Search results for: multi-element expression pattern

Authors: Mahmoodreza Tahamtan

Abstract:

Background: Malignant surface epithelial ovarian tumors (SEOT) account for approximately 90% of primary ovarian cancer. Wilms tumor gene (WT1) product was defined as a tumor suppressor gene, but today it is considered capable of performing oncogenic functions. There seems to be differences in WT1 expression patterns among SEOT subtypes. We evaluate the immunohistochemical expression of WT1 protein among different histologic subtypes of SEOT. Materials and Methods: Immunohistochemistry for WT1 was done on 35 serous cystadenocarcinomas, 9 borderline serous tumors, 3 mucinous cystadenocarcinomas, 10 borderline mucinous tumors, 7 endometrioid ovarian carcinomas, 3 clear cell carcinomas, 1 malignant Brenner tumor, 2 metastatic adenocarcinomas, and 6 endometrial adenocarcinomas. A tumor was considered negative if < 1% of tumor cells were stained.Positive reactions were graded as follows:1+,1%-24%; 2+,25%-49%; 3+,50%-74%; 4+,75%-100%. Results: Of the 35 cases of ovarian serous cystadenocarcinoma, 30(85.7%) were diffusely positive (3+,4+),4 showed reactivity of < 50% of the tumor cells (1+,2+), and one were negative. All 9 borderline serous tumors showed immunoreactivity with WT1. All the mucinous tumors(n:13), endometrioid carcinomas (n: 7), clear cell carcinomas (n: 3), metastatic adenocarcinomas (n: 2) and primary endometrial carcinomas (n:6) were negative. The single malignant Brenner tumor showed a positive reaction for WT1(4+) Conclusion: WT1 is a good marker to distinguish primary ovarian serous carcinomas from other surface epithelial tumors (especially endometrioid subtype) and metastatic carcinomas (especially endometrial serous carcinoma), other than malignant mesothelioma. We cannot rely to the degree of expression inorder to separate high grade borderline serous tumors from low grade ones.

Keywords: WT1, ovary, epithelial tumors, malignant

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Authors: Suddhasil Siddhanta, Debasish Nandy

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Child sex ratios pattern in the Asian Population is highly masculine mainly due to birth masculinity and gender bias in child mortality. The vast and the growing literature of female deficit in world population points out the diffusion of child sex ratio pattern in many Asian as well as neighboring European countries. However, little attention has been given to understand the common factors in different demographics in explaining child sex ratio pattern. Such a scholarship is extremely important as level of gender inequity is different in different country set up. Our paper tries to explain the major structural commonalities in the child masculinity pattern in two demographic billionaires - India and China. The analysis reveals that apart from geographical diffusion of sex selection technology, patrilocal social structure, as proxied by households with more than one generation in China and proportion of population aged 65 years and above in India, can explain significant variation of missing girl child in these two countries. Even after controlling for individual capacity building factors like educational attainment, or work force participation, the measure of social stratification is coming out to be the major determinant of child sex ratio variation. Other socio economic factors that perform much well are the agency building factors of the females, like changing pattern of marriage customs which is proxied by divorce and remarriage ratio for china and percentage of female marrying at or after the age of 20 years in India and the female workforce participation. Proportion of minorities in socio-religious composition of the population and gender bias in scholastic attainment in both these counties are also found to be significant in modeling child sex ratio variations. All these significant common factors associated with child sex ratio point toward the one single most important factor: the historical evolution of patriarchy and its contemporary perpetuation in both the countries. It seems that prohibition of sex selection might not be sufficient to combat the peculiar skewness of excessive maleness in child population in both these countries. Demand sided policies is therefore utmost important to root out the gender bias in child sex ratios.

Keywords: child sex ratios, gender bias, structural factors, prosperity, patrilocality

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Authors: Agnieszka H. Ludwig-Slomczynska, Michal T. Seweryn, Przemyslaw Kapusta, Ewelina Pitera, Katarzyna Cyganek, Urszula Mantaj, Lucja Dobrucka, Ewa Wender-Ozegowska, Maciej T. Malecki, Pawel Wolkow

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Obesity results from an imbalance between energy intake and its expenditure. Genome-Wide Association Study (GWAS) analyses have led to discovery of only about 100 variants influencing body mass index (BMI), which explain only a small portion of genetic variability. Analysis of gene epistasis gives a chance to discover another part. Since it was shown that interaction and communication between nuclear and mitochondrial genome are indispensable for normal cell function, we have looked for epistatic interactions between the two genomes to find their correlation with BMI. Methods: The analysis was performed on 366 T1DM patients using Illumina Infinium OmniExpressExome-8 chip and followed by imputation on Michigan Imputation Server. Only genes which influence mitochondrial functioning (listed in Human MitoCarta 2.0) were included in the analysis – variants of nuclear origin (MAF > 5%) in 1140 genes and 42 mitochondrial variants (MAF > 1%). Gene expression analysis was performed on GTex data. Association analysis between genetic variants and BMI was performed with the use of Linear Mixed Models as implemented in the package 'GENESIS' in R. Analysis of association between mRNA expression and BMI was performed with the use of linear models and standard significance tests in R. Results: Among variants involved in epistasis between mitochondria and nucleus we have identified one in mitochondrial transcription factor, TFB2M (rs6701836). It interacted with mitochondrial variants localized to MT-RNR1 (p=0.0004, MAF=15%), MT-ND2 (p=0.07, MAF=5%) and MT-ND4 (p=0.01, MAF=1.1%). Analysis of the interaction between nuclear variant rs6701836 (nuc) and rs3021088 localized to MT-ND2 mitochondrial gene (mito) has shown that the combination of the two led to BMI decrease (p=0.024). Each of the variants on its own does not correlate with higher BMI [p(nuc)=0.856, p(mito)=0.116)]. Although rs6701836 is intronic, it influences gene expression in the thyroid (p=0.000037). rs3021088 is a missense variant that leads to alanine to threonine substitution in the MT-ND2 gene which belongs to complex I of the electron transport chain. The analysis of the influence of genetic variants on gene expression has confirmed the trend explained above – the interaction of the two genes leads to BMI decrease (p=0.0308). Each of the mRNAs on its own is associated with higher BMI (p(mito)=0.0244 and p(nuc)=0.0269). Conclusıons: Our results show that nuclear-mitochondrial epistasis can influence BMI in T1DM patients. The correlation between transcription factor expression and mitochondrial genetic variants will be subject to further analysis.

