Characterization of post-transcriptional regulatory network of RNA-binding proteins using computational predictions and deep sequencing data

This report is divided into three parts: Data Analysis, Mathematical Modeling and Conclusion and future directions. In the Data Analysis part, various methods and tools for characterizing the post-transcriptional regulatory networks of RNA-binding proteins are discussed and applied. Chapter 2 introduces PAR-CLIP, a method for transcriptomewide identification of RNA binding proteins at nucleotide resolution. PAR-CLIP was successfully applied on RNA binding proteins and their binding specificity was characterized. Partly due to their vast volume, the data that were so far generated in CLIP experiments have not been put in a form that enables fast and interactive exploration of binding sites. To address this need, Chapter 3 presents CLIPZ, which is a database and analysis environment for various kinds of deep sequencing (and in particular CLIP) data, that aims to provide an open-access repository of information for post-transcriptional regulatory elements. Chapter 4 revisits various CLIP methods. A set of ideas in terms of both experimental protocols and data analysis are presented to improve the quality and reproducibility of such experiments. In general, cytoplasmic RNAs are isolated in CLIP experiments. Like many high-throughput experiments, CLIP has a certain amount of isolated RNAs which do not represent regulatory binding sites. To improve the quality of the obtained RNAs, a set of novel methods for data analysis are also suggested. These methods are added as new tools to the CLIPZ analysis platform. Argonaute CLIP data could in principle be beneficial in improving the microRNA target site predictions. However, several questions still remain which cannot be addressed using CLIP methods. For example: • Argonaute CLIP data by default does not reveal which microRNAs are more likely to interact to the mRNA binding site at the time of cross-linking. • As mentioned earlier, biochemical and structural studies of Thermus thermophilus Argonaute protein suggest that the protein-RNA interaction between microRNA and the Argonaute protein forms a physical structure that only some positions in the microRNA become accessible to the target binding site. Having inferred the interacting microRNA, it is also interesting to predict the most plausible secondary structure of the hybridized microRNA-mRNA complex. Mathematical Modeling part of the report contains Chapter 5. This chapter presents a novel mathematical model called MIRZA to address the above mentioned questions. An in-depth introduction to MIRZA is presented and its performance in terms of identifying functionally relevant targets of microRNAs is discussed. Finally, Conclusion and future directions part of the report contains Chapter 6 in which discusses the main findings of the projects and gives an outlook of where future work could be taken up

Nano-Crystalline Metal Matrix Nano-Composites Reinforced By Graphene and Alumina: Effect of Reinforcement Properties and Concentration on Mechanical Behavior

