Search results for: discovery studio 4.1/CDOCKER

Authors: Hassan Wajid, Syed T. Ahmed, Syed G. Haider Jr., Razia Latif, Ahsan Ali, Maira Anam

Abstract:

The phenomenon of Metamorphosis can be associated with any object, organism, or structure gradually and progressively going through the change of systemic or morphological form. This phenomenon can be integrated while teaching drawing to architecture students. In architectural drawings, metamorphosis’s main focus and purpose are not to completely imitate any object. In the process of drawing, the changes in systemic or morphological form happen until the complete process, and the visuals of the complete process change the drawing, opening up possibilities for the imagination of the perceivers. Metamorphosis in architectural drawings begins with an initial form and, through various noticeable stages, ends up final form or manifestation. How much of the initial form is manifested in the final form and progressively among various intermediate stages becomes an indication of the nature of metamorphosis as a phenomenon. It is important at this stage to clarify that the term metamorphosis is presently being coopted from its original domain, usually in life sciences. In this current exercise, the architectural drawings are to act as an operative analog process transforming one image of art and/or architecture in its broadest sense. That composition is claimed to have come from one source (individual work, a cultural artifact, civilizational remain). It dialectically meets, opposes, or confronts some carefully chosen alien opposites from a different domain. As an example, the layers of a detailed drawing of a Turkish prayer rug of 5 x 7 ratio over a detailed architectural plan of a religious, historical complex can be observed such that the two drawings, though at markedly different scales could dialectically converse with one another and through their mutual congruencies. In the final stage, the idea concludes contradictions across the scales to initiate the analogous roles of metamorphosed third reality, which suggests the previous un-acknowledged architectural or artistic identity. The proposed paper explores the trajectory of reproduction by analyzing drawings through detailed drawing stages and analyzes challenges as well as opportunities in the discovered realm of imagination. This description further aims at identifying factors influencing creativity and innovation in producing architectural drawings through the process of observing drawings from inception to the concluding stage.

Keywords: architectural drawings, metamorphosis, perceptions, discovery

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Authors: Alaaeddeen M. Seufi

Abstract:

Many have been published on therapeutic derivatives from living organisms including insects. In addition to traditional maggot therapy, more than 900 therapeutic products were isolated from insects. Most people look at insects as enemies and others believe that insects are friends. Many beneficial insects rather than Honey Bees, Silk Worms and Shellac insect could insure human-insect friendship. In addition, insects could be MicroFactories, Biosensors or Bioreactors. InsectFarm is an amazing example of the applied research that transfers insects from laboratory to market by Prof Mircea Ciuhrii and co-workers. They worked for 18 years to derive therapeutics from insects. Their research resulted in production of more than 30 commercial medications derived from insects (e.g. Imunomax, Noblesse, etc.). Two general approaches were followed to discover drugs from living organisms. Some laboratories preferred biochemical approach to purify components of the innate immune system of insects and insect metabolites as well. Then the purified components could be tested for many therapeutic trials. Other researchers preferred molecular approach based on proteomic studies. Components of the innate immune system of insects were then tested for their medical activities. Our Laboratory team preferred to induce insect immune system (using oral, topical and injection routes of administration), then a transcriptomic study was done to discover the induced genes and to identify specific biomarkers that can help in drug discovery. Biomarkers play an important role in medicine and in drug discovery and development as well. Optimum biomarker development and application will require a team approach because of the multifaceted nature of biomarker selection, validation, and application. This team uses several techniques such as pharmacoepidemiology, pharmacogenomics, and functional proteomics; bioanalytical development and validation; modeling and simulation to improve and refine drug development. Our Achievements included the discovery of four components of the innate immune system of Spodoptera littoralis and Musca domestica. These components were designated as SpliDef (defesin), SpliLec (lectin), SpliCec (cecropin) and MdAtt (attacin). SpliDef, SpliLec and MdAtt were confirmed as antimicrobial peptides, while SpliCec was additionally confirmed as anticancer peptide. Our current research is going on to achieve something in antioxidants and anticoagulants from insects. Our perspective is to achieve something in the mass production of prototypes of our products and to reach it to the commercial level. These achievements are the integrated contributions of everybody in our team staff.

Keywords: AMPs, insect, innate immunitty, therappeutics

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Authors: Shasline Gedeon, Tiffany W. Ardley, Ying Wang, Nathan J. Gesmundo, Katarina A. Sarris, Ana L. Aguirre