Keywords: body mass index, epistasis, mitochondria, type 1 diabetes

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Authors: A. Maruf Aytekin

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We present our approach on using continuous delivery pattern for release management. One of the key practices of agile and lean teams is the continuous delivery of new features to stakeholders. The main benefits of this approach lie in the ability to release new applications rapidly which has real strategic impact on the competitive advantage of an organization. Organizations that successfully implement Continuous Delivery have the ability to evolve rapidly to support innovation, provide stable and reliable software in more efficient ways, decrease the amount of resources need for maintenance, and lower the software delivery time and costs. One of the objectives of this paper is to elaborate a case study where IT division of Central Securities Depository Institution (MKK) of Turkey apply Continuous Delivery pattern to improve release management process.

Keywords: automation, continuous delivery, deployment, release management

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Authors: Samira Khalaji, , Fenneke Klein Jan, Kay-E. Gottschalk, Eugenia Makrantonaki, Karin Scharffetter-Kochanek

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Biological aging is a multi-dimensional process that takes place over a whole range of scales from the nanoscopic alterations within individual cells, over transformations in tissues and organs and to changes of the whole organism. On the single cell level, aging involves mutation of genes, differences in gene expression levels as well as altered posttranslational modifications of proteins. A variety of proteins is affected, including proteins of the cell cytoskeleton and migration machinery. Previous work quantified the expression of cytoskeleton proteins on the gene and protein levels in senescent and young fibroblasts. Their results show that senescent skin fibroblasts have an upregulated expression of the intermediate filament (IF) protein vimentin in contrast to actin and tubulin, which are downregulated. IFs play an important role in providing mechanical stability of cells. However, the mechanical properties of IFs depending on cellular senescence or age of the donor has not been studied so far. Hence, we employed passive microrheology on primary human dermal fibroblasts from female donors with age of 28 years (young) and 86 years (old) as model of in vivo aging and human normal dermal fibroblast from 11-year old male with CPD 17-35 (young) and CPD 58-59 (senescence) as a model of in vitro replicative senescence. In contrast to the expectations, our primary results show no significant differences in the viscoelastic properties of fibroblasts depending on age of the donor or cellular replicative senescence.

Keywords: aging, cytoskeleton, fibroblast, mechanical properties

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Authors: Mahsa Taghavi

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In the treatment of breast cancer, tamoxifen is a regularly prescribed medication. The effect of tamoxifen on breast cancer patients' EMT pathways was studied. In this study to see if it had any effect on the cancer cells' resistance to tamoxifen and to look for specific miRNAs associated with EMT. In this work, we used continuous and integrated bioinformatics analysis to choose the optimal GEO datasets. Once we had sorted the gene expression profile, we looked at the mechanism of signaling, the ontology of genes, and the protein interaction of each gene. In the end, we used the GEPIA database to confirm the candidate genes. after that, I investigated critical miRNAs related to candidate genes. There were two gene expression profiles that were categorized into two distinct groups. Using the expression profile of genes that were lowered in the EMT pathway, the first group was examined. The second group represented the polar opposite of the first. A total of 253 genes from the first group and 302 genes from the second group were found to be common. Several genes in the first category were linked to cell death, focal adhesion, and cellular aging. Two genes in the second group were linked to cell death, focal adhesion, and cellular aging. distinct cell cycle stages were observed. Finally, proteins such as MYLK, SOCS3, and STAT5B from the first group and BIRC5, PLK1, and RAPGAP1 from the second group were selected as potential candidates linked to tamoxifen's influence on the EMT pathway. hsa-miR-1204 and hsa-miR-639 have a very close relationship with the candidates genes according to the node degrees and betweenness index. With this, the action of tamoxifen on the EMT pathway was better understood. It's important to learn more about how tamoxifen's target genes and proteins work so that we can better understand the drug.

Keywords: tamoxifen, breast cancer, bioinformatics analysis, EMT, miRNAs

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Authors: Subhayan Maity

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Complete scenario of cosmic evolution from emergent phase to late time acceleration (i.e. non-singular ever expanding Universe) is a popular preference in the recent cosmology. Yet one can’t exclude the idea that other type of evolution pattern of the Universe may also be possible. Especially, the bouncing scenario is becoming a matter of interest now a days. The present work is an exhibition of such a different pattern of cosmic evolution where the evolution of Universe has been shown as a cyclic thermodynamic process. Under diffusion mechanism (non-equilibrium thermodynamic process), the cosmic evolution has been modelled as [ emergent - accelerated expansion - decelerated expansion - decelerated contraction - accelerated contraction - emergent] .

Keywords: non-equilibrium thermodynamics, non singular evolution of universe, cyclic evolution, diffusive fluid

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Authors: Ashis Pradhan, Mohan P. Pradhan

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Pattern Matching is useful for recognizing character in a digital image. OCR is one such technique which reads character from a digital image and recognizes them. Line segmentation is initially used for identifying character in an image and later refined by morphological operations like binarization, erosion, thinning, etc. The work discusses a recognition technique that defines a set of morphological operators based on its orientation in a character. These operators are further categorized into groups having similar shape but different orientation for efficient utilization of memory. Finally the characters are recognized in accordance with the occurrence of frequency in hierarchy of significant pattern of those morphological operators and by comparing them with the existing database of each character.