Metal matrix composites (MMCs) and Metal Matrix Nano-composites (MMNCs) are promising materials for a number of aerospace, defense, and automobile applications. Among all MMCs and MMNCs, aluminum is the most widely used matrix due to its low density coupled with high stiffness, high specific strength, high specific modulus and low thermal expansion coefficient. While high strengths have been shown in MMCs, they are known to have very limited ductility. However, there are indications that reducing reinforcement size to the nanoscale may improve strain to failure in addition to increase strength. Reducing grain size to the nanoscale has been found to improve material properties specially strength until grain size of around 10 nm. From this preliminary evidence, it would appear that nanocrystalline (NC) metallic materials and NC MMNCs may result in the best properties. Yet, in these materials, the effect of processing conditions and reinforcement type, size, and concentration on material performance is not well understood. Currently, mainly Powder Metallurgy (PM) techniques appear to be capable of generating NC metallic materials. Milling is used to mix matrix and reinforcement particles as well as reduce the size of particles. The majority of work in synthesizing NC metallic materials has employed cryomilling, which is milling of the metallic powders in a medium of liquid nitrogen (LN2) using stearic acid as a process control agent (PCA). After cryomilling, the milled powder is nanosize, but requires a high temperature/high vacuum degassing step to remove the PCA. However, there are several medium/PCA combinations that could be used that may produce the same results as the relatively complex and expensive LN2/Stearic acid combination. To date, these alternatives remain unexplored. To consolidate the milled powders techniques such as HIP, CIP, single action compaction, extrusion, and forging can be used. However, to achieve close to theoretical densities it is necessary to perform the consolidation at high temperature. The high temperature causes coarsening of the powder grains and results in a larger grain size. Since it appears that the grain size is one of the main factors in determining the strength and ductility of the material, it is important to understand how reinforcement additions affect grain growth. Furthermore, plastic deformation seems to be required to achieve maximum density. Plastic deformation results in work hardening, which strengthens the material at the expense of ductility. The effect of reinforcement additions on work hardening has also received limited attention. In order to better understand the effect of reinforcement type, size, and concentration on the processing and mechanical behavior of NC metals and MMNCs, pure Al was mixed with varying concentrations of graphene nanoplatelets (GNPs) and 47 nm alumina nanoparticles (Al2O3np). Instead of cryomilling, milling was conducted at room temperature in ethanol, where ethanol acted as both the medium and PCA. Degassing was accomplished by heating to only 135oC rather than to several hundred degrees. This processing method is considerably less complex and therefore less expensive and results in milled powders of the same size as those achieved by cryomilling followed by high temperature/high vacuum degassing. The consolidation of the powders was conducted by single action cold compaction and single action hot compaction. This method should minimize textural effects that are produced by other consolidation techniques such as extrusion. Relative density (i.e. the density of the sample divided by the theoretical density) of the final consolidated samples reached nearly 100% in all graphene-reinforced samples regardless of graphene concentration; whereas in Al2O3np-reinforced samples the achievable densities were in the range of 85-95% of theoretical density depending on Al2O3np concentration. These are similar to the relative densities achieved by LN2 cryomilling/HIP/extrusion processing and shows that the room temperature ethanol/cold compaction/hot compaction is a viable alternative synthesis method. As stated above, mechanical properties of the material are primarily governed by grain size and work-hardening and that it is likely that reinforcement additions have a significant effect on these properties. To understand the strengthening mechanisms of MMNCs, pure NC Al was reinforced with varying concentrations of Al2O3np and GNPs. The results show that i) room temperature milling in ethanol followed by a relatively low temperature drying treatment can produce NC Al and NC Al MMNCs with grain sizes comparable to materials produced by cryomilling, ii) grain boundary strengthening as described by the Hall-Petch relation accounts for the strength of Al- Al2O3np MMNCs, and iii) grain boundary strengthening, solute strengthening, and CTE mismatch strengthening also appear to contribute to the strength in Al-GNP MMNCs. To investigate the tribological behavior of aluminum matrix composites reinforced by GNPs and pure aluminum, pin-on-disk experiments were conducted on samples synthesized in the study. In the experiments, the influence of reinforcement, volume fraction, normal load, and sliding velocity on the tribological performance was investigated. Results showed that the wear rate of Al-1wt.% GNP is increased with increasing normal loads. However, the coefficient of friction (COF) of the Al-1wt.% GNP decreased with increasing normal loads. Formation of carbon film on the worn surface of Al-1wt.% GNP sample and morphology of the worn surfaces of aluminum and composite samples were analyzed by Optical Microscope (OM) and Scanning Electron Microscope (SEM). It was found that the graphene nanoplatelets reinforced nano-composites showed superior tribological properties and demonstrated the ability of the self-lubricating nature of the composite during tribological conditions. Moreover, diametrical compression of small disk specimens was used to understand the mechanical properties of metal matrix nano composites. Analysis was performed using an inverse method that couples digital image correlation and the analytical closed form formulation. This technique was capable of extracting the tension and compression modulus values in the metal matrix nanocomposite disk specimens. This method for characterization of metal matrix composites have the potential to accelerate the development and study of advanced composite materials

Reconnaissance of Archaeological Sites at Tuzkhormato Region Saladdin Governorate – Northern Iraq

