SVMs as input vectors under the MI setting. Based on experiments on five benchmark datasets, our strategy for adapting representation outperformed in comparison with original approach. In addition, task execution times (TETs) were reduced by more than 80% based on MissSVM. Hence, it is noteworthy to consider this representation adaptation to SVMs under MI-setting.

Keywords: support vector machine, Margin, Hausdorff distance, representation selection, multiple-instance learning, machine learning

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Authors: Bylhah Mugotitsa, Jim Todd, Agnes Kiragga, Jay Greenfield, Evans Omondi, Lukoye Atwoli, Reinpeter Momanyi

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The INSPIRE network aims to build an open, ethical, sustainable, and FAIR (Findable, Accessible, Interoperable, Reusable) data science platform, particularly for longitudinal mental health (MH) data. While studies have been done at the clinical and population level, there still exists limitations in data and research in LMICs, which pose a risk of underrepresentation of mental disorders. It is vital to examine the existing longitudinal MH data, focusing on how FAIR datasets are. This landscape analysis aimed to provide both overall level of evidence of availability of longitudinal datasets and degree of consistency in longitudinal studies conducted. Utilizing prompters proved instrumental in streamlining the analysis process, facilitating access, crafting code snippets, categorization, and analysis of extensive data repositories related to depression, anxiety, and psychosis in Africa. While leveraging artificial intelligence (AI), we filtered through over 18,000 scientific papers spanning from 1970 to 2023. This AI-driven approach enabled the identification of 228 longitudinal research papers meeting inclusion criteria. Quality assurance revealed 10% incorrectly identified articles and 2 duplicates, underscoring the prevalence of longitudinal MH research in South Africa, focusing on depression. From the analysis, evaluating data and metadata adherence to FAIR principles remains crucial for enhancing accessibility and quality of MH research in Africa. While AI has the potential to enhance research processes, challenges such as privacy concerns and data security risks must be addressed. Ethical and equity considerations in data sharing and reuse are also vital. There’s need for collaborative efforts across disciplinary and national boundaries to improve the Findability and Accessibility of data. Current efforts should also focus on creating integrated data resources and tools to improve Interoperability and Reusability of MH data. Practical steps for researchers include careful study planning, data preservation, machine-actionable metadata, and promoting data reuse to advance science and improve equity. Metrics and recognition should be established to incentivize adherence to FAIR principles in MH research

Keywords: longitudinal mental health research, data sharing, fair data principles, Africa, landscape analysis

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Authors: Sina Mahdavi

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Background and Objective: Multiple sclerosis (MS) is the most common inflammatory autoimmune disease of the central nervous system (CNS) that affects the myelination process in the CNS. Complex interactions of various "environmental or infectious" factors may act as triggers in autoimmunity and disease progression. The association between viral infections, especially Epstein-Barr virus (EBV) and MS, is one potential cause that is not well understood. In this study, we aim to summarize the available data on EBV infection in MS disease progression. Materials and Methods: For this study, the keywords "Multiple sclerosis," "Epstein-Barr virus," and "central nervous system" in the databases PubMed, Google Scholar, Sid, and MagIran between 2016 and 2022 were searched, and 14 articles were chosen, studied, and analyzed. Results: Demyelinated lesions isolated from MS patients contain EBNAs from EBV proteins. The EBNA1 domain contains a pentapeptide fragment identical to B-crystallin, a heat shock peptide, that is increased in peripheral B cells in response to B-crystallin infection, resulting in myelin-directed autoimmunity mediated by proinflammatory T cells. EBNA2, which is involved in the regulation of viral transcription, may enhance transcription from MS risk loci. A 7-fold increase in the risk of MS has been observed in EBV infection with HLA-DR15 synergy. Conclusion: EBV infection along with a variety of specific genetic risk alleles, cause inflammatory cascades in the CNS by infected B cells. There is a high expression of EBV during the course of MS, which indicates the relationship between EBV and MS, that this virus can play a role in the development of MS by creating an inflammatory state. Therefore, measures to modulate the expression of EBV may be effective in reducing inflammatory processes in demyelinated areas of MS patients.