Keywords: binary image, morphological patterns, frequency count, priority, reduction data set and recognition

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Authors: Rosa L. Figueroa, Christopher A. Flores, Qing Zeng-Treitler

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A regular expression consists of sequence characters which allow describing a text path. Usually, in clinical research, regular expressions are manually created by programmers together with domain experts. Lately, there have been several efforts to investigate how to generate them automatically. This article presents a text classification algorithm based on regexes. The algorithm named REX was designed, and then, implemented as a simplified method to create regexes to classify Spanish text automatically. In order to classify ambiguous cases, such as, when multiple labels are assigned to a testing example, REX includes an information gain method Two sets of data were used to evaluate the algorithm’s effectiveness in clinical text classification tasks. The results indicate that the regular expression based classifier proposed in this work performs statically better regarding accuracy and F-measure than Support Vector Machine and Naïve Bayes for both datasets.

Keywords: information gain, regular expressions, smith-waterman algorithm, text classification

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Authors: Kamila Duś-Szachniewicz, Kinga M. Walaszek, Paweł Skiba, Paweł Kołodziej, Piotr Ziółkowski

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Cell adhesion is of fundamental importance in the cell communication, signaling, and motility, and its dysfunction occurs prevalently during cancer progression. The knowledge of the molecular and cellular processes involved in abnormalities in cancer cells adhesion has greatly increased, and it has been focused mainly on cellular adhesion molecules (CAMs) and tumor microenvironment. Unfortunately, most of the data regarding CAMs expression relates to study on cells maintained in standard oxygen condition of 21%, while the emerging evidence suggests that culturing cells in ambient air is far from physiological. In fact, oxygen in human tissues ranges from 1 to 11%. The aim of this study was to compare the effects of physiological lymph node normoxia (5% O2), and hyperoxia (21% O2) on the expression of cellular adhesion molecules of primary diffuse large B-cell lymphoma cells (DLBCL) isolated from 10 lymphoma patients. Quantitative RT-PCR and immunohistochemistry were used to confirm the differential expression of several CAMs, including ICAM, CD83, CD81, CD44, depending on the level of oxygen. Our findings also suggest that DLBCL cells maintained at ambient O2 (21%) exhibit reduced growth rate and migration ability compared to the cells growing in normoxia conditions. Taking into account all the observations, we emphasize the need to identify the optimal human cell culture conditions mimicking the physiological aspects of tumor growth and differentiation.

Keywords: adhesion molecules, diffuse large B-cell lymphoma, physiological normoxia, quantitative RT-PCR

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Authors: Sandeep Kumar Agrawal, Aditi Bhattacharya, Janvie Manhas, Krushna Bhatt, Yatin Kholakiya, Nupur Khera, Ajoy Roychoudhury, Sudip Sen

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Autologous cultured explants of human oral mucosal epithelial cells (OMEC) are a potential therapeutic modality for limbal stem cell deficiency (LSCD). Injury or inflammation of the ocular surface in the form of burns, chemicals, Stevens Johnson syndrome, ocular cicatricial pemphigoid etc. can lead to destruction and deficiency of limbal stem cells. LSCD manifests in the form of severe ocular surface diseases (OSD) characterized by persistent and recurrent epithelial defects, conjuntivalisation and neovascularisation of the corneal surface, scarring and ultimately opacity and blindness. Most of the cases of OSD are associated with severe dry eye pertaining to diminished mucin and aqueous secretion. Mycophenolate mofetil (MMF) has been shown to upregulate the mucin expression in conjunctival goblet cells in vitro. The aim of this study was to evaluate the effects of MMF on mucin expression in primary cultures of oral mucosal epithelial cells. With institutional ethics committee approval and written informed consent, thirty oral mucosal epithelial tissue samples were obtained from patients undergoing oral surgery for non-malignant conditions. OMEC were grown on human amniotic membrane (HAM, obtained from expecting mothers undergoing elective caesarean section) scaffold for 2 weeks in growth media containing DMEM & Ham’s F12 (1:1) with 10% FBS and growth factors. In vitro dosage of MMF was standardised by MTT assay. Analysis of stem cell markers was done using RT-PCR while mucin mRNA expression was quantified using RT-PCR and q-PCR before and after treating cultured OMEC with graded concentrations of MMF for 24 hours. Protein expression was validated using immunocytochemistry. Morphological studies revealed a confluent sheet of proliferating, stratified oral mucosal epithelial cells growing over the surface of HAM scaffold. The presence of progenitor stem cell markers (p63, p75, β1-Integrin and ABCG2) and cell surface associated mucins (MUC1, MUC15 and MUC16) were elucidated by RT-PCR. The mucin mRNA expression was found to be upregulated in MMF treated primary cultures of OMEC, compared to untreated controls as quantified by q-PCR with β-actin as internal reference gene. Increased MUC1 protein expression was validated by immunocytochemistry on representative samples. Our findings conclude that OMEC have the ability to form a multi-layered confluent sheet on the surface of HAM similar to a cornea, which is important for the reconstruction of the damaged ocular surface. Cultured OMEC has stem cell properties as demonstrated by stem cell markers. MMF can be a novel enhancer of mucin production in OMEC. It has the potential to improve dry eye in patients undergoing OMEC transplantation for bilateral OSD. Further clinical trials are required to establish the role of MMF in patients undergoing OMEC transplantation.

