Miracle-dz/UniFAR-FTUs huggingface dataset:
HIV-1 Tat Protein-mediated Transactivation of the HIV-1 Long Terminal Repeat Promoter Is Potentiated by a Novel Nuclear Tat-interacting Protein of110 kDa, Tip110*

Human immunodeficiency virus type 1 (HIV-1) gene expression and replication is highly dependent on and modulated by interactions between viral and host cellular factors. Tat protein, encoded by one of the HIV-1 regulatory genes, tat, is essential for HIV-1 gene expression. A number of host cellular factors have been shown to interact with Tat in this process. During our attempts to determine the molecular mechanisms of Tat interaction with brain cells, we isolated a cDNA clone that encodes a novelTat-interacting protein of110 kDa or Tip110 from a human fetal brain cDNA library. GenBank™ BLAST search revealed that Tip110 was almost identical to a previously cloned KIAA0156 gene with unknown functions.In vivo binding of Tip110 with Tat was confirmed by immunoprecipitation and Western blotting, in combination with mutagenesis. The yeast three-hybrid RNA-protein interaction assay indicated no direct interaction of Tip110 with Tat transactivating response element RNA. Nevertheless, Tip110 strongly synergized with Tat on Tat-mediated chloramphenicol acetyltransferase reporter gene expression and HIV-1 virus production, whereas down-modulation of constitutive Tip110 expression inhibited HIV-1 virus production. Northern blot analysis showed that Tip110 mRNA was expressed in a variety of human tissues and cells. Moreover, digital fluorescence microscopic imaging revealed that Tip110 was expressed exclusively in the nucleus, and within a nuclear speckle structure that has recently been described for human cyclin T and CDK9, two critical components for Tat transactivation function on HIV-1 long terminal repeat promoter. Taken together, these data demonstrate that Tip110 regulates Tat transactivation activity through direct interaction, and suggest that Tip110 is an important cellular factor for HIV-1 gene expression and viral replication.
Detection of High Frequency Oscillations with Teager Energy in an Animal Model of Limbic Epilepsy

High frequency oscillations (HFO) in limbic epilepsy represent a marked difference between abnormal and normal brain activity. Faced with the difficult of visually detecting HFOs in large amounts of intracranial EEG data, it is necessary to develop an automated process. This paper presents Teager Energy as a method of finding HFOs. Teager energy is an ideal measure because unlike conventional energy it takes into account the frequency component of the signal as well as signal amplitude. This greatly aids in the dissection of HFOs out of the noise and other signals contained in the EEG. Therein, Teager energy analysis is able to detect high-frequency, low-amplitude components that conventional energy measurements would miss
International Journal of Advanced Research in Computer Science and Software Engineering

— Software defect prediction work focuses on the number of defects remaining in a software system. The software defect prediction model helps in early detection of defects and contributes to their efficient removal and producing a quality software system based on several metrics. A prediction of the number of remaining defects in an inspected are fact can be used for decision making. An accurate prediction of the number of defects in a software product during system testing contributes not only to the management of the system testing process but also to the estimation of the product’s required maintenance. Defective software modules cause software failures, increase development and maintenance costs, and decrease customer satisfaction. It strives to improve software quality and testing efficiency by constructing predictive models from code attributes to enable a timely identification of fault-prone modules. The main objective of paper is to help developers identify defects based on existing software metrics using data mining techniques and thereby improve the software quality. In this paper, we will discuss data mining techniques that are association mining, classification and clustering for software defect prediction. This helps the developers to detect software defects and correct them.
Neuro-fuzzy control of Quanser flexible link

In this study, neuro-fuzzy control of Quanser flexible link system is presented. Since flexible link has an under actuated nature, the PD-like and importance-based neuro-fuzzy (NF) controllers have to control the hub position so that it can attenuate the tip deflections. After simulation, both controllers are implemented on the Quanser flexible link system. As all different mathematical models of the flexible link deal with uncertainties, a comparison is made on the robustness of these controllers in addition to their performance.
Siberian tree-ring and stable isotope proxies as indicators of temperature and moisture changes after major stratospheric volcanic eruptions