Keywords: multiple sclerosis, Epstein-Barr virus, central nervous system, EBNAs

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Authors: Mohamad R. Moshtagh, Ahmad Bagheri

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Accurate fault detection in rotating machinery is of utmost importance to ensure optimal performance and prevent costly downtime in industrial applications. This study presents a robust fault detection system based on vibration data collected from rotating gears under various operating conditions. The considered scenarios include: (1) both gears being healthy, (2) one healthy gear and one faulty gear, and (3) introducing an imbalanced condition to a healthy gear. Vibration data was acquired using a Hentek 1008 device and stored in a CSV file. Python code implemented in the Spider environment was used for data preprocessing and analysis. Winner features were extracted using the Wiener feature selection method. These features were then employed in multiple machine learning algorithms, including Convolutional Neural Networks (CNN), Multilayer Perceptron (MLP), K-Nearest Neighbors (KNN), and Random Forest, to evaluate their performance in detecting and classifying faults in both the training and validation datasets. The comparative analysis of the methods revealed the superior performance of the Wiener-CNN approach. The Wiener-CNN method achieved a remarkable accuracy of 100% for both the two-class (healthy gear and faulty gear) and three-class (healthy gear, faulty gear, and imbalanced) scenarios in the training and validation datasets. In contrast, the other methods exhibited varying levels of accuracy. The Wiener-MLP method attained 100% accuracy for the two-class training dataset and 100% for the validation dataset. For the three-class scenario, the Wiener-MLP method demonstrated 100% accuracy in the training dataset and 95.3% accuracy in the validation dataset. The Wiener-KNN method yielded 96.3% accuracy for the two-class training dataset and 94.5% for the validation dataset. In the three-class scenario, it achieved 85.3% accuracy in the training dataset and 77.2% in the validation dataset. The Wiener-Random Forest method achieved 100% accuracy for the two-class training dataset and 85% for the validation dataset, while in the three-class training dataset, it attained 100% accuracy and 90.8% accuracy for the validation dataset. The exceptional accuracy demonstrated by the Wiener-CNN method underscores its effectiveness in accurately identifying and classifying fault conditions in rotating machinery. The proposed fault detection system utilizes vibration data analysis and advanced machine learning techniques to improve operational reliability and productivity. By adopting the Wiener-CNN method, industrial systems can benefit from enhanced fault detection capabilities, facilitating proactive maintenance and reducing equipment downtime.

Keywords: fault detection, gearbox, machine learning, wiener method

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Authors: Daria Zabolotnaya, Svetlana Degtyareva, Veronika Kanestri, Danila Konnov

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An adequate choice of the initial antiretroviral treatment determines the treatment efficacy. In the clinical guidelines in Russia non-nucleoside reverse transcriptase inhibitors (NNRTIs) are still considered to be an option for first-line treatment while pretreatment drug resistance (PDR) testing is not routinely performed. We conducted a cohort retrospective study in HIV-positive treatment naïve patients of the H-clinic (Moscow, Russia) who performed PDR testing from July 2017 to November 2021. All the information was obtained from the medical records anonymously. We analyzed the mutations in reverse transcriptase and protease genes. RT-sequences were obtained by AmpliSens HIV-Resist-Seq kit. Drug resistance was defined using the HIVdb Program v. 8.9-1. PDR was estimated using the Stanford algorithm. Descriptive statistics were performed in Excel (Microsoft Office, 2019). A total of 261 HIV-1 infected patients were enrolled in the study including 197 (75.5%) male and 64 (24.5%) female. The mean age was 34.6±8.3 years. The median CD4 count – 521 cells/µl (IQR 367-687 cells/µl). Data on risk factors of HIV-infection were scarce. The total quantity of strains containing mutations in the reverse transcriptase gene was 75 (28.7%). From these 5 (1.9%) mutations were associated with PDR to nucleoside reverse transcriptase inhibitors (NRTIs) and 30 (11.5%) – with PDR to NNRTIs. The number of strains with mutations in protease gene was 43 (16.5%), from these only 3 (1.1%) mutations were associated with resistance to protease inhibitors. For NNRTIs the most prevalent PDR mutations were E138A, V106I. Most of the HIV variants exhibited a single PDR mutation, 2 were found in 3 samples. Most of HIV variants with PDR mutation displayed a single drug class resistance mutation. 2/37 (5.4%) strains had both NRTIs and NNRTIs mutations. There were no strains identified with PDR mutations to all three drug classes. Though earlier data demonstrated a lower level of PDR in HIV treatment naïve population in Russia and our cohort can be not fully representative as it is taken from the private clinic, it reflects the trend of increasing PDR especially to NNRTIs. Therefore, we consider either pretreatment testing or giving the priority to other drugs as first-line treatment necessary.