Keywords: limbal stem cell deficiency, mycophenolate mofetil, mucin, ocular surface disease

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Authors: Bui Phuong Linh, Yuki Sakakibara, Ryuto Tanaka, Elizabeth H. Pigney, Taishi Hashiguchi

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NASH is an increasingly prevalent chronic liver disease that can progress to hepatocellular carcinoma and now is attracting interest worldwide. The STAM™ model is a clinically-correlated murine NASH model which shows the same pathological progression as NASH patients and has been widely used for pharmacological and basic research. The multiple parallel hits hypothesis suggests abnormalities in adipocytokines, intestinal microflora, and endotoxins are intertwined and could contribute to the development of NASH. In fact, NASH patients often exhibit gut dysbiosis and dysfunction in adipose tissue and metabolism. However, the analysis of the STAM™ model has only focused on the liver. To clarify whether the STAM™ model can also mimic multiple pathways of NASH progression, we analyzed the organ crosstalk interactions between the liver and the gut and the phenotype of adipose tissue in the STAM™ model. NASH was induced in male mice by a single subcutaneous injection of 200 µg streptozotocin 2 days after birth and feeding with high-fat diet after 4 weeks of age. The mice were sacrificed at NASH stage. Colon samples were snap-frozen in liquid nitrogen and stored at -80˚C for tight junction-related protein analysis. Adipose tissue was prepared into paraffin blocks for HE staining. Blood adiponectin was analyzed to confirm changes in the adipocytokine profile. Tight junction-related proteins in the intestine showed that expression of ZO-1 decreased with the progression of the disease. Increased expression of endotoxin in the blood and decreased expression of Adiponectin were also observed. HE staining revealed hypertrophy of adipocytes. Decreased expression of ZO-1 in the intestine of STAM™ mice suggests the occurrence of leaky gut, and abnormalities in adipocytokine secretion were also observed. Together with the liver, phenotypes in these organs are highly similar to human NASH patients and might be involved in the pathogenesis of NASH.

Keywords: Non-alcoholic steatohepatitis, hepatocellular carcinoma, fibrosis, organ crosstalk, leaky gut

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Authors: Okike Benjamin, E. J. D. Garba

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The protection of sensitive information against unauthorized access or fraudulent changes has been of prime concern throughout the centuries. Modern communication techniques, using computers connected through networks, make all data even more vulnerable to these threats. The researchers in this work propose a new encryption technique to be known as Merged Irregular Transposition Cipher. In this proposed encryption technique, a message to be encrypted will first of all be split into multiple parts depending on the length of the message. After the split, different keywords are chosen to encrypt different parts of the message. After encrypting all parts of the message, the positions of the encrypted message could be swapped to other position thereby making it very difficult to decrypt by any unauthorized user.

Keywords: information security, message splitting, pattern, sequence

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Authors: Bairam Khan, Premlata Vaishnava

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The ability to conceptualize one entity in terms of another allows us to communicate through metaphors. This central feature of human cognition has evolved with the development of language, and the processing of metaphors is without any conscious appraisal and is quite effortless. South Asians, like other speech communities, have been using the kitchenary [culinary] metaphor in a very simple yet interesting way and are known for bringing into new and unique constellations wherever they are. This composite feature of our language is used to communicate in a precise and compact manner and maneuvers the expression. The present study explores the role of kitchenary metaphors in the making and shaping of idioms by applying Cognitive Metaphor Theories. Drawing on examples from a corpus of adverts, print, and electronic media, the study looks at the metaphorical language used by real people in real situations. The overarching theme throughout the course is that kitchenary metaphors are powerful tools of expression in Hindi-Urdu.

Keywords: cognitive metaphor theories, kitchenary metaphors, hindi-urdu print, and electronic media, grammatical structure of kitchenary metaphors of hindi-urdu

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Authors: Ahmad Ali Shahid, M Shakil Shaukat

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Agriculture is the backbone of economy of Pakistan and Cotton is the major agricultural export and supreme source of raw fiber for our textile industry. To combat against the developing resistance in the target insects and combating these challenges wholesomely, a novel combination of pyramided/stacked genes was conceptualized and later realized, through the means of biotechnology i.e., transformation of three genes namely, Cry1Ac, Cry2A, and EPSP synthase (glyphosate tolerant) genes in the locally cultivated cotton variety. The progenies of the transformed plants were successfully raised and screened under the tunnel conditions for two generations and the present study focused on the screening of plants which were confirmed for containing all of these three genes and their expressions. Initially, the screening was done through glyphosate spray assay and the plants which were healthy and showed no damage on leaves were selected after 07 days of spray. In the laboratory, the DNA of these plants were isolated and subjected to amplification of the three genes. Thus, seventeen out of twenty were confirmed positive for Cry1Ac gene and ten out of twenty were positive for Cry2A gene and all twenty were positive for presence of EPSP synthase gene. Then, the ten plant samples which were confirmed with presence of all three genes were subjected to expression analysis of these proteins through ELISA. The results showed that eight out of ten plants were actively expressing the three transgenes. Real-time PCR was also done to quantify the expression levels of the EPSP synthase gene. Finally, eight plants were confirmed for the presence and active expression of all three genes in T3 generation of the triple gene transformed cotton. These plants may be subjected to T4 generation to develop a new stable variety in due course of time.

Keywords: agriculture, cotton, transformation, cry genes, ELISA, PCR

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Authors: L. Salvati, D. Smiraglia, S. Bajocco, M. Munafò

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This paper focuses on Land Use and Land Cover Changes (LULCC) occurred in the urban coastal regions of the Mediterranean basin in the last thirty years. LULCC were assessed diachronically (1975-2006) in two urban areas, Rome (Italy) and Athens (Greece), by using CORINE land cover maps. In strictly coastal territories a persistent growth of built-up areas at the expenses of both agricultural and forest land uses was found. On the contrary, a different pattern was observed in the surrounding inland areas, where a high conversion rate of the agricultural land uses to both urban and forest land uses was recorded. The impact of city growth on the complex pattern of coastal LULCC is finally discussed.