     هذه الدراسة تتطرق لأول مرة الى توثيق مواقع الآثار المنتشرة في مدينة طوزخورماتو وأطرافها، حيث هناك أكثر من (19) موقعا  أثريا  مقسمة  باتجاهين  الأول  تأخذ  مسارا  موازيا  لنهر نهر آق صو  تقريبا  من  خلف  جبال طوزخورماتو إلى نهر زغيتون (الجسر الرابط بين طوز وتكريت) والآخر عموديا عليها في منتصف المسار الأول وقد تم تحديد إحداثيات خمسة مواقع، وان هذه المواقع هي على شكل تلال بين كبيرة وصغيرة الحجم  منتشرة  على أسطحها قطع من الأواني الفخارية المتكسرة  وقسم منها ملونة بألوان  وكذلك هنالك الكثير من  قطع  حجر  الصوان حيث كانت تستخدم كأدوات القطع مثل السكاكين (في تل الشعير)، وإن هذه الآثار مرتفعة من مستوى سطح الأرض بدرجات متفاوتة اعتمادا على حجم منطقة البناء وان كل الأبنية  طينية،  لذا فان الحفاظ  على  الأبنية  ضعيفة  أمام المناخ ومن المحتمل أن تكون الأبنية مدفونة تحت التلال وان الأشياء الباقية هي الأواني الفخارية المتكسرة في فترة ما قبل الإسلام منتشرة على الأسطح، عدا الموقع الأثري لقلعة كاوور (الفترة الساسانية) على الجبل حيث البناء من الجص  وحجر الجبس. علما  بأنه لم  يدرس  أي  موقع  اثري  من هذه  المواقع  من  الناحية  الجيوفيزيائية  أو الجيولوجية كتحديد العمر أو الشكل الهندسي للبنايات المدفونة أو البحث عن الأشياء الثمينة كالذهب أو ما شابه ذلك.This study is talking for the first time about in this region to document the archaeological sites at Tuzkhormato and surroundings. There are more than (19) archaeological sites which took two trends  one of them is parallel to Aq-Su river, which starts from behind Tuzkhomato mountain and takes NE-SW direction at Shirash Tapa site and ending at Zeghaitoon river near the bridge of (Tikrit-Tuz) road, and another trend is perpendicular to the first one at about the mid-way distance of the first trend. Coordinations of (5) archaeological sites were located and studied, these sites are as a hill ranges in its shape between small to large and the broken pottery were spread widely on the surface of these sites and some of this pottery are colored, also there are chert cutter that is used as knives (at Tal-Al-Shaer) site only. These sites were uplifted from the surface level with uneven degree depending on the volume of the buildings at that site, and all the buildings were built from muds, so these buildings are weak to resist the climate. It is probable that all buildings were buried under these sites, and the destroyed pottery of pre-Islamic period was distributed over the archaeological sites. Only one site on the Tuzkhormato mountain built with blaster and gypsum rocks, this site is (Gawor Qalasi) which from (Sassanian) period. All these sites still are not studied geologically or geophysically for determination the ages of these sites or delineating the geometrical shapes of buried buildings or searching some of the precious things like gold or other things

H.E.L.L.A.: A Bay Area Critical Racial Affinity Group Committed to Healing, Empowerment, Love, Liberation, and Action

Despite repeated pleas for diversifying a predominantly White U.S. teacher workforce, a significant teacher diversity gap persists in almost every state of the country (Boser, 2014). Teachers of Color who enter the profession with commitments to social justice, in particular, face an array of racist structural and interpersonal challenges often leading to their burnout and in some cases push out from the field (Kohli & Pizarro, 2016). In response to neoliberal, color evasive, and apolitical approaches to teacher support, educators and organizers have reclaimed and reframed their pedagogies through critical professional development (Kohli, Picower, Martinez, & Ortiz, 2015) to center healing from the damaging impacts of oppression (Ginwright, 2015; Pour-Khorshid, 2016). This three-year ethnographic case study (Yin, 2003) of a California racial affinity group of 12 critical educators of Color (CEoC) committed to healing, empowerment, love, liberation and action (H.E.L.L.A.) offers insights about alternative approaches to teacher support rooted in critical-healing praxes (Cariaga, 2018). Relying on ethnographic approaches such as participant observation (Wilson, 1977), semi-structured interviews (Patton, 2002), and testimonios (Pour-Khorshid, 2016) as focal methods, I utilized grounded theory (Straus & Corbin, 1998) to examine: (a) the nature of learning and interactions that unfold over time, and (b) the personal and professional impact that members experienced through their participation. The findings from this research illuminate how the group explicitly centered 12 members’ experiences, needs, and collective knowledge to (a) engage in fugitive learning as an act of political and pedagogical resistance to White Supremacy; and in so doing, (b) cultivated a sacred space for soul care and collective healing. I conclude by discussing how and why critical racial affinity group spaces for CEoC offer a more holistic approach to support their personal, political, relational, and pedagogical growth and well-being

Physical Multi-Layer Phantoms for Intra-Body Communications

This paper presents approaches to creating tissue mimicking materials that can be used as phantoms for evaluating the performance of Body Area Networks (BAN). The main goal of the paper is to describe a methodology to create a repeatable experimental BAN platform that can be customized depending on the BAN scenario under test. Comparisons between different material compositions and percentages are shown, along with the resulting electrical properties of each mixture over the frequency range of interest for intra-body communications; 100 KHz to 100 MHz. Test results on a composite multi-layer sample are presented confirming the efficacy of the proposed methodology. To date, this is the first paper that provides guidance on how to decide on concentration levels of ingredients, depending on the exact frequency range of operation, and the desired matched electrical characteristics (conductivity vs. permittivity), to create multi-layer phantoms for intra-body communication applications

