Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular biology of the human immunodeficiency virus type 1

The immunodeficiency virus type 1 is a complex retrovirus. In addition to genes that specify the proteins of the virus particle and the replicative enzymes common to all retroviruses, HIV‐1 specifies at least six additional proteins that regulate the virus life cycle. Two of these regulatory genes, tat and rev, specify proteins essential for replication. These proteins bind to specific sequences of newly synthesized virus RNA and profoundly affect virus protein expression. Tat and rev appear to be prototypes of novel eukaryotic regulatory proteins. These two genes may play a central role in regulating the rate of virus replication. Three other viral genes, vif, vpu, and vpr, affect the assembly and replication capacity of newly made virus particles. These genes may play a critical role in spread of the virus from tissue to tissue and from person to person. Our understanding of the contribution of each of the virus structural proteins and regulatory genes to the complex life cycle of the virus in natural infections is incomplete. However, enough insight has been gained into the structure and function of each of these components to provide a firm basis for rational antiviral drug development. —Haseltine, W. A. Molecular biology of the human immunodeficiency virus type 1. FASEB J. 5: 2349–2360; 1991.
Carotid Artery Stenting 2013: Thumbs up

It has been customary for interventional cardiologists involved in carotid artery stenting, to underline non-inferiority of the percutaneous technique versus surgical carotid endarterectomy. To that end, all cause morbidity and mortality figures of both methods are compared. Surgery has, in most large randomized studies, had an edge over stenting in terms of cerebrovascular adverse events. This may have partly been due to occasional indiscriminate indication for stenting in lesions and/or vessels with unfavourable characteristics (severe target vessel tortuosity and calcification, Type III aortic arch, and so on). On one hand, the author pleads for improvement of the excellent results of endarterectomy, by subjecting all patients planned for surgery to a thorough preoperative cardiological work up, including generous invasive investigation, thus reducing the incidence of perioperative myocardial infarction, heart failure and cardiac death. On the other hand, we are convinced that the results of carotid stenting should then be compared to best practice surgery. The rate of neurological adverse event rate after carotid endarterectomy at our institution lies under 0.7% at 30 days postoperatively. Specifically, the goal should be that carotid stenting underbids surgical endarterectomy, also and mainly, in terms of cerebral and cerebrovascular adverse events. Cardiac morbidity and mortality as well as laryngeal nerve palsy should no more be the main arguments for the percutaneous approach. This should easily be possible if patient selection for carotid revascularisation would be approached according to morphological criteria, in analogy with the “Syntax”-score used to optimise revascularisation strategies in coronary artery disease.
How Does the Data Sampling Strategy Impact the Discovery of Information Diffusion in Social Media?

Platforms such as Twitter have provided researchers with ample opportunities to analytically study social phenomena. There are however, significant computational challenges due to the enormous rate of production of new information: researchers are therefore, often forced to analyze a judiciously selected “sample” of the data. Like other social media phenomena, information diffusion is a social process–it is affected by user context, and topic, in addition to the graph topology. This paper studies the impact of different attribute and topology based sampling strategies on the discovery of an important social media phenomena–information diffusion.We examine several widely-adopted sampling methods that select nodes based on attribute (random, location, and activity) and topology (forest fire) as well as study the impact of attribute based seed selection on topology based sampling. Then we develop a series of metrics for evaluating the quality of the sample, based on user activity (e.g. volume, number of seeds), topological (e.g. reach, spread) and temporal characteristics (e.g. rate). We additionally correlate the diffusion volume metric with two external variables–search and news trends. Our experiments reveal that for small sample sizes (30%), a sample that incorporates both topology and user context (e.g. location, activity) can improve on naive methods by a significant margin of ~15-20%.
Expression of CCAAT/Enhancer Binding Protein Beta in Muscle Satellite Cells Inhibits Myogenesis in Cancer Cachexia

Cancer cachexia is a paraneoplastic syndrome that causes profound weight loss and muscle mass atrophy and is estimated to be the cause of up to 30% of cancer deaths. Though the exact cause is unknown, patients with cancer cachexia have increased muscle protein catabolism. In healthy muscle, injury activates skeletal muscle stem cells, called satellite cells, to differentiate and promote regeneration. Here, we provide evidence that this mechanism is inhibited in cancer cachexia due to persistent expression of CCAAT/Enhancer Binding Protein beta (C/EBPβ) in muscle myoblasts. C/EBPβ is a bzip transcription factor that is expressed in muscle satellite cells and is normally downregulated upon differentiation. However, in myoblasts exposed to a cachectic milieu, C/EBPβ expression remains elevated, despite activation to differentiate, resulting in the inhibition of myogenin expression and myogenesis. In vivo, cancer cachexia results in increased number of Pax7+ cells that also express C/EBPβ and the inhibition of normal repair mechanisms. Loss of C/EBPβ expression in primary myoblasts rescues differentiation under cachectic conditions without restoring myotube size, indicating that C/EBPβ is an important inhibitor of myogenesis in cancer cachexia.
Modeling water futures using food security and environmental sustainability approaches

