Miracle-dz/UniFAR-FTUs huggingface dataset:
An analysis of pre‐ and post‐hatching maternal effects mediated by carotenoids in the blue tit

Maternal effects increase phenotypic plasticity in offspring traits and may therefore facilitate adaptation to environmental variability. Carotenoids have been hypothesized to mediate costs of reproduction in females as well as maternal effects. However, assessing potential transgenerational and population consequences of environmental availability of carotenoids requires a better understanding of mechanisms of maternal effects mediated by these antioxidant pigments. Manipulating dietary availability of carotenoids to egg‐laying female blue tits and subsequently cross‐fostering nestlings between female treatments allowed us to specifically investigate the relative importance of maternal effects through egg carotenoids and through post‐hatching care mediated by antioxidants in females. Nestling body size and mass and plasma antioxidants were not significantly affected by pre‐ or post‐hatching maternal effects mediated by antioxidants, although both types of maternal effects in interaction explained the variation in growth, as measured by wing length. Development of the ability to mount a cell‐mediated immune response as well as its temporal dynamics was influenced by both pre‐ and post‐hatching maternal effects, with an advantage to nestlings originating from, or reared by, carotenoid‐supplemented females. In addition, nestlings reared by carotenoid‐fed females had a lower blood sedimentation rate, indicating that they may have been less infected than nestlings from controls. Finally, prehatching maternal effects in interaction with nestling plasma carotenoid levels affected the development of carotenoid‐based plumage. Maternal effects mediated by carotenoids may thus act as a proximate factor in development and phenotypic plasticity in traits associated with nestling fitness, such as immune response and ability to metabolize and use antioxidants, and ultimately participate in the evolution of phenotypic traits.
Alpaca: intermittent execution without checkpoints

The emergence of energy harvesting devices creates the potential for batteryless sensing and computing devices. Such devices operate only intermittently, as energy is available, presenting a number of challenges for software developers. Programmers face a complex design space requiring reasoning about energy, memory consistency, and forward progress. This paper introduces Alpaca, a low-overhead programming model for intermittent computing on energy-harvesting devices. Alpaca programs are composed of a sequence of user-defined tasks. The Alpaca runtime preserves execution progress at the granularity of a task. The key insight in Alpaca is the privatization of data shared between tasks. Shared values written in a task are detected using idempotence analysis and copied into a buffer private to the task. At the end of the task, modified values from the private buffer are atomically committed to main memory, ensuring that data remain consistent despite power failures. Alpaca provides a familiar programming interface, a highly efficient runtime model, and places fewer restrictions on a target device's hardware architecture. We implemented a prototype of Alpaca as an extension to C with an LLVM compiler pass. We evaluated Alpaca, and directly compared to two systems from prior work. Alpaca eliminates checkpoints, which improves performance up to 15x, and avoids static multi-versioning, which improves memory consumption by up to 5.5x.
Boolean and current detection of MOS transistor with gate oxide short

We study the voltage and current behavior of Gate Oxide Short faults due to pinholes in the gate oxide. Our objective is to give a detailed analysis of the behavior of the GOS defect taking into account random parameters such as the GOS resistance, the GOS location and the GOS size. To facilitate an accurate analysis, we use a bi-dimensional array, and, since a complete analysis is desired, we derive characteristics of the GOS as a function of its resistance, location and size. Finally, we validate the model has been validated through measurements of GOS intentionally injected into a designed and manufactured circuit.
Multi-Nucleoside Reverse Transcriptase Inhibitor Resistant HIV Type-1 in a Patient from Sierra Leone Failing Stavudine, Lamivudine and Nevirapine

