Miracle-dz/UniFAR-FTUs huggingface dataset:
Population replacement gene drive characteristics for malaria elimination in a range of seasonal transmission settings: a modelling study

Background Gene drives are a genetic engineering method where a suite of genes is inherited at higher than Mendelian rates and has been proposed as a promising new vector control strategy to reinvigorate the fight against malaria in sub-Saharan Africa. Methods Using an agent-based model of malaria transmission with vector genetics, the impacts of releasing population-replacement gene drive mosquitoes on malaria transmission are examined and the population replacement gene drive system parameters required to achieve local elimination within a spatially-resolved, seasonal Sahelian setting are quantified. The performance of two different gene drive systems—“classic” and “integral”—are evaluated. Various transmission regimes (low, moderate, and high—corresponding to annual entomological inoculation rates of 10, 30, and 80 infectious bites per person) and other simultaneous interventions, including deployment of insecticide-treated nets (ITNs) and passive healthcare-seeking, are also simulated. Results Local elimination probabilities decreased with pre-existing population target site resistance frequency, increased with transmission-blocking effectiveness of the introduced antiparasitic gene and drive efficiency, and were context dependent with respect to fitness costs associated with the introduced gene. Of the four parameters, transmission-blocking effectiveness may be the most important to focus on for improvements to future gene drive strains because a single release of classic gene drive mosquitoes is likely to locally eliminate malaria in low to moderate transmission settings only when transmission-blocking effectiveness is very high (above ~ 80–90%). However, simultaneously deploying ITNs and releasing integral rather than classic gene drive mosquitoes significantly boosts elimination probabilities, such that elimination remains highly likely in low to moderate transmission regimes down to transmission-blocking effectiveness values as low as ~ 50% and in high transmission regimes with transmission-blocking effectiveness values above ~ 80–90%. Conclusion A single release of currently achievable population replacement gene drive mosquitoes, in combination with traditional forms of vector control, can likely locally eliminate malaria in low to moderate transmission regimes within the Sahel. In a high transmission regime, higher levels of transmission-blocking effectiveness than are currently available may be required.
Predicting and improving invoice-to-cash collection through machine learning/

Delinquent invoice payments can be a source of financial instability if it is poorly managed. Research in supply chain finance shows that effective invoice collection is positively correlated with the overall financial performance of companies. In this thesis I address the problem of predicting the delinquent invoice payments in advance with machine learning of historical invoice data. Specifically, this thesis demonstrates how supervised learning models can be used to detect the invoices that would have delay payments, as well as the problematic customers, which enables customized collection actions from the firm. The model from this thesis can predict with high accuracy if an invoice will be paid on time or not and also estimate the magnitude of the delay. This thesis builds and trains its invoice delinquency prediction capability based on the real-world invoice data from a Fortune 500 company. Thesis Supervisor: David Simichi-Levi Title: Professor of Civil and Environmental Engineering Thesis Supervisor: Asuman Ozdaglar Title: Professor of Electrical Engineering and Computer Science To my parents; Rao Yongjun and Hu Zhizheng Acknowledgments I would like to express my deepest gratitude to my thesis supervisors, Prof. David Simchi-Levi and Prof. Asuman Ozdaglar, for their invaluable patience, guidance and support over last two years. My plan to come to graduate school in this topic began many years back when I was an undergraduate summer research student at Northwestern University, where I was fortunate working with Prof. Daniel Abrams. I would like to thank him for encouraging me to pursue research of my interests even though it could have been (and had been) a difficult and rewarding journey. More personally, I am thankful to friends in MIT. Especially to Kim Yoo Joon, thank you for listening to all my agonies in life and suggesting solutions. I am lucky to have you as my classmate. To my roommate, Zhang Hongyi, for stimulating discussions that helped me forming ideas for my thesis. To my lifelong friends, Huang Yijie and Luo Feng, thank you for keeping me up-to-date on what lives outside of MIT are like. Finally, to my parents, thank you for your love and support throughout this journey. None of this could have been possible without you and for that I am dedicating this to you.
Challenges faced by the adoption of big data in the Dominican Republic construction industry: an empirical study