FROM URBAN LIVING LAB TO URBAN TRANSFORMATION

openQuesta ricerca approfondisce la crescente rilevanza globale del passaggio verso la sostenibilità nelle città, sottolineando le sfide con cui le amministrazioni locali si confrontano. Prendendo spunto dall'esperienza dell'autore in progetti finanziati dall'UE, lo studio si concentra sul Comune di Maia, con l'obiettivo di chiarire gli ostacoli e le strategie essenziali per raggiungere la sostenibilità urbana. Esamina l'iniziativa BaZe-Maia Living Lab, volta alla decarbonizzazione, mettendo in evidenza le complessità nell'attuare soluzioni ispirate ai living lab, soprattutto in considerazione di sfide come l'epidemia di COVID-19. Inoltre, l'alleanza di Maia con il consorzio SPARCS e la creazione del Piano d'Azione per l'Energia Sostenibile (SEAP) evidenziano i loro passi collettivi per modificare le abitudini urbane, aumentare l'efficienza energetica e ridurre al minimo gli sprechi. Questa esplorazione cerca di identificare gli elementi centrali che guidano tali sforzi, mettendo in luce gli ostacoli e suggerendo soluzioni. L'obiettivo principale è rafforzare la diffusione della conoscenza e integrare pratiche sostenibili innovative nel percorso di pianificazione urbana di Maia. La metodologia dello studio si basa su tecniche qualitative come interviste, analisi documentale e l'utilizzo del modello Morgenstadt per valutare le iniziative verdi di Maia, confrontandole con Lipsia. Un'analisi tematica dei documenti del progetto e delle opinioni degli stakeholder indica l'approccio proattivo di Maia alla co-progettazione, al coinvolgimento degli stakeholder, agli esperimenti e all'integrazione degli aspetti legati alla sostenibilità. Tuttavia, emergono difficoltà nell'avviare attività di co-progettazione e nel raggiungere gli obiettivi verdi strutturali. Un'analisi comparativa con Lipsia offre spunti illuminanti riguardo alla cooperazione completa, alla flessibilità, alle strategie finanziarie e alle visioni lungimiranti benefiche per Maia. Le principali raccomandazioni includono l'adozione di regolamenti completi, l'ampliamento dell'interazione degli stakeholder, il potenziamento delle capacità organizzative, il sfruttamento di collaborazioni esterne e risorse, l'istituzione di solide infrastrutture dati e la promozione delle innovazioni tecnologiche. Tuttavia, le difficoltà persistenti derivano dalla compartimentazione dei dipartimenti, dal coinvolgimento limitato e dalla visione della sostenibilità limitata all'ambito digitale. Questa indagine offre una comprensione più approfondita degli elementi diversificati che guidano i cambiamenti urbani verdi e fornisce una guida per superare gli ostacoli nella diffusione dei living lab. Ulteriori studi mirati potrebbero colmare le lacune osservate riguardo alle realizzazioni della co-progettazione e alle ristrutturazioni edilizie. La ricerca chiarisce l'intricato intreccio negli sforzi urbani verdi, sottolineando l'importanza di approcci unificati, coinvolgimento inclusivo degli stakeholder e rafforzamento delle capacità per indurre cambiamenti su vasta scala.This research delves into the escalating global relevance of transitioning towards sustainability in cities, underscoring the hurdles local administrations grapple with. Drawing from the author's involvement in projects funded by the EU, the study centers on the Municipality of Maia, aiming to clarify the obstacles and essential strategies for achieving urban sustainability. It examines the BaZe-Maia Living Lab initiative, which aims for decarbonization, highlighting the intricacies of enacting living lab-inspired solutions, especially given challenges like the COVID-19 outbreak. Additionally, Maia's alliance with the SPARCS consortium and the crafting of the Sustainable Energy Action Plan (SEAP) underscore their collective steps to modify urban habits, boost energy thriftiness, and minimize waste. This exploration seeks to identify the central elements guiding such endeavors, spotlighting impediments and suggesting solutions. The overarching goal is to fortify the dissemination of knowledge and weave groundbreaking sustainable practices into Maia's urban planning path. The methodology of the study hinges on qualitative techniques such as interviews, scrutinizing documents, and using the Morgenstadt blueprint to evaluate Maia's green undertakings, contrasting them with Leipzig. A thematic breakdown of project paperwork and the views of stakeholders indicates Maia's proactive approach to co-design, stakeholder involvement, trials, and integrating sustainability aspects. However, hitches emerge when initiating co-design activities and meeting structural green targets. A side-by-side analysis with Leipzig offers enlightening takeaways about all-encompassing cooperation, flexibility, financial strategies, and forward-thinking visions beneficial for Maia. Principal suggestions encompass the rollout of all-inclusive regulations, amplifying stakeholder interaction, fortifying organizational capabilities, capitalizing on outside collaborations and resources, instituting sturdy data infrastructures, and championing tech advancements. Yet, enduring difficulties arise from departmental silos, limited involvement, and viewing sustainability solely through a digital lens. This investigation offers a deeper understanding of the diverse elements steering green urban shifts and furnishes a blueprint to navigate roadblocks in living lab rollouts. More pinpointed studies might bridge observed voids concerning co-design realizations and building overhauls. The research clarifies the intricate interplay in urban green endeavors, emphasizing the value of unified approaches, inclusive stakeholder involvement, and strengthening capabilities to induce broad-based alterations