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Drug discovery and delivery involve drug targeting, an approach that helps find a drug against a chosen target through high throughput screening and other methods by way of identifying the physical properties of the potential lead compound. Physical properties of potential drug candidates have been an imperative focus since the unveiling of Lipinski's Rule of 5 for oral drugs. Throughout a compound's journey from discovery, clinical phase trials, then becoming a classified drug on the market, the desirable properties are optimized while minimizing/eliminating toxicity and undesirable properties. In the pharmaceutical industry, the ability to generate molecules in parallel with maximum efficiency is a substantial factor achieved through sp²-sp² carbon coupling reactions, e.g., Suzuki Coupling reactions. These reaction types allow for the increase of aromatic fragments onto a compound. More recent literature has found benefits to decreasing aromaticity, calling for more sp³-sp² carbon coupling reactions instead. The objective of this project is to provide a comparison between various sp³-sp² carbon coupling methods and reaction conditions, collecting data on production of the desired product. There were four different coupling methods being tested amongst three cores and 4-5 installation groups per method; each method ran under three distinct reaction conditions. The tested methods include the Photoredox Decarboxylative Coupling, the Photoredox Potassium Alkyl Trifluoroborate (BF3K) Coupling, the Photoredox Cross-Electrophile (PCE) Coupling, and the Weix Cross-Electrophile (WCE) Coupling. The results concluded that the Decarboxylative method was very difficult in yielding product despite the several literature conditions chosen. The BF3K and PCE methods produced competitive results. Amongst the two Cross-Electrophile coupling methods, the Photoredox method surpassed the Weix method on numerous accounts. The results will be used to build future libraries.

Keywords: drug discovery, high throughput chemistry, photoredox chemistry, sp³-sp² carbon coupling methods

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Authors: Michio Kurosu

Abstract:

Alterations in glycosylation not only directly impact cell growth and survival but also facilitate tumor-induced immunomodulation and eventual metastasis. Identification of cell type-specific glycoconjugates (tumor markers) has led to the discovery of new assay systems for certain cancers via immunodetection reagents. N- and O-linked glycans are the most abundant forms of glycoproteins. Recent studies of cancer immunotherapy are based on the immunogenicity of truncated O-glycan chains (e.g., Tn, sTn, T, and sLea/x). The prevalence of N-linked glycan changes in the development of tumor cells is known; however, therapeutic antibodies against N-glycans have not yet been developed. This is due to the lack of specificity of N-linked glycans between normal/healthy and cancer cells. Abnormal branching of N-linked glycans has been observed, particularly in solid cancer cells. While the discovery of drug-like glycosyltransferase inhibitors that block the biosynthesis of specific branching has a very low likelihood of success, altered glycosylation levels can be exploited by suppressing N-glycan biosynthesis through the inhibition of dolichyl-phosphate N-acetylglucosaminephosphotransferase1 (DPAGT1) activity. Inhibition of DPAGT1 function leads to changes of O-glycosylation on proteins associated with mitochondria and zinc finger binding proteins (indirect effects). On the basis of dynamic crosstalk between DPAGT1 and Snail/Slung/ZEB1 (a family of transcription factors that promote the repression of the adhesion molecules), we have developed pharmacologically acceptable selective DPAGT1 inhibitors. Tunicamycin kills a wide range of cancer and healthy cells in a non-selective manner. In sharp contrast, our DPAGT1 inhibitors display strong cytostatic effects against 16 solid cancers, which require the overexpression of DPAGT1 in their progression but do not affect the cell viability of healthy cells. The identified DPAGT1 inhibitors possess impressive anti-metastatic ability in various solid cancer cell lines and induce their mitochondrial structural changes, resulting in apoptosis. A prototype DPAGT1 inhibitor, APPB has already been proven to shrink solid tumors (e.g., pancreatic cancers, triple-negative breast cancers) in vivo while suppressing metastases and has strong synergistic effects when combined with current cytotoxic drugs (e.g., paclitaxel). At this conference, our discovery of selective DPAGT1 inhibitors with drug-like properties and proof-of-pharmaceutical concept studies of a novel DPAGT1 inhibitor are presented.

Keywords: DPAGT1 inhibitors, anti-metastatic drugs, natural product based drug designs, cytostatic effects

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Authors: T. Benyetho, L. El Abdellaoui, J. Terhzaz, H. Bennis, N. Ababssi, A. Tajmouati, A. Tribak, M. Latrach

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This work presents a new planar multiband antenna based on fractal geometry. This structure is optimized and validated into simulation by using CST-MW Studio. To feed this antenna we have used a CPW line which makes it easy to be incorporated with integrated circuits. The simulation results presents a good matching input impedance and radiation pattern in the GSM band at 900 MHz and ISM band at 2.4 GHz. The final structure is a dual band fractal antenna with 70 x 70 mm² as a total area by using an FR4 substrate.

Keywords: Antenna, CPW, fractal, GSM, multiband

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Authors: S. Nandagopalan, N. Pradeep

Abstract:

The aim of this paper is to propose a general framework for storing, analyzing, and extracting knowledge from two-dimensional echocardiographic images, color Doppler images, non-medical images, and general data sets. A number of high performance data mining algorithms have been used to carry out this task. Our framework encompasses four layers namely physical storage, object identification, knowledge discovery, user level. Techniques such as active contour model to identify the cardiac chambers, pixel classification to segment the color Doppler echo image, universal model for image retrieval, Bayesian method for classification, parallel algorithms for image segmentation, etc., were employed. Using the feature vector database that have been efficiently constructed, one can perform various data mining tasks like clustering, classification, etc. with efficient algorithms along with image mining given a query image. All these facilities are included in the framework that is supported by state-of-the-art user interface (UI). The algorithms were tested with actual patient data and Coral image database and the results show that their performance is better than the results reported already.