The adoption of Big Data (BD) in the construction industry has been identified as a possible solution to the demand of the current needs of projects, but the integration of this technology has proven to be a challenge specially in industries such as construction that are not technological driven. The understanding of the key elements for the BD adoption has become the focus of many industries that seek to exploit the benefits offered by this technology. Therefore, this paper aims to explore the challenges faced by the adoption of BD in the Dominican Republic (DR) construction industry. To identify these challenges qualitative research was undertaken due to the paucity of scientific data. Twenty-one individuals representing 19 companies who have great impact in the DR construction sector were interviewed. From the analysis six main challenges were identified. They are: lack BD awareness, high cost of investment, resistance to change, lack of government support and regulation, lack of technological expertise, and security concerns of BD. The challenges identified in this study, will serve to help companies better plan their technology adoption process, mainly considering aspects such as the need to tackle the lack of awareness by disseminating and promoting the concept of BD which will not only generate a better understanding of technology by making sure that present and future professionals understand the technology and its benefits. This study provides insight in the challenges to overcome for a successful adoption of BD technology, which would help companies to prepare for a future adoption.
CONSTITUYENTES DE MAREA EN LA BAHÍA DE SANTA MARTA (COLOMBIA)

Se realizo un analisis de la onda de marea en la bahia de Santa Marta. La onda de marea fue medida mediante la ayuda de un mareografo WLR 7 de la familia Aandera. A partir de las series de tiempo obtenidas se determino la amplitud y la fase de los constituyentes principales de la marea mediante un analisis de armonicos efectuado con la tecnica de ajuste de minimos cuadrados. Se encontro una marea con caracteristicas mixta principalmente diurna conformada por 12 constituyentes, de ellos seis son de caracter diurno (K1, O1, P1, Q1, J1, OO1) y cinco de caracter semidiurno (M2, S2, K2, N2, Mu2) ademas de la Componente lunisolar sinodica quincenal (Msf).
Numerical simulation and parametric study of UOE pipe forming process

The UOE process is widely recognized as an effective approach to manufacture large-diameter submerged-arc welding pipes. During the UOE process, the plate is crimped along its edge, pressed into U and O shape, welded closed and then expanded to obtain a circular pipe. In this study, the mechanical properties tests are carried out on the API X80 pipeline steel to establish the constitutive model. A two-dimensional finite element model of the UOE forming process is established under plane strain assumption. The deformed geometry of different forming steps and the distribution of equivalent plastic strain are obtained. The model is validated in practical manufacturing by comparing the forming quality, which shows a significant coherence in their geometric configurations. In particular, the effect of process parameters on the forming quality is analyzed. Those parameters are the yield strength of the plate, the location of C-die, the initial location of U-rollers, the displacement of U-rollers, the location o.
Software Ecosystems: Analyzing and Managing Business Networks in the Software Industry

This book describes the state-of-the-art of software ecosystems. It constitutes a fundamental step towards an empirically based, nuanced understanding of the implications for management, governance, and control of software ecosystems.This is the first book of its kind dedicated to this emerging field and offers guidelines on how to analyze software ecosystems; methods for managing and growing; methods on transitioning from a closed software organization to an open one; and instruments for dealing with open source, licensing issues, product management and app stores. It is unique in bringing together industry experiences, academic views and tackling challenges such as the definition of fundamental concepts of software ecosystems, describing those forces that influence its development and lifecycles, and the provision of methods for the governance of software ecosystems.This book is an essential starting point for software industry researchers, product managers, and entrepreneurs.Contributors: T. Aaltonen, T.A. Alspaugh, C. Alves, M. Anvaari, H.U. Asuncion, O. Barbosa, S. Biffl, S. Brinkkemper, M.A. Cusumano, E. den Hartigh, D. Dhungana, R.P. dos Santos, A. Finkelstein, M. Goeminne, I. Groher, I. Hammouda, S. Jansen, A. Jimnez Salas, J. Kabbedijk, M. Kauppinen, T. Kilamo, Y. -R. Li, L. Luinenburg, T. Mens, T. Mikkonen, K.M. Popp, W. Scacchi, E. Schludermann, J. Souer, M. Tol, J. van Angeren, G. van Capelleveen, M. Viljainen, W. Visscher, C. Werner
SSI Analysis of Long-Term UHI Development Due To Urbanization Affecting Urban Ecosystem and Local Climate Change Through City of Izmir Case