We report a 33-year-old HIV type-1 (HIV-1)-infected male from Sierra Leone who harboured extensive drug resistance mutations to all nucleoside reverse transcriptase inhibitors (NRTIs) and non-NRTIs, including the multi-NRTI-resistance Q151M complex, K65R, M184I and Y181I, after using standard first-line generic fixed-dose stavudine, lamivudine and nevirapine (Triomune™) for 36 months. In the context of non-B subtypes in resource-limited countries, first-line stavudine-containing regimens have been associated with more extensive and complex mutation patterns, compared with subtype B viruses. Whether the extensive and complex NRTI resistance patterns found among African patients failing first-line antiretroviral therapy is explained by viral genetic diversity or by different patient monitoring strategies remains to be elucidated. Emerging multi-NRTI resistance in sub- Saharan Africa would not only compromise second-line treatment options and the success of anti-retroviral rollout, but could also contribute to the spread of drug- resistant variants worldwide.
Greener and Smarter Phones for Future Cities: Characterizing the Impact of GPS Signal Strength on Power Consumption

Smart cities appear as the next stage of urbanization aiming to not only exploit physical and digital infrastructure for urban development but also the intellectual and social capital as its core ingredient for urbanization. Smart cities harness the power of data from sensors in order to understand and manage city systems. The most important of these sensing devices are smartphones as they provide the most important means to connect the smart city systems with its citizens, allowing personalization n and cocreation. The battery lifetime of smartphones is one of the most important parameters in achieving good user experience for the device. Therefore, the management and the optimization of handheld device applications in relation to their power consumption are an important area of research. This paper investigates the relationship between the energy consumption of a localization application and the strength of the global positioning system (GPS) signal. This is an important focus, because location-based applications are among the top power-hungry applications. We conduct experiments on two android location-based applications, one developed by us, and the other one, off the shelf. We use the results from the measurements of the two applications to derive a mathematical model that describes the power consumption in smartphones in terms of SNR and the time to first fix. The results from this study show that higher SNR values of GPS signals do consume less energy, while low GPS signals causing faster battery drain (38% as compared with 13%). To the best of our knowledge, this is the first study that provides a quantitative understanding of how the poor strength (SNR) of satellite signals will cause relatively higher power drain from a smartphone's battery.
A semantic interoperability framework for software as a service systems in cloud computing environments / Reza Rezaei

In cloud computing environments, one of the most important barriers to the adoption of software as a service systems is interoperability. Generally, in cloud computing environments at software as a service level, interoperability refers to the ability of software as a service systems on one cloud provider to communicate with software as a service systems on another cloud provider. The current software as a service systems in cloud computing environments have not been built with interoperability as a primary concern. Software as a service systems in cloud computing environments are poorly developed to meet the interoperability challenges. A common tactic for enabling interoperability is the use of an interoperability framework or model. During the past few years, at software as a service level, various interoperability frameworks and models have been developed to provide interoperability between systems. The syntactic interoperability of software as a service systems have already been intensively researched. However, not enough consideration has been given to semantic interoperability issues. Both syntactic and semantic interoperability are necessary prerequisites to achieve interoperability. Achieving semantic interoperability is a challenge within the world of software as a service in cloud computing environments. Therefore, a semantic interoperability framework for software as a service systems in cloud computing environments is needed. In this thesis, we develop a semantic interoperability framework for software as a service systems in cloud computing environments. For this purpose, we illustrate how current technologies, such as service oriented architecture, can represent an adequate foundation for implementing such framework. The capabilities and value of service oriented architecture for semantic interoperability between software as a service systems in cloud computing environments will be studied and demonstrated. iv In order to evaluate the effectiveness of the proposed semantic interoperability framework for software as a service systems in cloud computing environments, extensive experimentation and statistical analysis have been performed. Overall, the effectiveness of semantic interoperability of software as a service systems in cloud computing environments with the proposed framework shows a significant improvement in comparison with the existing models and frameworks.
Differential expression of vesicular monoamine transporter (VMAT) 1 and 2 in gastrointestinal endocrine tumours