Keywords: active contour, Bayesian, echocardiographic image, feature vector

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Authors: Mehravar Javid

Abstract:

This article delves straight into the fascinating role of dream interpretation in psychotherapy, particularly in the context of trauma and healing. By applying a detailed case study of a 19-year-old Iranian woman who has been undergoing therapy, it can explore to what extent her vivid and symbolic dreams – featuring mermaids, hanging fetuses, and themes of control and domination – serve as a reflection of her innermost fears, unresolved traumas, and struggles with identity and sexuality. Another fact to be highlighted is that the dreams, rich in metaphor and symbolism, offer a unique outlook into the patient's subconscious mind, revealing layers of her psychological state that might otherwise remain obscured and vague. On the other hand, the article examines how the therapist navigates these dreamscapes by utilizing them as a tool to understand and address the patient's deep-seated emotional conflicts, traumatic experiences, and identity issues. By analyzing these dreams, we can demonstrate how such dreams can be a crucial part of the healing process, providing insights that facilitate emotional recovery and self-discovery. This discovery underscores the significance of dreams in psychotherapy, highlighting their potential as a powerful medium for unraveling the complexities of the human psyche and aiding in the journey toward mental health and recovery.

Keywords: dream, interpreting, trauma, healing

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Authors: Alyona Cerfontyne, Levita D'Souza, Lefteris Patlamazoglou

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Unlike adoption and donor-assisted reproduction, misattributed paternity occurring within the context of spontaneous conception and outside of formally recognised practices of having a child remains largely an understudied phenomenon. In adulthood, to discover misattributed paternity, i.e., that the man you call your father is not related to you genetically, can have profound implications for everyone affected. Until the advent of direct-to-consumer DNA testing 20 years ago, such discoveries were relatively rare. Despite the growing number of individuals uncovering their biogenetic paternity through genetic testing, there is very limited research on misattributed paternity from the perspective of adult children affected by it. No research exists on how to support these individuals through counselling post-discovery. Framed as insider action research, this study aimed to explore the perceived psychosocial consequences of misattributed paternity discoveries and coping strategies used by individuals who discover their misattributed paternity status in adulthood. In total, 12 individuals with misattributed paternity participated in semi-structured interviews in July-August 2022. The collected data was analysed using reflexive thematic analysis. The study’s results indicate that discovering misattributed paternity in adulthood can be likened to a watershed moment forever changing the trajectory of one’s life. Psychological experiences consistent with trauma, as well as grief and loss, re-evaluation of close family relationships, reestablishment of one’s identity, as well as experiencing a profound need to belong are the key themes emerging from the analysis of psychosocial experiences. Post-discovery, individuals with misattributed paternity employ a wide range of emotional and problem-focused coping strategies, amongst which seeking connection with those who understand, searching for information on the new biogenetic family and finding new meanings to life are most prominent. The study contributes both to the academic and practical knowledge of experiences of misattributed paternity and highlights the importance of further research on the topic.

Keywords: discovery of misattributed paternity, misattributed paternity, paternal discrepancy, psychosocial consequences, coping

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Authors: Amira Bousselmi

Abstract:

This article presents a PIFA antenna designed for geolocation applications (GNSS) operating on 1.278 GHz, 2.8 GHz, 5.7 GHz and 10 GHz. To improve the performance of the antenna, an artificial magnetic conductor structure (AMC) was used. Adding the antenna with AMC resulted in a measured gain of 4.78 dBi. The results of simulations and measurements are presented. CST Microwave Studio is used to design and compare antenna performance. An antenna design methodology, design and characterization of the AMC surface are described as well as the simulated and measured performances of the AMC antenna are then discussed. Finally, in Section V, there is a conclusion.

Keywords: antenna multiband, global navigation system, AMC, Galeleo

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Authors: S. Nandagopalan, N. Pradeep

Abstract:

The aim of this paper is to propose a general framework for storing, analyzing, and extracting knowledge from two-dimensional echocardiographic images, color Doppler images, non-medical images, and general data sets. A number of high performance data mining algorithms have been used to carry out this task. Our framework encompasses four layers namely physical storage, object identification, knowledge discovery, user level. Techniques such as active contour model to identify the cardiac chambers, pixel classification to segment the color Doppler echo image, universal model for image retrieval, Bayesian method for classification, parallel algorithms for image segmentation, etc., were employed. Using the feature vector database that have been efficiently constructed, one can perform various data mining tasks like clustering, classification, etc. with efficient algorithms along with image mining given a query image. All these facilities are included in the framework that is supported by state-of-the-art user interface (UI). The algorithms were tested with actual patient data and Coral image database and the results show that their performance is better than the results reported already.