Global water scarcity is becoming a constraint for human development. Therefore there is a need to enhance water productivity of the irrigated and rainfed agriculture to meet the increasing food demand due to the population growth. This paper describes modeling efforts to assess present and future water needs for food, people and environment. This exercise is being carried out by the International Commission on Irrigation and Drainage (ICID) in five countries, China, Egypt, India, Mexico, and Pakistan, which together cover 51% of irrigated area and 43% population in the world. This paper presents two modeling frameworks including the food security approach of the International Water Management Institute (IWMI) through policy dialogue model (PODIUM), an environmental approach i.e. the Basin wide Holistic Integrated Water Assessment (BHIWA) model and its system dynamic version using VenSim environment.
Reformulating the repository, Digital Intangible Heritage, empathic design and Greek/Unani medicinal practices

Within the emerging domain of Digital Intangible Heritage, my research focuses on the continuity of cultural knowledge by proposing a new model for access to indigenous methodologies. Through the creation of a digital repository of Greek/Unani medicinal practices and an experimental web-based interface to this archive, the research defines a new framework for the description, representation and transmission of these practices. The Unani medicinal system is entrenched in the Middle Eastern and South Asian regions. Through analytic documentation of these practices, I intend to reveal the intricate relationships between a traditional Unani physician's life experience and clinical practices. For example, I will examine the lifestyle practices of a physician in relation to his diagnostic understanding of lifestyle diseases. Following analytic documentation using a range of digital capture tools and the classification of this material using an extended metadata schema - Dublin Core -the research challenge here is to create a sympathetic interactive information architecture for the repository. Drawing on `empathic design', `design probes' and `experiencing prototyping' the experimental web-based application intends to provide users with an intuitive interface through which to retrieve knowledge and experiences related to accomplished Unani physicians.
Modeling of Lithium-Ion Battery for Energy Storage System Simulation

Batteries are the power providers for almost all portable computing devices. They can also be used to build energy storage systems for large-scale power applications. In order to design battery systems for energy-optimal architectures and applications with maximized battery lifetime, system designers require computer aided design tools that can implement mathematical battery models, predict the battery behavior and thus help the designers search for the optimal schemes. This paper presents a lithium-ion battery model which can be used on SIMPLORER software to simulate the behavior of the battery under dynamic conditions. Based on measured battery data, a mathematical model of the battery is developed which takes into account battery operating temperature and the rates of the battery charge/discharge currents. In addition, thermal characteristics of the battery are also studied.
Spitzer Mid-Infrared Spectra of Cool-Core Galaxy Clusters

We have obtained mid-infrared spectra of nine cool-core galaxy clusters with the Infrared Spectrograph aboard the Spitzer Space Telescope. X-ray, ultraviolet and optical observations have demonstrated that each of these clusters hosts a cooling flow which seems to be fueling vigorous star formation in the brightest cluster galaxy. Our goal is to use the advantages of the mid-infrared band to improve estimates of star formation. Our spectra are characterized by diverse morphologies ranging from classic starbursts to flat spectra with surprisingly weak dust features. Although most of our sample are known from optical/UV data to be active star-formers, they lack the expected strong mid-infrared continuum. Star formation may be proceeding in unusually dust-deficient circumgalactic environments such as the interface between the cooling flow and the relativistic jets from the active galactic nucleus.
Spectral structure of singular spectrum decomposition for time series

Singular spectrum analysis (SSA) is a nonparametric and adaptive spectral decomposition of a time series. The singular value decomposition of the trajectory matrix and the anti-diagonal averaging leads to a time-series decomposition. In this algorithm, a single free parameter, window length $K$, is involved which is the FIR filter length for the time series. There are no generally accepted criterion for the proper choice of the window length $K$. Moreover, the proper window length depends on the specific problem which we are interested in. Thus, it is important to monitor the spectral structure of the SSA decomposition and its window length dependence in detail for the practical application. In this paper, based on the filtering interpretation of SSA, it is shown that the decomposition of the power spectrum for the original time series is possible with the filters constructed from the eigenvectors of the lagged-covariance matrix. With this, we can obtain insights into the spectral structure of the SSA decomposition and it helps us for the proper choice of the window length in the practical application of SSA.
Description Logics ’ 96 , Boston , MA Using Description Logics for Consistency-based Diagnosis