Neuroendocrine tumours are characterized by their capacity to produce hormones, which are stored in vesicles and secretory granules. Demonstration of granule/vesicle proteins in tumours is taken as evidence of neuroendocrine differentiation. Vesicular monoamine transporters (VMAT1 and VMAT2) mediate the transport of amines into vesicles of neurons and endocrine cells. The expression of VMAT1 and VMAT2 and the usefulness of VMAT1 and VMAT2 in the histopathological diagnosis of gastrointestinal endocrine tumours have not been fully explored. This study therefore investigated the expression of VMAT1 and VMAT2 in 211 human gastrointestinal tumours by immunocytochemistry and western blotting. VMAT1 and/or VMAT2 were demonstrated in the majority of amine‐producing endocrine tumours of gastric, ileal, and appendiceal origin. Serotonin‐producing endocrine tumours (ileal and appendiceal carcinoids) expressed predominantly VMAT1, while histamine‐producing endocrine tumours (gastric carcinoids) expressed VMAT2 almost exclusively. In peptide‐producing endocrine tumours such as rectal carcinoids and endocrine pancreatic tumours, only a small number of immunopositive tumour cells were observed. No labelling was found in non‐endocrine tumours, including gastric, colorectal and pancreatic adenocarcinomas and gastrointestinal stromal tumours. In conclusion, VMAT1 and VMAT2 are differentially expressed by gastrointestinal endocrine tumours, with a pattern specific for each tumour type, reflecting their neuroendocrine differentiation and origin. VMAT1 and VMAT2 may therefore become valuable markers in the classification of neuroendocrine tumours and may also indicate patients suitable for radioisotope treatment operating via these transporter systems. Copyright © 2001 John Wiley & Sons, Ltd.
Foamy virus vector integration sites in normal human cells

Foamy viruses (FVs) or spumaviruses are retroviruses that have been developed as vectors, but their integration patterns have not been described. We have performed a large-scale analysis of FV integration sites in unselected human fibroblasts (n = 1,008) and human CD34+ hematopoietic cells (n = 1,821) by using a bacterial shuttle vector and a comparable analysis of lentiviral vector integration sites in CD34+ cells (n = 1,331). FV vectors had a distinct integration profile relative to other types of retroviruses. They did not integrate preferentially within genes, despite a modest preference for integration near transcription start sites and a significant preference for CpG islands. The genomewide distribution of FV vector proviruses was nonrandom, with both clusters and gaps. Transcriptional profiling showed that gene expression had little influence on integration site selection. Our findings suggest that FV vectors may have desirable integration properties for gene therapy applications.
Developing predictive assays: The phenotypic screening “rule of 3”

Not all phenotypic assays are created equal; critically evaluating the disease relevance of the assay system, stimulus, and readout can help design the most predictive ones. Phenotypic drug discovery approaches can positively affect the translation of preclinical findings to patients. However, not all phenotypic assays are created equal. A critical question then follows: What are the characteristics of the optimal assays? We analyze this question and propose three specific criteria related to the disease relevance of the assay—system, stimulus, and end point—to help design the most predictive phenotypic assays.
Title Dual-cap Mushroom-like Metasurface used in CP Reconfigurable Monopole Antenna for Performance Enhancement

A dual-cap mushroom-like metasurface (MS) is proposed. The proposed MS is called dual-cap mushroom-like MS because each unit cell has a simple patch with a centered via on one side of the substrate and a meandered slot on the other side, while conventional mushroom-like MS has one side of the substrate being a plain conducting plate. The operating frequency and bandwidth of the unit cells are analyzed using an equivalent circuit which is verified using the software tools Advanced Design System (ADS) and CST. Results show that the meander slot on the other side of the substrate introduces inductive effects to lower down the operating frequency and increase the operating bandwidth of the unit cells. Comparison is made with other unit cells. The proposed MS is then used as a reflector in the design of a planar circular-polarization reconfiguration (CPR) monopole antenna for the Global Navigation Satellite System (GNSS). Simulation results show that, by placing at only 0. 09λ0 from the antenna, the MS can increase the boresight gain and the operating bandwidth from 0.4 to 6.6 dBi, and 1.46-1.79 GHz to 1.42-1.88 GHz, respectively.
Fair QoS multi-resource allocation for wireless LAN