Background Urbanization provides several opportunities to human being to live better and comfortable life. On the other hand, it also comes with some costs and side effects like worsening climate conditions. In the local sense, the previous climatic conditions in the rural areas can be called the natural when the subsequent climatic conditions after the widespread urbanization and the absorption of these natural areas are compared. So, during the urbanization process, the natural conditions of the pre-urban areas are getting worse due to the civic activities in the cities. One of the side effects of urbanization is thermal pollution caused by certain urban activities and sectoral urban designs and also related patterns on the land surfaces of cities. Thus, thermal pollution changes city’s local climate over time and negatively affects the city’s comfort level at least locally. There are several researches focusing on that issue in cities. Each one made its contribution to the area to build up a strong knowledge. One great contribution comes from the researches focusing on analyzing time serious thermal data with continuous distribution over cities. Method Here in this research is introduced and suggested a Simulated Single Image (SSI) method based on Simulated Single Data (SSD) statistical analyze approach for the studies based on time serious data. Therefore, SSI method using time series data was applied to Remote Sensing (RS) LANDSAT satellites’ bands especially to time series’ thermal bands of Izmir city to reveal where generally Urban Hot Spots (UHS) appear and Urban Heat Islands (UHI) develop in the city. Stereo representation of the study region is also used to visually examine the topographical effect on UHI distribution in the city. Since all those analyses depend on SSI analyse, all analyses represent over and over time confirmation. Conclusions The study clearly demonstrated that industrial regions and roads with large surfaces, somehow bare lands even with spare bushes, empty but sparse grassy urban lands and more significantly the urban land parts faced to certain directions are the main urban land cover and structure types contributing UHSs to appear and UHI developments in the city that are strongly confirmed over and over again with long term data. Thus, these contributing factors adversely affect the previous natural climate in the lands that latter swallowed by the city and then let UHSs to appear and UHIs to develop at and around where these urban land cover structures are located or seen in the city over time. Those city parts are the riskiest zones that city authorities take serious actions for caring their city chronical climate (thermal) conditions and to focus on for returning these zones back into their previous natural climate and environment conditions. There are also some nature-based solutions that are given and suggested in the conclusion section of the paper for compensation of the effects caused by those contributors in the city.
Influence of load characteristics on the power/voltage stability of HVDC systems. I. Basic equations and relationships

The influence of load characteristics on the power stability of a specific HVDC system configuration has been shown. This points to a more fundamental influence of load characteristics on the power/voltage stability of HVDC systems in general. Thus, a fundamental analysis of the influence of load characteristics on the power/voltage stability of three typical HVDC system configurations is carried out in this two-part work. Three aspects are treated; (i) the basic power/voltage stability equations incorporating load characteristics, the effect of load characteristics and system parameters; (ii) the relationships between the maximum power and voltage sensitivity based methods for all the configurations incorporating load characteristics; and (iii) the most unfavourable load characteristics with respect to degrading power/voltage stability margins and the sensitivity of these margins to load characteristics. This paper presents points (i) and (ii) while part II deals with point (iii).
Bioinformatic Analysis of Lytic Polysaccharide Monooxygenases Reveals the Pan-Families Occurrence of Intrinsically Disordered C-Terminal Extensions