Cytotoxicity of the Urine of Different Camel Breeds on the Proliferation of Lung Cancer Cells, A549

Objective: Cancer is a disease characterized by uncontrolled cellular proliferation and differentiation. Nearly all conventional cancer treatments have undesirable negative impacts, and safer chemotherapeutics would be advantageous. Consequently, the goal of current study was to evaluate and compare the effects of urine derived from two different camel breeds on proliferation of cultured human cancer cells. Human lung adenocarcinoma cells (A549) were cultured in the presence or absence of varied dilutions of urine obtained from two different camel breeds (Magateer and Majaheem). Within breeds, we compared the effects of sex and age of donor camels on urine cytotoxicity to A549 cells. After 48 hrs, surviving A549 cells were enumerated using the sulfarhodamine assay. A549 cell survival was lower using urine from Magateer versus Majaheem camels (84.8% versus 94.2% of starting cell number, respectively; n=20 for both groups, p<0.001). When evaluating the effect of camel age, urine from older Magateer camels was significantly more effective in inhibiting A549 proliferation than was urine from younger camels of this breed. An age-related effect was not observed for Majaheem camels. When comparing sex-effects on camel urine inhibition of A549 proliferation (n=10 in each group), we observed a trend towards more A549 inhibition using female versus male urine, in both camel breeds; however, this difference did not reach statistical significance. The present study confirms previous studies that showed that camel urine can inhibit the growth of cancer cells. It also provides the first evidence that there are slight differences in the cancer cell growth-inhibitory effect of camel urine depending on the camel breed, age, and, possibly, sex. Keywords: Camel breeds, Urine, Cancer cells, Cytotoxicity

The Impact of Knowledge Management Strategies on Organizational Ambidexterity Mediated by Organizational Learning Capability

Background: This study intends to investigate the relationship between organizational ambidexterity and knowledge management practices, with a focus on travel and tourism industries specifically. The research is conducted using a descriptive-correlation approach and involves 72 businesses located in Qom, Mashhad, and Tehran. A total of 369 managers and personnel from these organizations participated in the study, providing valuable insights into the dynamics of knowledge management and its impact on organizational learning and ambidexterity within the tourism sector. Methods: In this study, descriptive-correlation research methodology was used. Data were collected through a questionnaire distributed to 369 managers and personnel from 72 tourism organizations. The questionnaire focused on assessing the participants' perspectives on knowledge management strategies, organizational learning capability, and organizational ambidexterity. This quantitative approach allowed for the examination of relationships and mediation effects within the specified variables. Findings: The results of the study show substantial correlation between organizational ambidexterity, learning ability, and knowledge management techniques. It was found to be fascinating that the relationship between organizational ambidexterity and knowledge management strategies in the tourism setting was partially mediated by organizational learning capacity. Conclusion: In conclusion, tourism companies should place a high priority on implementing both explicit and tacit knowledge management strategies in order to attain structural ambidexterity. Effective HRM procedures as well as the advancement of knowledge management and information technology infrastructures must serve as the cornerstones of these strategies. Encouraging learning, unlearning, relearning, experimentation, and knowledge sharing are pivotal for enhancing organizational learning capability and, consequently, achieving organizational ambidexterity. This study underscores the need for a holistic approach that integrates human and technological elements to foster a dynamic and adaptable organizational structure in the tourism sector