We consider the problem of allocating two network resources (wireless bandwidth and backhaul router buffer) to support fair QoS in WLAN. We transform the QoS requirements to multi-resource demands and apply the DRF scheme to achieve fair allocation of the two different types of resources. We define a QoS utility function which measures the user QoS satisfaction. We briefly prove the property of resource-based strategy proofness of DRF, the corresponding mathematical expression is used to prove QoS-based strategy-proofness in terms of both resource share and user QoS. Finally our simulation results confirm the properties of DRF and demonstrate that our DRF-based approach performs better than several multi-resource allocation schemes with respect to both fairness and utility.
Activation by Fusion of the Glutaminase and Synthetase Subunits of Escherichia coli Carbamyl-phosphate Synthetase*

Escherichia coli carbamyl-phosphate synthetase consists of two subunits that act in concert to synthesize carbamyl phosphate. The 40-kDa subunit is an amidotransferase (GLN subunit) that hydrolyzes glutamine and transfers ammonia to the 120-kDa synthetase subunit (CPS subunit). The enzyme can also catalyze ammonia-dependent carbamyl phosphate synthesis if provided with exogenous ammonia. In mammalian cells, homologous amidotransferase and synthetase domains are carried on a single polypeptide chain called CAD. Deletion of the 29-residue linker that bridges the GLN and CPS domains of CAD stimulates glutamine-dependent carbamyl phosphate synthesis and abolishes the ammonia-dependent reaction (Guy, H. I., and Evans, D. R. (1997) J. Biol. Chem. 272, 19906–19912), suggesting that the deletion mutant is trapped in a closed high activity conformation. Since the catalytic mechanisms of the mammalian and bacterial proteins are the same, we anticipated that similar changes in the function of the E. coli protein could be produced by direct fusion of the GLN and CPS subunits. A construct was made in which the intergenic region between the contiguous carA and carB genes was deleted and the sequences encoding the carbamyl-phosphate synthetase subunits were fused in frame. The resulting fusion protein was activated 10-fold relative to the native protein, was unresponsive to the allosteric activator ornithine, and could no longer use ammonia as a nitrogen donor. Moreover, the functional linkage that coordinates the rate of glutamine hydrolysis with the activation of bicarbonate was abolished, suggesting that the protein was locked in an activated conformation similar to that induced by the simultaneous binding of all substrates.
Phonon Density of States of Iron up to 153 Gigapascals

We report phonon densities of states (DOS) of iron measured by nuclear resonant inelastic x-ray scattering to 153 gigapascals and calculated from ab initio theory. Qualitatively, they are in agreement, but the theory predicts density at higher energies. From the DOS, we derive elastic and thermodynamic parameters of iron, including shear modulus, compressional and shear velocities, heat capacity, entropy, kinetic energy, zero-point energy, and Debye temperature. In comparison to the compressional and shear velocities from the preliminary reference Earth model (PREM) seismic model, our results suggest that Earth's inner core has a mean atomic number equal to or higher than pure iron, which is consistent with an iron-nickel alloy.
The Yeast RNA Polymerase II-associated Factor Iwr1p Is Involved in the Basal and Regulated Transcription of Specific Genes*

RNA polymerase II (RNA pol II) is a multisubunit enzyme that requires many auxiliary factors for its activity. Over the years, these factors have been identified using both biochemical and genetic approaches. Recently, the systematic characterization of protein complexes by tandem affinity purification and mass spectroscopy has allowed the identification of new components of well established complexes, including the RNA pol II holoenzyme. Using this approach, a novel and highly conserved factor, Iwr1p, that physically interacts with most of the RNA pol II subunits has been described in yeast. Here we show that Iwr1p genetically interacts with components of the basal transcription machinery and plays a role in both basal and regulated transcription. We report that mutation of the IWR1 gene is able to bypass the otherwise essential requirement for the transcriptional regulator negative cofactor 2, which occurs with different components of the basal transcription machinery, including TFIIA and subunits of the mediator complex. Deletion of the IWR1 gene leads to an altered expression of specific genes, including phosphate-responsive genes and SUC2. Our results show that Iwr1p is a nucleocytoplasmic shuttling protein and suggest that Iwr1p acts early in the formation of the pre-initiation complex by mediating the interaction of certain activators with the basal transcription apparatus.
Advanced document analysis and automatic classification of PDF documents