Keywords: active contour, bayesian, echocardiographic image, feature vector

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Authors: A. El Hamdouni, J. Zbitou, A. Tajmouati, L. El Abdellaoui, A. Errkik, A. Tribak, M. Latrach

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This paper presents a novel fractal antenna structure proposed for UWB (Ultra – Wideband) applications. The frequency band 3.1-10.6 GHz released by FCC (Federal Communication Commission) as the commercial operation of UWB has been chosen as frequency range for this antenna based on coplanar waveguide (CPW) feed and circular shapes fulfilled according to fractal geometry. The proposed antenna is validated and designed by using an FR4 substrate with overall area of 34 x 43 mm2. The simulated results performed by CST-Microwave Studio and compared by ADS (Advanced Design System) show good matching input impedance with return loss less than -10 dB between 2.9 GHz and 11 GHz.

Keywords: Fractal antenna, Fractal Geometry, CPW Feed, UWB, FCC

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Authors: Hema Bhardwaj, D. Srinivasa Rao

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Technology for analysing, processing, and extracting meaningful data from enormous and complicated datasets can be termed as "big data." The technique of big data mining and big data analysis is extremely helpful for business movements such as making decisions, building organisational plans, researching the market efficiently, improving sales, etc., because typical management tools cannot handle such complicated datasets. Special computational and statistical issues, such as measurement errors, noise accumulation, spurious correlation, and storage and scalability limitations, are brought on by big data. These unique problems call for new computational and statistical paradigms. This research paper offers an overview of the literature on big data mining, its process, along with problems and difficulties, with a focus on the unique characteristics of big data. Organizations have several difficulties when undertaking data mining, which has an impact on their decision-making. Every day, terabytes of data are produced, yet only around 1% of that data is really analyzed. The idea of the mining and analysis of data and knowledge discovery techniques that have recently been created with practical application systems is presented in this study. This article's conclusion also includes a list of issues and difficulties for further research in the area. The report discusses the management's main big data and data mining challenges.

Keywords: big data, data mining, data analysis, knowledge discovery techniques, data mining challenges

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Authors: Elena G. Salina, Vadim A. Makarov

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With the emergence of primary resistance to the current drugs and wide distribution of latent tuberculosis infection, a need for new compounds with a novel mode of action is growing steadily. Copper-mediated innate immunity and antibacterial toxicity propose novel strategies in TB drug discovery and development. Transcriptome of M. tuberculosis was obtained by RNA-seq, intracellular copper content was measured by ISP MS and complexes of 1-hydroxy-2-thiopyridines with copper were detected by HPLC.1-hydroxy-2-thiopyridine derivatives were found to be highly active in vitro against both actively growing and dormant non-culturable M. tuberculosis. Transcriptome response to 1-hydroxy-2-thiopyridines revealed signs of copper toxicity in M. tuberculosis bacilli. Indeed, Cu was found to accumulate inside cells treated with 1-hydroxy-2-thiopyridines. These compounds were found to form stable charged lipophylic complexes with Cu²⁺ ions which transport into mycobacterial cell. Subsequent metabolic destruction of the complex led to transformation of 1-hydroxy-2-thiopyridines into 2-methylmercapto-2-ethoxycarbonylpyridines, which did not possess antitubercular activity and releasing of free Cu²⁺ in the cytoplasm. 1-hydroxy-2-thiopyridines are a potent class of Cu-dependent inhibitors of M. tuberculosis which may control M. tuberculosis infection by impairment of copper homeostasis. Acknowledgment: This work was financially supported by the Ministry of Education and Science of the RussianFederation (Agreement No 14.616.21.0065; unique identifier RFMEFI61616X0065).

Keywords: copper toxicity, drug discovery, M. tuberculosis inhibitors, 2-thiopyridines

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Authors: Reem Al-Shidhani, Isabelle S. R. Storer, Michael J. Bromley, Lydia Tabernero

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Invasive fungal diseases are an increasing global health concern that contributes to the high mortality rates in immunocompromised patients. The rising of antifungal resistance severely lowers the efficacy of the limited antifungal agents available. New antifungal drugs that target new mechanisms are necessary to tackle the current shortfalls. Amongst post- modifications, phosphorylation is a predominant and an outstanding protein alteration in all eukaryotes. In fungi, protein phosphorylation plays a vital role in many signal transduction pathways, including cell cycle, cell growth, metabolism, transcription, differentiation, proliferation, and virulence. The investigation of Aspergillus fumigatus phosphatases revealed seven genes essential for viability. Inhibiting one of these phosphatases is a new interesting route to develop novel antifungal drugs. In this study, we carried out an early drug discovery process targeting oneessential phosphatase, GlcA. Here, we report the identification of new GlcA inhibitors that show antifungal activity. These important finding open a new avenue to the development of novel antifungals to expand the current narrow arsenal of clinical candidates.