Lytic polysaccharide monooxygenases (LPMOs) are monocopper enzymes secreted by many organisms and viruses. LPMOs catalyze the oxidative cleavage of different types of polysaccharides and are today divided into eight families (AA9–11, AA13–17) within the Auxiliary Activity enzyme class of the CAZy database. LPMOs minimal architecture encompasses a catalytic domain, to which can be appended a carbohydrate-binding module. Intriguingly, we observed that some LPMO sequences also display a C-terminal extension of varying length not associated with any known function or fold. Here, we analyzed 27,060 sequences from different LPMO families and show that 60% have a C-terminal extension predicted to be intrinsically disordered. Our analysis shows that these disordered C-terminal regions (dCTRs) are widespread in all LPMO families (except AA13) and differ in terms of sequence length and amino-acid composition. Noteworthily, these dCTRs have so far only been observed in LPMOs. LPMO-dCTRs share a common polyampholytic nature and an enrichment in serine and threonine residues, suggesting that they undergo post-translational modifications. Interestingly, dCTRs from AA11 and AA15 are enriched in redox-sensitive, conditionally disordered regions. The widespread occurrence of dCTRs in LPMOs from evolutionarily very divergent organisms, hints at a possible functional role and opens new prospects in the field of LPMOs.
Heterogeneity in Lateral Distribution of Polycations at the Surface of Lipid Membrane: From the Experimental Data to the Theoretical Model

Natural and synthetic polycations of different kinds attract substantial attention due to an increasing number of their applications in the biomedical industry and in pharmacology. The key characteristic determining the effectiveness of the majority of these applications is the number of macromolecules adsorbed on the surface of biological cells or their lipid models. Their study is complicated by a possible heterogeneity of polymer layer adsorbed on the membrane. Experimental methods reflecting the structure of the layer include the electrokinetic measurements in liposome suspension and the boundary potential of planar bilayer lipid membranes (BLM) and lipid monolayers with a mixed composition of lipids and the ionic media. In the review, we systematically analyze the methods of experimental registration and theoretical description of the laterally heterogeneous structures in the polymer layer published in the literature and in our previous studies. In particular, we consider a model based on classical theory of the electrical double layer, used to analyze the available data of the electrokinetic measurements in liposome suspension with polylysines of varying molecular mass. This model suggests a few parameters related to the heterogeneity of the polymer layer and allows determining the conditions for its appearance at the membrane surface. A further development of this theoretical approach is discussed.
In-plane acoustic reflectors for reducing effective anchor loss in lateral–extensional MEMS resonators

In this paper, novel in-plane acoustic reflectors are proposed to enhance the quality factor (Q) in lateral-mode micromachined resonators. Finite element coupled-domain simulation is used to model anchor loss and to estimate the relative change in the resonator's performance without and with the inclusion of acoustic reflectors. Several 27 and 110 MHz AlN-on-silicon resonators are fabricated and measured to validate the theoretical and simulated data. An average Q enhancement of up to 560% is reported for specific designs with reflectors over the same resonators without reflectors. The measured results trend well with the simulated data and support that the acoustic reflectors can reduce the overall anchor loss with minimum modification in the resonator design.
JCT With Contractor's Design form of contract: a study in use

This paper presents the results of a detailed study of projects using the JCT With Contractor's Design (WCD) form of contract. Initially 49 projects were investigated to discover how the WCD contract is being used: for what kind of projects, by whom, in what circumstances, and what management approaches are being used. Fourteen projects were then selected to be investigated in more detail on their performance in terms of time, cost, quality and management. The variables were assessed in absolute terms and were then compared to what might have been expected if the contract had been managed in the conventional manner, i.e. using the JCT 80 Standard form of building contract. The conclusion of the study was that out of all the WCD projects investigated none had experienced serious problems and only a small proportion had encountered any difficulties at all in using the WCD approach.
Favipiravir Inhibits Mayaro Virus Infection in Mice