Keywords: land use changes, coastal region, Rome prefecture, Attica, southern Europe

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Authors: Azzah Aldeghather, Sara Alkhodair

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In the modern urban planning and architecture landscape, with western ideologies and styles becoming the mainstay of experience and definitions globally, the Islamic world requires a methodology that defines its expression, which transcends cultural, societal, and national styles. This paper will propose a methodology as an objective system to define, evaluate and apply traditional Islamic knowledge to Islamic urban planning and architecture, providing the Islamic world with a system to manifest its approach to design. The methodology is expressed as Four Pillars which are based on traditional meanings of Arab words roughly translated as Pillar One: The Principles (Al Mabade’), Pillar Two: The Foundations (Al Asas), Pillar Three: The Purpose (Al Ghaya), Pillar Four: Presence (Al Hadara). Pillar One: (The Principles) expresses the unification (Tawheed) pillar of Islam: “There is no God but God” and is comprised of seven principles listed as: 1. Human values (Qiyam Al Insan), 2. Universal language as sacred geometry, 3. Fortitude© and Benefitability©, 4. Balance and Integration: conjoining the opposites, 5. Man, time, and place, 6. Body, mind, spirit, and essence, 7. Unity of design expression to achieve unity, harmony, and security in design. Pillar Two: The Foundations is based on two foundations: “Muhammad is the Prophet of God” and his relationship to the renaming of Medina City as a prototypical city or place, which defines a center space for collection conjoined by an analysis of the Medina Charter as a base for the humanistic design. Pillar Three: The Purpose (Al Ghaya) is comprised of four criteria: The naming of the design as a title, the intention of the design as an end goal, the reasoning behind the design, and the priorities of expression. Pillar Four: Presence (Al Hadara) is usually translated as a civilization; in Arabic, the root of Hadara is to be present. This has five primary definitions utilized to express the act of design: Wisdom (Hikma) as a philosophical concept, Identity (Hawiya) of the form, and Dialogue (Hiwar), which are the requirements of the project vis-a-vis what the designer wishes to convey, Expression (Al Ta’abeer) the designer wishes to apply, and Resources (Mawarid) available. The Proposal will provide examples, where applicable, of past and present designs that exemplify the manifestation of the Pillars. The proposed methodology endeavors to return Islamic urban planning and architecture design to its a priori position as a leading design expression adaptable to any place, time, and cultural expression while providing a base for analysis that transcends the concept of style and external form as a definition and expresses the singularity of the esoteric “Spiritual” aspects in a rational, principled, and logical manner clearly addressed in Islam’s essence.

Keywords: Islamic architecture, Islamic design, Islamic urban planning, principles of Islamic design

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Authors: Nisha Sharma, Mili Kaur, Ashutosh Halder, Seema Kaushal, Manoj Kumar, Manish Jain

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Purpose: To investigate microRNAs (miRNA) as an epigenomic etiological factor in idiopathic non-obstructive azoospermia (NOA). In order to achieve the same, an association was seen between occupational exposure to radiation, thermal, and chemical factors and idiopathic cases of non-obstructive azoospermia, and later, testicular differential miRNA expression profiling was done in exposure group NOA cases. Method: It is a prospective study in which 200 apparent idiopathic male factor infertility cases, who have been advised to undergo testicular fine needle aspiration (FNA) evaluation, are recruited. A detailed occupational history was taken to understand the possible type of exposure due to the nature and duration of work. A total of 26 patients were excluded upon XY-FISH and Yq microdeletion tests due to the presence of genetic causes of infertility, 6 hypospermatogeneis (HS), six Sertoli cell-only syndrome (SCOS), and six normospermatogeneis patients testicular FNA samples were used for RNA isolation followed by small RNA sequencing and nCounter miRNA expression analysis. Differential miRNA expression profile of HS and SCOS patients was done. A web-based tool, miRNet, was used to predict the interacting compounds or chemicals using the shortlisted miRNAs with high fold change. The major limitation encountered in this study was the insufficient quantity of testicular FNA sample used for total RNA isolation, which resulted in a low yield and RNA integrity number (RIN) value. Therefore, the number of RNA samples admissible for differential miRNA expression analysis was very small in comparison to the total number of patients recruited. Results: Differential expression analysis revealed 69 down-regulated and 40 up-regulated miRNAs in HS and 66 down-regulated and 33 up-regulated miRNAs in SCOS in comparison to normospermatogenesis controls. The miRNA interaction analysis using the miRNet tool showed that the differential expression profiles of HS and SCOS patients were associated with arsenic trioxide, bisphenol-A, calcium sulphate, lithium, and cadmium. These compounds are reproductive toxins and might be responsible for miRNA-mediated epigenetic deregulation leading to NOA. The association between occupational risk factor exposure and the non-exposure group of NOA patients was not statistically significant, with ꭓ2 (3, N= 178) = 6.70, p= 0.082. The association between individual exposure groups (radiation, thermal, and chemical) and various sub-types of NOA is also not significant, with ꭓ2 (9, N= 178) = 15.06, p= 0.089. Functional analysis of HS and SCOS patients' miRNA profiles revealed some important miR-family members in terms of male fertility. The miR-181 family plays a role in the differentiation of spermatogonia and spermatocytes, as well as the transcriptional regulation of haploid germ cells. The miR-34 family is expressed in spermatocytes and round spermatids and is involved in the regulation of SSCs differentiation. Conclusion: The reproductive toxins might adopt the miRNA-mediated mechanism of disease development in idiopathic cases of NOA. Chemical compound induced; miRNA-mediated epigenetic deregulation can give a future perspective on the etiopathogenesis of the disease.