Keywords: HIV, resistance, mutations, treatment

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Authors: Pushpendra Kumar, Sanjeev Kumar, R. Balasubramanian

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Estimation of optical flow from a sequence of images using variational methods is one of the most successful approach. Discontinuity between different motions is one of the challenging problem in flow estimation. In this paper, we design a new anisotropic diffusion operator, which is able to provide smooth flow over a region and efficiently preserve discontinuity in optical flow. This operator is designed on the basis of intensity differences of the pixels and isotropic operator using exponential function. The combination of these are used to control the propagation of flow. Experimental results on the different datasets verify the robustness and accuracy of the algorithm and also validate the effect of anisotropic operator in the discontinuity preserving.

Keywords: optical flow, variational methods, computer vision, anisotropic operator

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Authors: Ashima Sharma, Tapan K. Chaudhuri

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Human Serum Albumin (HSA) is one of the most demanded therapeutic protein with immense biotechnological applications. The current source of HSA is human blood plasma. Blood is a limited and an unsafe source as it possesses the risk of contamination by various blood derived pathogens. This issue led to exploitation of various hosts with the aim to obtain an alternative source for the production of the rHSA. But, till now no host has been proven to be effective commercially for rHSA production because of their respective limitations. Thus, there exists an indispensable need to promote non-animal derived rHSA production. Of all the host systems, Escherichia coli is one of the most convenient hosts which has contributed in the production of more than 30% of the FDA approved recombinant pharmaceuticals. E. coli grows rapidly and its culture reaches high cell density using inexpensive and simple substrates. The fermentation batch turnaround number for E. coli culture is 300 per year, which is far greater than any of the host systems available. Therefore, E. coli derived recombinant products have more economical potential as fermentation processes are cheaper compared to the other expression hosts available. Despite of all the mentioned advantages, E. coli had not been successfully adopted as a host for rHSA production. The major bottleneck in exploiting E. coli as a host for rHSA production was aggregation i.e. majority of the expressed recombinant protein was forming inclusion bodies (more than 90% of the total expressed rHSA) in the E. coli cytosol. Recovery of functional rHSA form inclusion body is not preferred because it is tedious, time consuming, laborious and expensive. Because of this limitation, E. coli host system was neglected for rHSA production for last few decades. Considering the advantages of E. coli as a host, the present work has targeted E. coli as an alternate host for rHSA production through resolving the major issue of inclusion body formation associated with it. In the present study, we have developed a novel and innovative method for enhanced soluble and functional production of rHSA in E.coli (~60% of the total expressed rHSA in the soluble fraction) through modulation of the cellular growth, folding and environmental parameters, thereby leading to significantly improved and enhanced -expression levels as well as the functional and soluble proportion of the total expressed rHSA in the cytosolic fraction of the host. Therefore, in the present case we have filled in the gap in the literature, by exploiting the most well studied host system Escherichia coli which is of low cost, fast growing, scalable and ‘yet neglected’, for the enhancement of functional production of HSA- one of the most crucial biomolecule for clinical and biotechnological applications.

Keywords: enhanced functional production of rHSA in E. coli, recombinant human serum albumin, recombinant protein expression, recombinant protein processing

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Authors: Ali K. M. Al-Nasrawi, Uday A. Al-Hamdany, Sarah M. Hamylton, Brian G. Jones, Yasir M. Alyazichi