Abstract. Stratospheric volcanic eruptions have far-reaching impacts on global climate and society. Tree rings can provide valuable climatic information on these impacts across different spatial and temporal scales. To detect temperature and hydroclimatic changes after strong stratospheric Common Era (CE) volcanic eruptions for the last 1500 years (535 CE unknown, 540 CE unknown, 1257 CE Samalas, 1640 CE Parker, 1815 CE Tambora, and 1991 CE Pinatubo), we measured and analyzed tree-ring width (TRW), maximum latewood density (MXD), cell wall thickness (CWT), and δ13C and δ18O in tree-ring cellulose chronologies of climate-sensitive larch trees from three different Siberian regions (northeastern Yakutia – YAK, eastern Taimyr – TAY, and Russian Altai – ALT). All tree-ring proxies proved to encode a significant and specific climatic signal of the growing season. Our findings suggest that TRW, MXD, and CWT show strong negative summer air temperature anomalies in 536, 541–542, and 1258–1259 at all studied regions. Based on δ13C, 536 was extremely humid at YAK, as was 537–538 in TAY. No extreme hydroclimatic anomalies occurred in Siberia after the volcanic eruptions in 1640, 1815, and 1991, except for 1817 at ALT. The signal stored in δ18O indicated significantly lower summer sunshine duration in 542 and 1258–1259 at YAK and 536 at ALT. Our results show that trees growing at YAK and ALT mainly responded the first year after the eruptions, whereas at TAY, the growth response occurred after 2 years. The fact that differences exist in climate responses to volcanic eruptions – both in space and time – underlines the added value of a multiple tree-ring proxy assessment. As such, the various indicators used clearly help to provide a more realistic picture of the impact of volcanic eruption on past climate dynamics, which is fundamental for an improved understanding of climate dynamics, but also for the validation of global climate models.
Paratuberculosis in Farmed Deer: Case Reports and DNA Characterization of Isolates of Mycobacterium Paratuberculosis

Mycobacterium paratuberculosis was isolated from farmed deer in New Zealand on 21 occasions over a 7-year period. The number of cases increased during the last 3 years of the study. Clinical paratuberculosis was observed in 5 deer, 3 other cases came from grossly normal animals that reacted to a tuberculin skin test, and the remaining 13 animals had tuberculous lesions that were identified at meat inspection. Pathologic features of the lesions in these 13 cases included necrosis and mineralization in lymph nodes draining the gastrointestinal tract. The histologic changes in these lesions were very similar to those caused by Mycobacterium bovis and members of the M. avium complex. Characterization of 20 of the isolates of M. paratuberculosis by restriction endonuclease analysis and DNA hybridization revealed that 3 of these isolates were identical to New Zealand sheep isolates and 17 were the same as cattle isolates. The source of the cervine infections was not determined.
The multidimensional database system RasDaMan

RasDaMan is a universal — i.e., domain-independent — array DBMS for multidimensional arrays of arbitrary size and structure. A declarative, SQL-based array query language offers flexible retrieval and manipulation. Efficient server-based query evaluation is enabled by an intelligent optimizer and a streamlined storage architecture based on flexible array tiling and compression. RasDaMan is being used in several international projects for the management of geo and healthcare data of various dimensionality.
Location-Based Analysis of Developers and Technologies on GitHub

GitHub is a popular platform for collaboration on open source projects. It also provides a rich API to query various aspects of the public activity. This combination of a popular social coding website with a rich API presents an opportunity for researchers to gather empirical data about software development practices. There are an overwhelmingly large number of competing platforms to choose from in software development. Knowing which are gaining widespread adoption is valuable both for individual developers trying to increase their employability, as well as software engineers deciding which technology to use in their next big project. In terms of a developer's employability and an employer's ability to find available developers in their economic region, it is important to identify the most common technologies by geographic location. In this paper, analyses are done on GitHub data taking into account the developers' location and their technology usage. A web-based tool has been developed to interact with and visualize this data. In its current state of development, the tool summarizes the amount of code developers have in their public repositories broken down by programming language, and summarizes data about programmers using specific programming languages. This allows website visitors to get an immediate picture of the programming language usage in their region of interest. Future research could expand this work to technologies beyond programming languages such as frameworks and libraries.
Multi-Resolution Data Fusion for Super-Resolution Electron Microscopy