Keywords: microRNA, non-obstructive azoospermia (NOA), occupational exposure, hypospermatogenesis (HS), Sertoli cell only syndrome (SCOS)

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Authors: Mohamed A. Morsy, Azza A. K. El-Sheikh, Abdulla Y. Al-Taher

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The aim of the present study is to investigate the effect of resveratrol (RES) on methotrexate (MTX)-induced testicular damage. RES (10 mg/kg/day) was given for 8 days orally and MTX (20 mg/kg i.p.) was given at day 4 of experiment, with or without RES in rats. MTX decreased serum testosterone, induced histopathological testicular damage, increased testicular tumor necrosis factor-α level and expression of nuclear factor-κB and cyclooxygenase-2. In MTX/RES group, significant reversal of these parameters was noticed, compared to MTX group. Testicular expression of multidrug resistance protein (Mrp) 3 was three- and five-folds higher in RES- and MTX/RES-treated groups, respectively. In vitro, using prostate cancer cells, each of MTX and RES alone induced cytotoxicity with IC50 0.18 ± 0.08 and 20.5 ± 3.6 µM, respectively. RES also significantly enhanced cytotoxicity of MTX. In conclusion, RES appears to have dual beneficial effect, as it promotes MTX tumor cytotoxicity, while protecting the testes, probably via up-regulation of testicular Mrp3 as a novel mechanism.

Keywords: resveratrol, methotrexate, multidrug resistance protein 3, tumor necrosis factor-α, nuclear factor-κB, cyclooxygenase-2

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Authors: Bairam Khan, Premlata Vaishnava

Abstract:

The ability to conceptualize one entity in terms of another allows us to communicate through metaphors. This central feature of human cognition has evolved with the development of language, and the processing of metaphors is without any conscious appraisal and is quite effortless. South Asians, like other speech communities, have been using the kitchenary [culinary] metaphor in a very simple yet interesting way and are known for bringing into new and unique constellations wherever they are. This composite feature of our language is used to communicate in a precise and compact manner and maneuvers the expression. The present study explores the role of kitchenary metaphors in the making and shaping of idioms by applying Cognitive Metaphor Theories. Drawing on examples from a corpus of adverts, print, and electronic media, the study looks at the metaphorical language used by real people in real situations. The overarching theme throughout the course is that kitchenary metaphors are powerful tools of expression in Hindi-Urdu.

Keywords: cognitive metaphor theory, source domain, target domain, signifier- signified, kitchenary, ethnocultural elements of south asia and hindi- urdu language

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Authors: Danna Jia, Bin Li

Abstract:

Background: Atopic dermatitis (AD) is a chronic and refractory inflammatory skin disease characterized by relapsing eczematous and pruritic skin lesions. The global prevalence of AD ranges from 1~ 20%, and its incidence rates are increasing. It affects individuals from infancy to adulthood, significantly impacting their daily lives and social activities. Despite its major health burden, the precise mechanisms underlying AD remain unknown. Understanding the genetic differences associated with AD is crucial for advancing diagnosis and targeted treatment development. This study aims to identify candidate genes of AD by using bioinformatics analysis. Methods: We conducted a comprehensive analysis of four pooled transcriptomic datasets (GSE16161, GSE32924, GSE130588, and GSE120721) obtained from the Gene Expression Omnibus (GEO) database. Differential gene expression analysis was performed using the R statistical language. The differentially expressed genes (DEGs) between AD patients and normal individuals were functionally analyzed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Furthermore, a protein-protein interaction (PPI) network was constructed to identify candidate genes. Results: Among the patient-level gene expression datasets, we identified 114 shared DEGs, consisting of 53 upregulated genes and 61 downregulated genes. Functional analysis using GO and KEGG revealed that the DEGs were mainly associated with the negative regulation of transcription from RNA polymerase II promoter, membrane-related functions, protein binding, and the Human papillomavirus infection pathway. Through the PPI network analysis, we identified eight core genes: CD44, STAT1, HMMR, AURKA, MKI67, and SMARCA4. Conclusion: This study elucidates key genes associated with AD, providing potential targets for diagnosis and treatment. The identified genes have the potential to contribute to the understanding and management of AD. The bioinformatics analysis conducted in this study offers new insights and directions for further research on AD. Future studies can focus on validating the functional roles of these genes and exploring their therapeutic potential in AD. While these findings will require further verification as achieved with experiments involving in vivo and in vitro models, these results provided some initial insights into dysfunctional inflammatory and immune responses associated with AD. Such information offers the potential to develop novel therapeutic targets for use in preventing and treating AD.

Keywords: atopic dermatitis, bioinformatics, biomarkers, genes

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Authors: Naureen Akhtar

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The stability of the protein in detergent-containing solution is the key for its successful crystallisation. Fluorescence-detection size-exclusion chromatography (FSEC) is a potential approach for screening monodispersity as well as the stability of protein in a detergent-containing-solution. In this present study, covalently linked Green Fluorescent Protein (GFP) to bacterial nitrate transporter, NarU from Escherichia coli was studied for pre-crystallisation trials by FSEC. Immobilised metal ion affinity chromatography (IMAC) and gel filtration were employed for their purification. The main objectives of this study were over-expression, detergent screening and crystallisation of nitrate transporter proteins. This study could not produce enough proteins that could realistically be taken forward to achieve the objectives set for this particular research. In future work, different combinations of variables like vectors, tags, creation of mutant proteins, host cells, position of GFP (N- or C-terminal) and/or membrane proteins would be tried to determine the best combination as the principle of technique is still promising.