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Surface elevation dynamics have always responded to disturbance regimes. Creating Digital Elevation Models (DEMs) to detect surface dynamics has led to the development of several methods, devices and data clouds. DEMs can provide accurate and quick results with cost efficiency, in comparison to the inherited geomatics survey techniques. Nowadays, remote sensing datasets have become a primary source to create DEMs, including LiDAR point clouds with GIS analytic tools. However, these data need to be tested for error detection and correction. This paper evaluates various DEMs from different data sources over time for Apple Orchard Island, a coastal site in southeastern Australia, in order to detect surface dynamics. Subsequently, 30 chosen locations were examined in the field to test the error of the DEMs surface detection using high resolution global positioning systems (GPSs). Results show significant surface elevation changes on Apple Orchard Island. Accretion occurred on most of the island while surface elevation loss due to erosion is limited to the northern and southern parts. Concurrently, the projected differential correction and validation method aimed to identify errors in the dataset. The resultant DEMs demonstrated a small error ratio (≤ 3%) from the gathered datasets when compared with the fieldwork survey using RTK-GPS. As modern modelling approaches need to become more effective and accurate, applying several tools to create different DEMs on a multi-temporal scale would allow easy predictions in time-cost-frames with more comprehensive coverage and greater accuracy. With a DEM technique for the eco-geomorphic context, such insights about the ecosystem dynamic detection, at such a coastal intertidal system, would be valuable to assess the accuracy of the predicted eco-geomorphic risk for the conservation management sustainability. Demonstrating this framework to evaluate the historical and current anthropogenic and environmental stressors on coastal surface elevation dynamism could be profitably applied worldwide.

Keywords: DEMs, eco-geomorphic-dynamic processes, geospatial Information Science, remote sensing, surface elevation changes,

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Authors: Reham Khalaf-Nazzal, Imad Dweikat, Paula Gimenez, Iker Oyenarte, Alfonso Martinez-Cruz, Domonik Muller

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Metal cation transport mediator (CNNM) gene family comprises 4 isoforms that are expressed in various human tissues. Structurally, CNNMs are complex proteins that contain an extracellular N-terminal domain preceding a DUF21 transmembrane domain, a ‘Bateman module’ and a C-terminal cNMP-binding domain. Mutations in CNNM2 cause familial dominant hypomagnesaemia. Growing evidence highlights the role of CNNM2 in neurodevelopment. Mutations in CNNM2 have been implicated in epilepsy, intellectual disability, schizophrenia, and others. In the present study, we aim to elucidate the function of CNNM2 in the developing brain. Thus, we present the genetic origin of symptoms in two family cohorts. In the first family, three siblings of a consanguineous Palestinian family in which parents are first cousins, and consanguinity ran over several generations, presented a varying degree of intellectual disability, cone-rod dystrophy, and autism spectrum disorder. Exome sequencing and segregation analysis revealed the presence of homozygous pathogenic mutation in the CNNM2 gene, the parents were heterozygous for that gene mutation. Magnesium blood levels were normal in the three children and their parents in several measurements. They had no symptoms of hypomagnesemia. The CNNM2 mutation in this family was found to locate in the CBS1 domain of the CNNM2 protein. The crystal structure of the mutated CNNM2 protein was not significantly different from the wild-type protein, and the binding of AMP or MgATP was not dramatically affected. This suggests that the CBS1 domain could be involved in pure neurodevelopmental functions independent of its magnesium-handling role, and this mutation could have affected a protein partner binding or other functions in this protein. In the second family, another autosomal dominant CNNM2 mutation was found to run in a large family with multiple individuals over three generations. All affected family members had hypomagnesemia and hypermagnesuria. Oral supplementation of magnesium did not increase the levels of magnesium in serum significantly. Some affected members of this family have defects in fine motor skills such as dyslexia and dyslalia. The detected mutation is located in the N-terminal part, which contains a signal peptide thought to be involved in the sorting and routing of the protein. In this project, we describe heterogenous clinical phenotypes related to CNNM2 mutations and protein functions. In the first family, and up to the authors’ knowledge, we report for the first time the involvement of CNNM2 in retinal photoreceptor development and function. In addition, we report the presence of a neurophenotype independent of magnesium status related to the CNNM2 protein mutation. Taking into account the different modes of inheritance and the different positions of the mutations within CNNM2 and its different structural and functional domains, it is likely that CNNM2 might be involved in a wide spectrum of neuropsychiatric comorbidities with considerable varying phenotypes.