Using quantitative models of simple mechanisms as an example domain, we show how the basic principles of consistency-based diagnosis can be implemented using description logics with expressive concrete domains. In addition, description logics provide the inference services necessary to organize and validate model libraries, an aspect that is neglected in consistency-based diagnosis until now. 1 Description Logics for Diagnosis Consistency-based diagnosis 1 [7; 10] is a method for the diagnosis of technical devices based on descriptions of the corr t and faulty behavior of components. Therefore, for represen ting, simulating and diagnosing the simple bike drive train i n Fig.1 at least the following knowledge must be represented within such a system: 1. The differenttypes of components , e.g. wheels, gearwheels, chains, along with their attributeslike forceF , radiusr and torqueM . 2 2. Thestructureof assemblies, e.g the kinematic structure of the mechanisms using kinematic pairs. 3. Physical lawslikeM = r F andconstraintsimposed on the attributes likeF 0 andr > 0. 4. Thenormal and faulty behaviors (often called models in consistency-based diagnosis) of components and assemblies, e.g. the propagation of torques from one wheel to another ( M1 = M2) in a rotational pair. Based on this representation diagnosisis mainly the task of identifying the models of behavior that are consistent with a set of observed parameter values. This is most often done by simulatinghypothetized behaviors and comparing the results with the observed values. Also called model-based diagnosis In this paper we are modeling these attributes using scalar n umeric values resulting in quantitative models of behavior. Alternatively a qualitative modeling using symbolic values as it is used in qualitative physics is possible. In this paper we argue that description logics (DL) are well suited for consistency-based diagnosis. They provide a ric h and expressive representation language, that is able to ful fill the representation needs. The TBox contains the descriptio ns of the different component types and the models of correct and faulty behavior. Concrete devices are modeled as a set of assertions within the ABox. Furthermore the powerful Tand ABox inference services such as consistency , object classification3 andclassificationcan be used for simulation and diagnosis. Moreover, for certain languages (e.g. ALCF(D)) sound and complete algorithms for these inferences could be given (see e.g. [3]).
Fossilization of English in PNG

Fossilization is when there is a permanent cessation of a person learning a new target language. Certain incorrect forms of the language are fossilized into the person’s language production. After a while, these incorrect forms are accept as correct. There are many reasons why language learners never reach target-like proficiency of the new target language. In Papua New Guinea, there are many examples of fossilisation in the use of English. These non-standard fossilized forms may emerge due to the transfer of the phonetic sounds of the mother tongue. Fossilization may occur with the lack of syntactic knowledge, therefore, the some speakers have difficulty in constructing a correct form of the English sentence. Semantic fossilization is common when words are imported from a local language into English. The most common reason for fossilization is that adequate communication is achieved so there is no motivation to continue learning the various forms of the new language. Changing these commonly accepted forms is very difficult.
Towards a framework for automatic geographic feature extraction from Twitter

Interactive social media platforms offer a tremendous amount of volunteered, user-generated content (Flickr, Twitter, etc.). Together with volunteered geographic information (VGI) they potentially provide a valuable source of information which is increasingly recognized, but particularly in GIScience not utilized to its full potential. Twitter as one location-based social network in particular, provides the ability to sense geo-processes and to gain knowledge about the individual user perception towards geographic objects. A georeferenced tweet represents a proxy of a real world observation and contains spatial, temporal and semantic information. These social sensor measurements depend on particular tweet locations and are influenced by the individual user perception of urban space. Although there is a growing research body conducting Twitter analysis, a key challenge remains whether this noisy biased data source forms a representative sample for the knowledge discovery of geographic information. Location information retrieved from Twitter data is spatio-temporally and semantically uncertain. One of the main research aims is therefore to investigate whether geographic features from tweets can be detected and extracted. Furthermore, we explore whether the inferred geometries of features match with real world spatial objects (e.g. points of interest). In this work we propose a framework to infer geographic features from unstructured georeferenced Twitter data using semantic topic modelling and spatial clustering techniques. Given the detected and extracted geographic features from Twitter, we applied a geometry computation and compared the results with map features from OpenStreetMap.
Re-modulating water allocation in a complex multi-reservoir system under current and climate change scenarios