Keywords: invasive fungal diseases, phosphatases, GlcA, competitive inhibitors

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Authors: Luís Antonio de Almeida Rodriguez, José Maria Parente de Oliveira, Ednelson Oliveira

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In the last two decades, the world’s aviation authorities have made several attempts to create consensus about a global and accepted approach for applying semantics to web services registry descriptions. This problem has led communities to face a fat and disorganized infrastructure to describe aeronautical web services. It is usual for developers to implement ad-hoc connections among consumers and providers and manually create non-standardized service compositions, which need some particular approach to compose and semantically discover a desired web service. Current practices are not precise and tend to focus on lightweight specifications of some parts of the OWL-S and embed them into syntactic descriptions (SOAP artifacts and OWL language). It is necessary to have the ability to manage the use of both technologies. This paper presents an implementation of the ontology OWL-S that describes a Brazilian Aeronautical Web Service Registry, which makes it able to publish, advertise, make multi-criteria semantic discovery aligned with the ideas of the System Wide Information Management (SWIM) Program, and invoke web services within the Air Traffic Management context. The proposal’s best finding is a generic approach to describe semantic web services. The paper also presents a set of functional requirements to guide the ontology development and to compare them to the results to validate the implementation of the OWL-S Ontology.

Keywords: aeronautical web services, OWL-S, semantic web services discovery, ontologies

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Authors: Bing Li, Zhi Li, Yilong Yang

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Web classification can promote the quality of service discovery and management in the service repository. It is widely used to locate developers desired services. Although traditional classification methods based on supervised learning models can achieve classification tasks, developers need to manually mark web services, and the quality of these tags may not be enough to establish an accurate classifier for service classification. With the doubling of the number of web services, the manual tagging method has become unrealistic. In recent years, the attention mechanism has made remarkable progress in the field of deep learning, and its huge potential has been fully demonstrated in various fields. This paper designs a multi-head attention graph convolutional network (MHAGCN) service classification method, which can assign different weights to the neighborhood nodes without complicated matrix operations or relying on understanding the entire graph structure. The framework combines the advantages of the attention mechanism and graph convolutional neural network. It can classify web services through automatic feature extraction. The comprehensive experimental results on a real dataset not only show the superior performance of the proposed model over the existing models but also demonstrate its potentially good interpretability for graph analysis.

Keywords: attention mechanism, graph convolutional network, interpretability, service classification, service discovery

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Authors: Christina Williams, Mehari Weldemariam, Ann M. Farese, Thomas J. MacVittie, Maureen A. Kane

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Radiation exposure results in dose-dependent and time-dependent multi-organ damage. Drug development of medical countermeasures (MCM) for radiation-induced injury occurs under the FDA Animal Rule because human efficacy studies are not ethical or feasible. The FDA Animal Rule requires the representation of both sexes and describes several uses for biomarkers in MCM drug development studies. Currently, MCMs are limited and there is no FDA-approved biomarker for any radiation injury. Sex as a variable is essential to identifying biomarkers and developing effective MCMs for acute radiation exposure (ARS) and delayed effects of acute radiation exposure (DEARE). These studies aim to address the death of information on sex differences that have not been determined by studies that included only male, single-sex cohorts. Studies have reported differences in radiosensitivity according to sex. As such, biomarker discovery for radiation-induced damage must consider sex as a variable. This study evaluated the plasma proteomic profile of Rhesus macaque non-human primates after different exposures and doses, as well as time points after radiation. Exposures and doses included total body irradiation between 5-7.5 Gy and partial body irradiation with 5% bone marrow sparing at 9, 9.5 and 10 Gy. Timepoints after irradiation included days 1, 3, 60, and 180, which encompassed both acute radiation syndromes and delayed effects of acute radiation exposure. Bottom-up proteomic analyses of plasma included equal numbers of males and females. In the control animals, few proteomic differences are observed between the sexes. In the irradiated animals, there are a few sex differences, with changes mostly consisting of proteins upregulated in the female animals. Multiple canonical pathways were upregulated in irradiated animals relative to the control animals when subjected to pathway analysis, but differential responses between the sexes are limited. These data provide critical baseline differences according to sex and establish sex differences in non-human primate models relevant to drug development of MCM under the FDA Animal Rule.

Keywords: ionizing radiation, sex differences, plasma proteomics, biomarker discovery

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Authors: Olanrewaju B. Lasisi

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The position of Ijebu-Ode, the historical capital of the Ijebu Kingdom, at the center of gravity of Ijebu land is enclosed by the 180-km-long earthwork and suggests a centrally controlled project. This paper reflects on the first stratigraphic drawing of the banks and ditches of this earthwork, and place its construction mechanism in a chronological framework. Nine radiocarbon dates obtained at the site suggest that the earthwork was built in the late 14th or early 15th century. This suggests a relationship with the Ijebu Kingdom, which pre-existed the opening of the Atlantic trade but first became visible only in the Portuguese records in the 1480s. In June 2017, more earthworks were found but within the core of Ijebu Land. This most recent finding points to an extension of territory from the center to the outlying villages. One central question about this discovery of monumental architectures that was functional around the 14th century or before is in its mode of construction. Apparently, iron tools must have been used in the construction of ‘a 20m deep ditch that runs 180km in circumference.’ Thus, the discovery of iron-working sites around the vicinity of the earthwork is a pointer to this building process that is up till now shrouded in mystery. By comparing the chronology of Ijebu earthworks with the evidence of Iron working in south western Nigeria around the first half of the first millennium AD, it can be thought that the rise in polity triggered the knowledge of metallurgy in the region.