Keywords: magnesium transport, autosomal recessive, autism, neurodevelopment, CBS domain

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Authors: Emre Bayamlıoğlu

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Apart from being the subject of neighboring rights when broadcasted on TV or of cinematographic work when fixed to a tangible medium including a hard drive, the copyright eligibility of a sports performance, and eventually the sporting event has once again given rise to controversy following the CJEU judgment in the Murphy case. Most of the arguments which deny copyright protection for sports performances focus on the fact that unlike movies, plays, television programs, or operas, athletic events are competitive and have no underlying script. The first part of the paper aims to explain that such rhetoric is rather weak simply for the fact that, several types of performances such as improvised musical or dramatic shows are still protected by copyright despite the fact that they are not based on a script. The second part argues that the core reason for the denial copyright protection was the functionality aiming certain practical results such as winning the game, scoring, eliminating an opponent, obstructing a shot and etc., but no scientific or artistic expression in whatsoever form. The paper further argues that expanding copyright protection to functional performances would give rise to unintended copyright claims by the athletes on tackles, shoots, passes, crosses etc. resulting with further restrictions on reporting and photographing of sporting events. The final part provides a policy analysis of the trend to broaden the scope of copyright to cover sports performances. It is argued that such expansion will clearly undermine the ratio legis of copyright laws since it will give rise to excessive commodification of information beyond the needs of a viable market economy. Therefore, remedies other than copyright protection such as unfair competition and unjust enrichment provides sufficient redress for the damages to be sustained by the investors of sporting events.

Keywords: copyright eligibility, idea-expression dichotomy, sports performance

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Authors: Salma A. Mahmoud

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Epigenetic, or alteration in gene expression influenced by extragenetic factors, has emerged as one of the most promising areas that will address some of the gaps in our current knowledge in understanding patterns of human variation. In the last decade, the research investigating epigenetic mechanisms in many fields has flourished and witnessed significant progress. It paved the way for a new era of integrated research especially between anthropology/archeology and life sciences. Skeletal remains are considered the most significant source of information for studying human variations across history, and by utilizing these valuable remains, we can interpret the past events, cultures and populations. In addition to archeological, historical and anthropological importance, studying bones has great implications in other fields such as medicine and science. Bones also can hold within them the secrets of the future as they can act as predictive tools for health, society characteristics and dietary requirements. Bones in their basic forms are composed of cells (osteocytes) that are affected by both genetic and environmental factors, which can only explain a small part of their variability. The primary objective of this project is to examine the epigenetic landscape/signature within bones of archeological remains as a novel marker that could reveal new ways to conceptualize chronological events, gender differences, social status and ecological variations. We attempted here to address discrepancies in common variants such as methylome as well as novel epigenetic regulators such as chromatin remodelers, which to our best knowledge have not yet been investigated by anthropologists/ paleoepigenetists using plethora of techniques (biological, computational, and statistical). Moreover, extracting epigenetic information from bones will highlight the importance of osseous material as a vector to study human beings in several contexts (social, cultural and environmental), and strengthen their essential role as model systems that can be used to investigate and construct various cultural, political and economic events. We also address all steps required to plan and conduct an epigenetic analysis from bone materials (modern and ancient) as well as discussing the key challenges facing researchers aiming to investigate this field. In conclusion, this project will serve as a primer for bioarcheologists/anthropologists and human biologists interested in incorporating epigenetic data into their research programs. Understanding the roles of epigenetic mechanisms in bone structure and function will be very helpful for a better comprehension of their biology and highlighting their essentiality as interdisciplinary vectors and a key material in archeological research.

Keywords: epigenetics, archeology, bones, chromatin, methylome

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Authors: Joseph M. Rich, Vinay A. Duddalwar, Assad A. Oberai