Keywords: transporters, detergents, over-expression, crystallography

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Authors: Maryam Jaberi, Siavosh Shayan, Mojtaba Yamani

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Habble-Rud River basin (HR), up to 100 km length, one of the largest watersheds which drain into deserts to the north of Central Iran (Dasht-e Kavir). This stream is oblique with the NE-SW trending, flow in the southern range of central Alborz Mountains and the northern border of Central Iran. The end of the ~17 km suddenly change direction and with the southern trending to have a morphology which meanders passes through the Alborz Mountain ridge and flows into the Garmsar plain where it forms one of the largest alluvial fans in Iran, i.e. the vast Garmsar alluvial fan with an area of 476 km2. This study was carried out through morphometric analyses, longitudinal river profiles, and study of geomorpholic evidence such as fluvial terraces, gypsum-salt domes, seismic data, and satellite images. This study aimed to investigate the changes in the pattern of rivers in the southern part of the HR river basin. The southern part of HR river basin located at the southern foothills of the Central Alborz is characterized the thrust faults (Sorkheh-Kalut and Garmsar faults), folds,diapirs and arid climate. The activity of more than 10 salt domes that belong to the Oligocene-Miocene period has considerably influenced the pattern of streams in this region. Dissolution of these domes has not only reduced the quality of water and soil resources, but also has led to the formation of badlands and gullies.Our results indicated that the pattern of rivers in the southern part of HR river basin was influenced by discharge of the HR river in Quaternary, geological structure, subsidence of Central Iran and vertical uplift of Alborz mountain. These agents caused the formation meanders in the southern part of the HR River and evaluation of the seasonal rivers like Shoor-Darre and Garmabsar.

Keywords: geomorphologic evaluation, rivers pattern, Habble-Rud River basin, seasonal rivers

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Authors: Ebtehal Aljedaani, Maha Aljohani

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Privacy and security patterns are both important for developing software that protects users' data and privacy. Privacy patterns are designed to address common privacy problems, such as unauthorized data collection and disclosure. Security patterns are designed to protect software from attack and ensure reliability and trustworthiness. Using privacy and security patterns, software engineers can implement security and privacy by design principles, which means that security and privacy are considered throughout the software development process. These patterns are available to translate "security & privacy-by-design" into practical advice for software engineering. Previous research on privacy and security patterns has typically focused on one category of patterns at a time. This paper aims to bridge this gap by merging the two categories and identifying their similarities and differences. To do this, the authors conducted a systematic literature review of 25 research papers on privacy and security patterns. The papers were analysed based on the category of the pattern, the classification of the pattern, and the security requirements that the pattern addresses. This paper presents the results of a comprehensive review of privacy and security design patterns. The review is intended to help future IT designers understand the relationship between the two types of patterns and how to use them to design secure and privacy-preserving software. The paper provides a clear classification of privacy and security design patterns, along with examples of each type. The authors found that there is only one widely accepted classification of privacy design patterns, while there are several competing classifications of security design patterns. Three types of security design patterns were found to be the most commonly used.

Keywords: design patterns, security, privacy, classification of patterns, security patterns, privacy patterns

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Authors: Femy M. Makkar, S. Chandrakaran, N. Sankar

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The concept of reinforced earth has been used in the field of geotechnical engineering since 1960s, for many applications such as, construction of road and rail embankments, pavements, retaining walls, shallow foundations, soft ground improvement and so on. Conventionally, planar geosynthetic materials such as geotextiles and geogrids were used as the reinforcing elements. Recently, the use of three dimensional reinforcements becomes one of the emerging trends in this field. So, in the present investigation, three dimensional geogrid is proposed as a reinforcing material. Laboratory scaled plate load tests are conducted on a model square footing resting on 3D geogrid reinforced sand bed. The performance of 3D geogrids in triangular and square pattern was compared with conventional geogrids and the improvement in bearing capacity and reduction in settlement and heave are evaluated. When single layer of reinforcement was placed at an optimum depth of 0.25B from the bottom of the footing, the bearing capacity of conventional geogrid reinforced soil improved by 1.85 times compared to unreinforced soil, where as 3D geogrid reinforced soil with triangular pattern and square pattern shows 2.69 and 3.05 times improvement respectively compared to unreinforced soil. Also, 3D geogrids performs better than conventional geogrids in reducing the settlement and heave of sand bed around the model footing.

Keywords: 3D reinforcing elements, bearing capacity, heavy, settlement

Procedia PDF Downloads 302

Authors: Sadegh Lotfieblisofla, Arash Khodabakhshi

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Tissue plasminogen activator (tPA) as a serine protease plays an important role in the fibrinolytic system and the dissolution of fibrin clots in human body. The production of this drug in plants such as tobacco could reduce its production costs. In this study, expression of tPA gene and protein targeting to different plant cell compartments, using various signal peptides has been investigated. For high level of expression, Kozak sequence was used after CaMV35S in the beginning of the gene. In order to design the final construction, Extensin, KDEL (amino acid sequence including Lys-Asp-Glu-Leu) and SP (γ-zein signal peptide coding sequence) were used as leader signals to conduct this protein into apoplast, endoplasmic reticulum and cytosol spaces, respectively. Cloned human tPA gene under the CaMV (Cauliflower mosaic virus) 35S promoter and NOS (Nopaline Synthase) terminator into pBI121 plasmid was transferred into tobacco explants by Agrobacterium tumefaciens strain LBA₄₄₀₄. The presence and copy number of genes in transgenic tobacco was proved by Southern blotting. Enzymatic activity of the rt-PA protein in transgenic plants compared to non-transgenic plants was confirmed by Zymography assay. The presence and amount of rt-PA recombinant protein in plants was estimated by ELISA analysis on crude protein extract of transgenic tobacco using a specific antibody. The yield of recombinant tPA in transgenic tobacco for SP, KDEL, Extensin signals were counted 0.50, 0.68, 0.69 microgram per milligram of total soluble proteins.