Keywords: archaeology, earthworks, Ijebu, metallurgy

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Authors: Abdul Musaweer Habib, Habibul Hasan Mazumder, Saiful Islam, Sohel Sikder, Omar Faruk Sikder

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The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1499 proteins of Fusobacterium nucleatum, which has no homolog in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the KEGG Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the 3-D structure of these three proteins. Finally, determination of ligand binding sites of the key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against Fusobacterium nucleatum.

Keywords: colorectal cancer, drug target, Fusobacterium nucleatum, homology modeling, ligands

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Authors: Surajit Bhattacharya, Daniel Veltri, Atit A. Patel, Daniel N. Cox

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miRNAs have emerged as key post-transcriptional regulators of gene expression, however identification of biologically-relevant target genes for this epigenetic regulatory mechanism remains a significant challenge. To address this knowledge gap, we have developed a novel tool in R, Intra-miR-ExploreR, that facilitates integrated discovery of miRNA targets by incorporating target databases and novel target prediction algorithms, using statistical methods including Pearson and Distance Correlation on microarray data, to arrive at high confidence intragenic miRNA target predictions. We have explored the efficacy of this tool using Drosophila melanogaster as a model organism for bioinformatics analyses and functional validation. A number of putative targets were obtained which were also validated using qRT-PCR analysis. Additional features of the tool include downloadable text files containing GO analysis from DAVID and Pubmed links of literature related to gene sets. Moreover, we are constructing interaction maps of intragenic miRNAs, using both micro array and RNA-seq data, focusing on neural tissues to uncover regulatory codes via which these molecules regulate gene expression to direct cellular development.

Keywords: miRNA, miRNA:mRNA target prediction, statistical methods, miRNA:mRNA interaction network

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Authors: M. Khazini, M.Damou, Z. Souar

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In this paper, octagon antenna ultra wideband (UWB) low band wearable antenna designs have been proposed for in-body to on-body communication channel of wireless. Single element antenna, dual elements, are designed and compared in free space and in body proximity. Conformal design has been focused. Liquid crystal polymer (LCP) is a material that has gained attention as a potential high-performance microwave substrate and packaging material. This investigation uses several methods to determine the electrical properties of LCP for millimeter-wave frequencies.

Keywords: ultra wideband, wearable antenna, slot antenna, liquid crystal polymer (LCP), CST studio

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Authors: Reza Ferdousi, Reza Safdari, Yadollah Omidi

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Drug-drug interactions (DDIs) are main cause of the adverse drug reactions and nature of the functional and molecular complexity of drugs behavior in human body make them hard to prevent and treat. With the aid of new technologies derived from mathematical and computational science the DDIs problems can be addressed with minimum cost and efforts. Market basket analysis is known as powerful method to identify co-occurrence of thing to discover patterns and frequency of the elements. In this research, we used market basket analysis to identify important bio-elements in DDIs occurrence. For this, we collected all known DDIs from DrugBank. The obtained data were analyzed by market basket analysis method. We investigated all drug-enzyme, drug-carrier, drug-transporter and drug-target associations. To determine the importance of the extracted bio-elements, extracted rules were evaluated in terms of confidence and support. Market basket analysis of the over 45,000 known DDIs reveals more than 300 important rules that can be used to identify DDIs, CYP 450 family were the most frequent shared bio-elements. We applied extracted rules over 2,000,000 unknown drug pairs that lead to discovery of more than 200,000 potential DDIs. Analysis of the underlying reason behind the DDI phenomena can help to predict and prevent DDI occurrence. Ranking of the extracted rules based on strangeness of them can be a supportive tool to predict the outcome of an unknown DDI.

Keywords: drug-drug interaction, market basket analysis, rule discovery, important bio-elements

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Authors: Kai-Cheng Hsu, Tzu-Ying Sung, Jinn-Moon Yang

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Colorectal cancer (CRC) is one of the main causes of cancer death in the world. Although several drugs have been developed to treat colorectal cancer, such as Regorafenib and 5-FU, their efficacy is often limited by the development of drug resistance. Therefore, development of new drugs with new scaffolds is necessary to treat CRC. Here, we used site-moiety maps to identify inhibitors against PIM1, LIMK1, SRC, and mTOR, which are often overexpressed in CRC. A site-moiety map represents physicochemical properties and moiety preferences of a binding site through anchors. An anchor contains three elements: (1) conserved interacting residues of a binding pocket; (2) moiety preference of the binding pocket; and (3) the type (e.g., hydrogen-bonding or van der Waals interactions) of interaction between the moieties and the binding pocket. Then, we performed a structure-based virtual screening of ~260,000 compounds and selected compound candidates with high site-moiety map scores for bioassays. Among these candidates, compound 1 and compound 2 inhibited the growth of CRC cells with IC50 values of <10 μM. The experimental result of enzyme-based assays indicated that compound 1 is a dual inhibitor against PIM1 (IC50 6 μM) and LIMK1(IC50 11 μM). Compound 2 was predicted as a SRC inhibitor and will be further validated. The compounds inhibited different protein targets compared to the current drugs. We believe that the compounds provide a starting point to design new drugs for CRC treatment.