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Prostate adenocarcinoma is the most common cancer in males, with osseous metastases as the commonest site of metastatic prostate carcinoma (mPC). Treatment monitoring is based on the evaluation and characterization of lesions on multiple imaging studies, including Computed Tomography (CT). Monitoring of the osseous disease burden, including follow-up of lesions and identification and characterization of new lesions, is a laborious task for radiologists. Deep learning algorithms are increasingly used to perform tasks such as identification and segmentation for osseous metastatic disease and provide accurate information regarding metastatic burden. Here, nnUNet was used to produce a model which can segment CT scan images of prostate adenocarcinoma vertebral bone metastatic lesions. nnUNet is an open-source Python package that adds optimizations to deep learning-based UNet architecture but has not been extensively combined with transfer learning techniques due to the absence of a readily available functionality of this method. The IRB-approved study data set includes imaging studies from patients with mPC who were enrolled in clinical trials at the University of Southern California (USC) Health Science Campus and Los Angeles County (LAC)/USC medical center. Manual segmentation of metastatic lesions was completed by an expert radiologist Dr. Vinay Duddalwar (20+ years in radiology and oncologic imaging), to serve as ground truths for the automated segmentation. Despite nnUNet’s success on some medical segmentation tasks, it only produced an average Dice Similarity Coefficient (DSC) of 0.31 on the USC dataset. DSC results fell in a bimodal distribution, with most scores falling either over 0.66 (reasonably accurate) or at 0 (no lesion detected). Applying more aggressive data augmentation techniques dropped the DSC to 0.15, and reducing the number of epochs reduced the DSC to below 0.1. Datasets have been identified for transfer learning, which involve balancing between size and similarity of the dataset. Identified datasets include the Pancreas data from the Medical Segmentation Decathlon, Pelvic Reference Data, and CT volumes with multiple organ segmentations (CT-ORG). Some of the challenges of producing an accurate model from the USC dataset include small dataset size (115 images), 2D data (as nnUNet generally performs better on 3D data), and the limited amount of public data capturing annotated CT images of bone lesions. Optimizations and improvements will be made by applying transfer learning and generative methods, including incorporating generative adversarial networks and diffusion models in order to augment the dataset. Performance with different libraries, including MONAI and custom architectures with Pytorch, will be compared. In the future, molecular correlations will be tracked with radiologic features for the purpose of multimodal composite biomarker identification. Once validated, these models will be incorporated into evaluation workflows to optimize radiologist evaluation. Our work demonstrates the challenges of applying automated image segmentation to small medical datasets and lays a foundation for techniques to improve performance. As machine learning models become increasingly incorporated into the workflow of radiologists, these findings will help improve the speed and accuracy of vertebral metastatic lesions detection.

Keywords: deep learning, image segmentation, medicine, nnUNet, prostate carcinoma, radiomics

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Authors: Kang-Mo Jung

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Least squares support vector machine (LS-SVM) is a penalized regression which considers both fitting and generalization ability of a model. However, the squared loss function is very sensitive to even single outlier. We proposed a weighted absolute deviation loss function for the robustness of the estimates in least absolute deviation support vector machine. The proposed estimates can be obtained by a quadratic programming algorithm. Numerical experiments on simulated datasets show that the proposed algorithm is competitive in view of robustness to outliers.

Keywords: least absolute deviation, quadratic programming, robustness, support vector machine, weight

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Authors: Mustafa Sertçelik, Turan Çalban, Hacali Necefoğlu, Sabri Çolak

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In this study, Chevreul’s salt solubility and its dissolution kinetics in ammonium chloride solutions were investigated. Chevreul’s salt that we used in the studies was obtained by using the optimum conditions (ammonium sulphide concentration; 0,4 M, copper sulphate concentration; 0,25 M, temperature; 60°C, stirring speed; 600 rev/min, pH; 4 and reaction time; 15 mins) determined by T. Çalban et al. Chevreul’s salt solubility in ammonium chloride solutions and the kinetics of dissolution were investigated. The selected parameters that affect solubility were reaction temperature, concentration of ammonium chloride, stirring speed, and solid/liquid ratio. Correlation of experimental results had been achieved using linear regression implemented in the statistical package program statistica. The effect of parameters on Chevreul’s salt solubility was examined and integrated rate expression of dissolution rate was found using kinetic models in solid-liquid heterogeneous reactions. The results revealed that the dissolution rate of Chevreul’s salt was decreasing while temperature, concentration of ammonium chloride and stirring speed were increasing. On the other hand, dissolution rate was found to be decreasing with the increase of solid/liquid ratio. Based on result of the applications of the obtained experimental results to the kinetic models, we can deduce that Chevreul’s salt dissolution rate is controlled by diffusion through the ash (or product layer). Activation energy of the reaction of dissolution was found as 74.83 kJ/mol. The integrated rate expression along with the effects of parameters on Chevreul's salt solubility was found to be as follows: 1-3(1-X)2/3+2(1-X)= [2,96.1013.(CA)3,08 .(S/L)-038.(W)1,23 e-9001,2/T].t

Keywords: Chevreul's salt, copper, ammonium chloride, ammonium sulphide, dissolution kinetics

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