Mayaro virus (MAYV) is an emergent alphavirus that causes MAYV fever. It is often associated with debilitating symptoms, particularly arthralgia and myalgia. MAYV infection is becoming a considerable health issue that, unfortunately, lacks a specific antiviral treatment. Favipiravir, a broad-spectrum antiviral drug, has recently been shown to exert anti-MAYV activity in vitro. In the present study, the potential of Favipiravir to inhibit MAYV replication in an in vivo model was evaluated. Immunocompetent mice were orally administrated 300 mg/kg/dose of Favipiravir at pre-, concurrent-, or post-MAYV infection. The results showed a significant reduction in infectious viral particles and viral RNA transcripts in the tissues and blood of the pre- and concurrently treated infected mice. A significant reduction in the presence of both viral RNA transcript and infectious viral particles in the tissue and blood of pre- and concurrently treated infected mice was observed. By contrast, Favipiravir treatment post-MAYV infection did not result in a reduction in viral replication. Interestingly, Favipiravir strongly decreased the blood levels of the liver disease markers aspartate- and alanine aminotransferase in the pre- and concurrently treated MAYV-infected mice. Taken together, these results suggest that Favipiravir is a potent antiviral drug when administered in a timely manner.
Internalization of Islamic Values in Developing Students' Actual Morals

This study aims to explore the efforts of madrasah teachers to internalize Islamic values in developing students' actual morals. Using a case study research by conducting in-depth interviews with 8 madrasah tsanawiyah teachers and analyzing them with data cleaning, transcripts, coding and categorization, and interpretation. This research resulted in: First, duha sunnah and fardhu prayer in congregation, and get used to respect the teacher, to manage the syahwiya power of students, resulting in "iffah" which gave birth to the morals of jud, syakha', qana'ah, amanah, zuhud, rahmah, hilm, and al-afwu. Second, get used to dzikrullah, and accustom shiyam sunnah, to curb the hammiya power of students, resulting syaja'ah, ‘adalah, ihsan, insyaf, rahmah, and hilm. Third, get used to muhadharah activities, and Islamic integrative learning, to educate students' powers of mufakkara, thus giving birth to wisdom and fathanah behavior. It can be concluded that the internalization of Islamic values in developing students' actual morals is duha sunnah and fardhu prayer in congregation, get used to respect the teacher, get used to dzikrullah, accustom shiyam sunnah, muhadharah activity, and Islamic integrative learning, to curb the spiritual power of shahwiya, manage power of hammiya, and educating students powers of mufakkara, thus giving birth to the behavior of' iffah, jud, syakha', qana'ah, amanah, zuhud, rahmah, hilm, al-afwu, syaja'ah, 'adalah, ihsan, insyaf, mujahadah, sabr, wisdom, and fathanah. The results of this study have implications for the theory of "Islamic moral development" which can be applied to all madrasah education in Indonesia and the Islamic world.
SYMBIOSIS: synthetic manipulable biobricks via orthogonal serine integrase systems

Serine integrases are emerging as one of the most powerful biological tools for synthetic biology. They have been widely used across genome engineering and genetic circuit design. However, developing serine integrase-based tools for directly/precisely manipulating synthetic biobricks is still missing. Here, we report SYMBIOSIS, a versatile method that can robustly manipulate DNA parts in vivo and in vitro. First, we proposed a “Keys match Locks” model to demonstrate that three orthogonal serine integrases are able to irreversibly and stably switch on seven synthetic biobricks with high accuracy in vivo. Then, we demonstrated that purified integrases can facilitate the assembly of “Donor” and “Acceptor” plasmids in vitro to construct composite plasmids. Finally, we used SYMBIOSIS to assemble different chromoprotein genes and create novel colored Escherichia coli. We anticipate that our SYMBIOSIS strategy will accelerate synthetic biobricks manipulation, genetic circuit design, and multiple plasmids assembly for synthetic biology with broad potential applications.