Keywords: colorectal cancer, drug discovery, site-moiety map, virtual screening, PIM1, LIMK1

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Authors: Fatima Zahra Moussa, Yamina Belhadef, Souheyla Ferouani

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In this work, we present a new form of miniature circular patch antenna based on CSRR metamaterials with an extended bandwidth proposed for 5 GHz Wi-Fiapplications. A reflection coefficient of -35 dB and a radiation pattern of 7.47 dB are obtained when simulating the initial proposed antenna with the CST microwave studio simulation software. The notch insertion technique in the radiating element was used for matching the antenna to the desired frequency in the frequency band [5150-5875] MHz.An extension of the bandwidth from 332 MHz to 1423 MHz was done by the DGS (defected ground structure) technique to meet the user's requirement in the 5 GHz Wi-Fi frequency band.

Keywords: patch antenna, miniaturisation, CSRR, notches, wifi, DGS

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Authors: Gabriela V. Angeles Perez, Jose Castillejos Lopez, Araceli L. Reyes Cabello, Emilio Bravo Grajales, Adriana Perez Espinosa, Jose L. Quiroz Fabian

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Road traffic accidents are among the principal causes of traffic congestion, causing human losses, damages to health and the environment, economic losses and material damages. Studies about traditional road traffic accidents in urban zones represents very high inversion of time and money, additionally, the result are not current. However, nowadays in many countries, the crowdsourced GPS based traffic and navigation apps have emerged as an important source of information to low cost to studies of road traffic accidents and urban congestion caused by them. In this article we identified the zones, roads and specific time in the CDMX in which the largest number of road traffic accidents are concentrated during 2016. We built a database compiling information obtained from the social network known as Waze. The methodology employed was Discovery of knowledge in the database (KDD) for the discovery of patterns in the accidents reports. Furthermore, using data mining techniques with the help of Weka. The selected algorithms was the Maximization of Expectations (EM) to obtain the number ideal of clusters for the data and k-means as a grouping method. Finally, the results were visualized with the Geographic Information System QGIS.

Keywords: data mining, k-means, road traffic accidents, Waze, Weka

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Authors: Cem Çindaş, Serkan Şimşek

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In this paper, the study and design of a 3-dB 90° directional coupler operating in the S-band is proposed. The coupler employs symmetrical multi-section coupled lines designed in a stripline technique. Design is realized in AWR Design Environment and CST Microwave Studio. Using these two programs played a key role in attaining outcomes swiftly and precisely. The simulation results show that the coupler maintains amplitude consistency within ± 0.3 dB, isolation and reflection losses better than 16 dB, and phase difference between two output ports of 88º±0.6˚ in the 1.7 – 4.35 GHz range. This simulation results indicate an improvement is achieved in fractional bandwidth (FBW) performance around the center frequency of f0 = 3 GHz.

Keywords: coupled stripline, directional coupler, multi-section coupler, symmetrical coupler

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Authors: Paolo Fantozzi, Luigi Laura, Umberto Nanni

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The problem of Entity relation discovery in structured data, a well covered topic in literature, consists in searching within unstructured sources (typically, text) in order to find connections among entities. These can be a whole dictionary, or a specific collection of named items. In many cases machine learning and/or text mining techniques are used for this goal. These approaches might be unfeasible in computationally challenging problems, such as processing massive data streams. A faster approach consists in collecting the cooccurrences of any two words (entities) in order to create a graph of relations - a cooccurrence graph. Indeed each cooccurrence highlights some grade of semantic correlation between the words because it is more common to have related words close each other than having them in the opposite sides of the text. Some authors have used sliding windows for such problem: they count all the occurrences within a sliding windows running over the whole text. In this paper we generalise such technique, coming up to a Weighted-Distance Sliding Window, where each occurrence of two named items within the window is accounted with a weight depending on the distance between items: a closer distance implies a stronger evidence of a relationship. We develop an experiment in order to support this intuition, by applying this technique to a data set consisting in the text of the Bible, split into verses.