This thesis explores the domain of document analysis and document classification within the PDF document environment The main focus is the creation of a document classification technique which can identify the logical class of a PDF document and so provide necessary information to document class specific algorithms (such as document understanding techniques). The thesis describes a page decomposition technique which is tailored to render the information contained in an unstructured PDF file into a set of blocks. The new technique is based on published research but contains many modifications which enable it to competently analyse the internal document model of PDF documents. A new level of document processing is presented: advanced document analysis. The aim of advanced document analysis is to extract information from the PDF file which can be used to help identify the logical class of that PDF file. A blackboard framework is used in a process of block labelling in which the blocks created from earlier segmentation techniques are classified into one of eight basic categories. The blackboard's knowledge sources are programmed to find recurring patterns amongst the document's blocks and formulate document-specific heuristics which can be used to tag those blocks. Meaningful document features are found from three information sources: a statistical evaluation of the document's esthetic components; a logical based evaluation of the labelled document blocks and an appearance based evaluation of the labelled document blocks. The features are used to train and test a neural net classification system which identifies the recurring patterns amongst these features for four basic document classes: newspapers; brochures; forms and academic documents. In summary this thesis shows that it is possible to classify a PDF document (which is logically unstructured) into a basic logical document class. This has important ramifications for document processing systems which have traditionally relied upon a priori knowledge of the logical class of the document they are processing.
Low-complexity multi-way and reconfigurable cyclic shift network of QC-LDPC decoder for Wi-Fi/WIMAX applications

This paper proposes a cyclic shift decomposition (CSD) algorithm to perform multi-way cyclic shifts with low complexity in the quasi-cyclic low-density parity-check (QCLDPC) decoder. The proposed algorithm decomposes the cyclic shift into a common cyclic shift and a private cyclic shift. Based on the proposed CSD algorithm, a low-complexity multi-way and reconfigurable cyclic shift network (CSN) for QC-LDPC codes is proposed. The proposed CSN is composed of the shared component, which performs the common cyclic shift, and the repeated component, which performs the private cyclic shift. Each component can support reconfigurability for given QCLDPC codes. By introducing the single-path shared component, only the complexity of the multi-path repeated component increases linearly as the number of multi-way paths increases. A complexity analysis of each component is also proposed. Based on the complexity analysis, the proposed CSN can perform multi-way and reconfigurable cyclic shifts with low complexity in the QC-LDPC decoder. The implementation results show that the areas of the proposed four-way CSN are 0.227 mm2 and 0.276 mm2 for the IEEE 802.11n/ac and IEEE 802.16e QC-LDPC codes, respectively, with 130 nm CMOS technology. The area saving per each-way is from 13.8% to 86.5% compared with previously presented works.
Survey on Data Processing and Scheduling in Hadoop

is an explosion in the volume of data in the world. The amount of data is increasing by leaps and bounds. The sources are individuals, social media, organizations, etc. The data may be structured, semi-structured or unstructured. Gaining knowledge from this data and using it for competitive advantage is the primary focus of all the organizations. In the last few years Big Data has found its way in almost every field, from government to private sectors, industry to academia. The major challenges associated with Big Data are data organization, modeling, data analysis and retrieval. Hadoop is a widely used software framework used for the large scale management and analysis of data. The main components of Hadoop: HDFS and MapReduce, enable the distributed storage and processing of data over a large number of commodity servers. This paper provides an overview of MapReduce and its capabilities and discusses the related issues.