Water resource planning and management at watershed scale should be aimed at guaranteeing soil and water conservation, together with the organization, use and management of water resources for protecting the environment and for the economic and social development. Nevertheless, appropriate approaches and tools for identifying the most efficient solutions often are not adopted, and water resource is allocated for fulfilling water demands from different stakeholders with no clear rules and aims, especially when complex water supply systems are managed. In this study irrigation and hydropower water demands are analyzed in a large-scale complex system located in Eastern Calabria (Southern Italy), i.e. the Neto-Tacina Rivers System involving 2 watersheds (total area about 1500 km2), 3 irrigation systems (about 235 km2 of irrigable fields, more than 70 km2 actually irrigated), 9 reservoirs, 3 intakes and a system of three consecutive hydropower plants. Specifically, current configuration considering water concessions presently awarded to the companies managing the hydropower plants is analyzed. Then, by means of: 1) statistical tools, 2) a GIS-based distributed hydrological model and, 3) software tools for integrated water resources planning, an alternative and more efficient water resources allocation is proposed. Furthermore, the new system reliability is tested by considering two future water availability scenarios, derived from the most recent high resolution climate change data for the analyzed region, provided by regional downscaling experiments with grid resolutions finer than 20 km.
Theoretical and Computational Fluid Dynamics Streamline Topologies in Stokes Flow Within Lid-Driven Cavities

Stokes flow in a rectangular cavity with two moving lids (with equal speed but in opposite directions) and aspect ratio A (height to width) is considered. An analytic solution for the streamfunction, ψ, expressed as an infinite series of Papkovich–Fadle eigenfunctions is used to reveal changes in flow structures as A is varied. Reducing A from A = 0.9 produces a sequence of flow transformations at which a saddle stagnation point changes to a centre (or vice versa) with the generation of two additional stagnation points. To obtain the local flow topology as A → 0, we expand the velocity field about the centre of the cavity and then use topological methods. Expansion coefficients depend on the cavity aspect ratio which is considered as a separation parameter. The normal-form transformations result in a much simplified system of differential equations for the streamlines encapsulating all features of the original system. Using the simplified system, streamline patterns and their bifurcations are obtained, as A → 0.
Development of MERCURY version 2.0 robotic arms for rehabilitation applications

MERCURY is a robotic platform comprised of two mechatronic robotic arm manipulators, a body machine interface (BMI) in the form of a wearable hardware sensor sleeve and a brain computer interface (BCI). It is a prototype system primarily aimed at research in human-robotic interfaces, medical rehabilitation and assistive technologies for patients with Spinal Cord Injury. This paper discusses improvements implemented in the second generation of the system, following evaluation of results obtained from pilot testing the first generation robotic setup. The system now integrates two of the second generation MERCURY robotic arms. The main improvements are digitization of control signals, the addition of anthropomorphic hands in place of pincers, two additional degrees of freedom, improved telecommunications and BCI control.
Serum Monocyte Chemoattractant Protein-1 Concentrations Associate With Diabetes Status but Not Arterial Stiffness in Children With Type 1 Diabetes

OBJECTIVE The relationship between circulating markers of inflammation and arterial stiffness in children with type 1 diabetes is not well studied. We tested whether inflammatory monocyte chemoattractant protein (MCP)-1 concentrations correlate with arterial stiffness or type 1 diabetes status. RESEARCH DESIGN AND METHODS MCP-1 concentrations and radial tonometry data were available for 98 children with type 1 diabetes and 55 healthy control subjects. Arterial stiffness was calculated as augmentation index corrected for a heart rate of 75 (AI75). Correlation between MCP-1 and AI75 and differences in MCP-1 concentrations between case and control subjects were tested. RESULTS MCP-1 was significantly higher in children with type 1 diabetes than in control subjects (P < 0.001). However, there were no correlations between MCP-1 and AI75 in the overall sample or upon stratification by type 1 diabetes status (range P = 0.28–0.66). CONCLUSIONS Circulating MCP-1 was not associated with arterial stiffness but was significantly elevated in children with type 1 diabetes, indicating a proinflammatory state in children as young as 10 years. The clinical significance of MCP-1 elevation in type 1 diabetes needs further investigation.
Impulse Purchasing Behaviors of the Turkish Consumers in Websites as a Dynamic Consumer Model: Technology Products Example

This paper examines the concept of impulse purchasing behavior online basically. The phenomenon of impulse purchasing has been researched in consumer research as well as for example in psychology and economics since the 1950s. A detailed review and analysis of the literature asserts that there are some unsolved issues regarding the state of knowledge on impulse purchasing behavior. Furthermore, nowadays consumers buy an increasing amount of purchases on the Internet. The current conceptualizations of impulse purchase behavior do not adequately capture impulse purchase behavior over the Internet. Today several researchers have claimed that the phenomenon of impulse purchasing should be examined also in the context of online shopping environment. This article aims to reveal that what attitudes of the customers are the points in question while purchasing on internet in terms of impulse buying. The results of our exploratory research are consistent with our conceptualization, and present a strong base for future research.