Keywords: cooccurrence graph, entity relation graph, unstructured text, weighted distance

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Authors: Abdullah M. Algarni, Yashwant K. Malaiya

Abstract:

Some of the key aspects of vulnerability-discovery, dissemination, and disclosure-have received some attention recently. However, the role of interaction among the vulnerability discoverers and vulnerability acquirers has not yet been adequately addressed. Our study suggests that a major percentage of discoverers, a majority in some cases, are unaffiliated with the software developers and thus are free to disseminate the vulnerabilities they discover in any way they like. As a result, multiple vulnerability markets have emerged. In some of these markets, the exchange is regulated, but in others, there is little or no regulation. In recent vulnerability discovery literature, the vulnerability discoverers have remained anonymous individuals. Although there has been an attempt to model the level of their efforts, information regarding their identities, modes of operation, and what they are doing with the discovered vulnerabilities has not been explored. Reports of buying and selling of the vulnerabilities are now appearing in the press; however, the existence of such markets requires validation, and the natures of the markets need to be analysed. To address this need, we have attempted to collect detailed information. We have identified the most prolific vulnerability discoverers throughout the past decade and examined their motivation and methods. A large percentage of these discoverers are located in Eastern and Western Europe and in the Far East. We have contacted several of them in order to collect first-hand information regarding their techniques, motivations, and involvement in the vulnerability markets. We examine why many of the discoverers appear to retire after a highly successful vulnerability-finding career. The paper identifies the actual vulnerability markets, rather than the hypothetical ideal markets that are often examined. The emergence of worldwide government agencies as vulnerability buyers has significant implications. We discuss potential factors that can impact the risk to society and the need for detailed exploration.

Keywords: risk management, software security, vulnerability discoverers, vulnerability markets

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Authors: Damou Mehdi, Nouri Keltouma, Fahem Mohammed

Abstract:

In this paper, the concept of substrate integrated waveguide (SIW) technology is used to design filter for 30 GHz communication systems. SIW is created in the substrate of RT/Duroid 5880 having relative permittivity ε_r= 2.2 and loss tangent tanφ = 0.0009. Four Via are placed on the century filter the structures of SIW are modeled using and have been optimized in software HFSS (High Frequency Structure Simulator), à transition is designed for a Ka-band transceiver module with a 28.5GHz center frequency, . and then the results are verified using another simulation CST Microwave Studio (Computer Simulation Technology). The return loss are less than -18 dB, and -13 dB respectively. The insertion loss is divided equally -1.2 dB and -1.4 respectively.

Keywords: transition, microstrip, substrat integrated wave guide, filter, via

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Authors: Nicole C. Valdez, Vincent L. Borromeo, Conrad C. Chong, Ahmad F. Mazahery

Abstract:

Breast cancer is the most prevalent cancer worldwide, where the majority of cases are estrogen-receptor positive and involve 2 receptor proteins. The binding of estrogen to estrogen receptor alpha (ERα) promotes breast cancer growth, while it's binding to estrogen-receptor beta (ERβ) inhibits tumor growth. While natural products have been a promising source of chemotherapeutic agents, the challenge remains in finding a bioactive compound that specifically targets cancer cells, minimizing side effects on normal cells. Flavonoids are natural products that act as phytoestrogens and induce the same response as estrogen. They are able to compete with estrogen for binding to ERα; however, it has a higher binding affinity for ERβ. Their abundance in nature and low toxicity make them a potential candidate for breast cancer treatment. This study aimed to determine which particular flavonoids can specifically recognize ERβ and potentially be used for breast cancer treatment through molecular docking. A total of 206 flavonoids comprised of 97 isoflavones and 109 flavanones were collected from ZINC15, while the 3D structures of ERβ and ERα were obtained from Protein Data Bank. These flavonoid subclasses were chosen as they bind more strongly to ERs due to their chemical structure. The structures of the flavonoid ligands were converted using Open Babel, while the estrogen receptor protein structures were prepared using Autodock MGL Tools. The optimal binding site was found using BIOVIA Discovery Studio Visualizer before docking all flavonoids on both ERβ and ERα through Autodock Vina. Genistein is a flavonoid that exhibits anticancer effects by binding to ERβ, so its binding affinity was used as a baseline. Eriodictyol and 4”,6”-Di-O-Galloylprunin both exceeded genistein’s binding affinity for ERβ and was lower than its binding affinity for ERα. Of the two, eriodictyol was pursued due to its antitumor properties on a lung cancer cell line and on glioma cells. It is able to arrest the cell cycle at the G2/M phase by inhibiting the mTOR/PI3k/Akt cascade and is able to induce apoptosis via the PI3K/Akt/NF-kB pathway. Protein pathway and gene analysis were also conducted using ChEMBL and PANTHER and it was shown that eriodictyol might induce anticancer effects through the ROS1, CA7, KMO, and KDM1A genes which are involved in cell proliferation in breast cancer, non-small cell lung cancer, and other diseases. The high binding affinity of eriodictyol to ERβ, as well as its potential affected genes and antitumor effects, therefore, make it a candidate for the development of new breast cancer treatment. Verification through in vitro experiments such as checking the upregulation and downregulation of genes through qPCR and checking cell cycle arrest using a flow cytometry assay is recommended.

Keywords: breast cancer, estrogen receptor, flavonoid, molecular docking

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