Keywords: tPA, recombinant, transgenic, tobacco

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Authors: Naomi Seidu, Edward Poluyi, Chibuikem Ikwuegbuenyi, Eghosa Morgan

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The current poor prognosis of glioblastoma has called for the need for an improvement in treatment methods in order to improve its survival rate. Despite the different interventions currently available for this tumor, the average survival is still only a few months. (12-15). The aim is to create a more favorable prognosis and have a reduction in the resistance to treatment currently being experienced, even with surgical interventions and chemotherapy. From the available literature, there is a relationship between the presence of HOX genes (Homeobox genes) and glioblastoma, which could be attributable to the increasing treatment resistance. Hence silencing these genes can be a key to improving survival rates of glioblastoma. A series of studies have highlighted the role that HOX genes play in glioblastoma prognosis. Promotion of human glioblastoma initiation, aggressiveness, and resistance to Temozolomide has been associated with HOXA9. The role of HOX gene expression in cancer stem cells should be studied as it could provide a means of designing CSC-targeted therapies, as CSCs play a part in the initiation and progression of solid tumors.

Keywords: GBM- glioblastoma, HOXA gene- homeobox genes cluster, signaling pathways, temozolomide

Procedia PDF Downloads 105

Authors: Elizabeth Bourgeois

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During social distancing, fashion and self-expression have been pushed further into virtual environments. In VR spaces, identities can be curated easily, untethered from the necessities of life and work. Personal styles reach a wider audience and follow new rules. Digital platforms leave some, but not all, 'real world' clothing constraints behind. Virtual aesthetics are set by the user and the software. Gen Z is a native user, applying face filters on Instagram and Snapchat and styling outfits and skins in apps like Gacha Life, Roblox, and Fortnite. These games cultivate space for community and personal style. Loosely tied to human forms, each app has physical aesthetics, with clear vernacular dress defining it. There are ecosystems of makers, consumers, and critics. Designer-modelers create original assets, brands, and luxury items. Fashion and beauty are ephemeral but always reflect the idealization of form and self. Online communities have already established new beauty ideals that impact live fashion trends. Fashion houses develop AR filters, gaming hairstyles challenge real-world colorists, and musicians perform virtual concerts in their avatar forms. In these times, social media and gaming communities promote the expression of public identity. The online dress is no longer tied to 'real' bodies or cloth. In virtual worlds, there are still tribes, status symbols, gender identities, and roles, but free of fabric, form, and static social structure, there is room for fantastic invention.

Keywords: virtual reality, fashion, Gen Z, social media, gaming

Procedia PDF Downloads 135

Authors: Cheng-Cao Sun, Shu-Jun Li, De-Jia Li

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Through analysis of a published micro-array-based high-throughput assessment, we discovered that miR-1275 was markedly down-regulated in nasopharyngeal carcinoma (NPC) tissues. However, little is known about its effect and mechanism involved in NPC development and progression. In this study, we investigated the role of miR-1275 on the development of NPC. The results indicated that miR-1275 was significantly down-regulated in primary NPC tissues, and very low levels were found in NPC cell lines. Ectopic expression of miR-1275 in NPC cell lines significantly suppressed cell growth as evidenced by cell viability assay and colony formation assay, through inhibition of HOXB5. In addition, miR-1275 suppresses G1/S transition through inhibition of HOXB5. Further, oncogene HOXB5 was revealed to be a putative target of miR-1275, which was inversely correlated with miR-1275 expression in NPC. Collectively, our study demonstrates that as a tumor suppressor, miR-1275 played a pivotal role on NPC through inhibiting cell proliferation, and suppressing G1/S transition by targeting oncogenic HOXB5.

Keywords: microRNA-1275 (miR-1275), HOXB5, nasopharyngeal carcinoma, proliferation

Procedia PDF Downloads 264

Authors: Marjan Mahdavi-Roshan, Arsalan Salari, Mahboobeh Gholipour, Moona Naghshbandi

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Background and objectives: Before any nutritional intervention, it is necessary to have the prospect of eating habits of people with cardiovascular risk factors. In this study, we assessed the adherence of healthy diet based on Mediterranean dietary pattern and related factors in adults in the north of Iran. Methods: This study was conducted on 550 men and women with cardiovascular risk factors that referred to Heshmat hospital in Rasht, northern Iran. Information was collected by interview and reading medical history and measuring anthropometric indexes. The Mediterranean Diet Adherence Screener was used for assessing dietary adherence, this screener was modified according to religious beliefs and culture of Iran. Results: The mean age of participants was 58±0.38 years. The mean of body mass index was 27±0.01 kg/m², and the mean of waist circumference was 98±0.2 cm. The mean of dietary adherence was 5.76±0.07. 45% of participants had low adherence, and just 4% had suitable adherence. The mean of dietary adherence in men was significantly higher than women (p=0. 07). Participants in rural area and high educational participants insignificantly had an unsuitable dietary Adherence. There was no significant association between some cardiovascular disease risk factors and dietary adherence. Conclusion: Education to different group about dietary intake correction and using a Mediterranean dietary pattern that is similar to dietary intake in the north of Iran, for controlling cardiovascular disease is necessary.

Keywords: dietary adherence, Mediterranean dietary pattern, cardiovascular disease, north of Iran

Procedia PDF Downloads 252