Perhaps surprisingly, all electron microscopy (EM) data collected to date is less than a cubic millimeter – presenting a huge demand in the materials and biological sciences to image at greater speed and lower dosage, while maintaining resolution. Traditional EM imaging based on homogeneous raster scanning severely limits the volume of high-resolution data that can be collected, and presents a fundamental limitation to understanding physical processes such as material deformation and crack propagation. ,,,,,, We introduce a multi-resolution data fusion (MDF) method for super-resolution computational EM. Our method combines innovative data acquisition with novel algorithmic techniques to dramatically improve the resolution/ volume/speed trade-off. The key to our approach is to collect the entire sample at low resolution, while simultaneously collecting a small fraction of data at high resolution. The high-resolution measurements are then used to create a material-specific model that is used within the “plug-andplay” framework to dramatically improve resolution of the low-resolution data. We present results using FEI electron microscope data that demonstrate super-resolution factors of 4x-16x, while substantially maintaining high image quality and reducing dosage.
Aging, HCI, & Personal Perceptions of Time

While aging has become an influential area of research in HCI, the science of human longevity presents itself as an untapped framework through which HCI researchers may further investigate. The present work presents preliminary research on older adults' personal perception of time in context with their personal perception of technology. Researchers worked to thus investigate the underlying socioemotional effects of technology during the aging process. Initial results suggest research opportunities in regards to HCI's awareness of and potential influence upon personal perception of 'time'. Beginning with a sample of older adults previously interested in technical innovation, we point to (1) the processes behind intention to learn about novel technologies and (2) personal perception of "time" or longevity coinciding with said investment. We pose questions and aim to inspire discussion and future investigations into time as a foundation for self-reflection and perception.
Inotropic Action of the Puberty Hormone Kisspeptin in Rat, Mouse and Human: Cardiovascular Distribution and Characteristics of the Kisspeptin Receptor

Kisspeptins, the ligands of the kisspeptin receptor known for its roles in reproduction and cancer, are also vasoconstrictor peptides in atherosclerosis-prone human aorta and coronary artery. The aim of this study was to further investigate the cardiovascular localisation and function of the kisspeptins and their receptor in human compared to rat and mouse heart. Immunohistochemistry and radioligand binding techniques were employed to investigate kisspeptin receptor localisation, density and pharmacological characteristics in cardiac tissues from all three species. Radioimmunoassay was used to detect kisspeptin peptide levels in human normal heart and to identify any pathological changes in myocardium from patients transplanted for cardiomyopathy or ischaemic heart disease. The cardiac function of kisspeptin receptor was studied in isolated human, rat and mouse paced atria, with a role for the receptor confirmed using mice with targeted disruption of Kiss1r. The data demonstrated that kisspeptin receptor-like immunoreactivity localised to endothelial and smooth muscle cells of intramyocardial blood vessels and to myocytes in human and rodent tissue. [125I]KP-14 bound saturably, with subnanomolar affinity to human and rodent myocardium (KD = 0.12 nM, human; KD = 0.44 nM, rat). Positive inotropic effects of kisspeptin were observed in rat, human and mouse. No response was observed in mice with targeted disruption of Kiss1r. In human heart a decrease in cardiac kisspeptin level was detected in ischaemic heart disease. Kisspeptin and its receptor are expressed in the human, rat and mouse heart and kisspeptins possess potent positive inotropic activity. The cardiovascular actions of the kisspeptins may contribute to the role of these peptides in pregnancy but the consequences of receptor activation must be considered if kisspeptin receptor agonists are developed for use in the treatment of reproductive disorders or cancer.
Toward the neurocomputer: image Processing and pattern recognition with neuronal cultures

Information processing in the nervous system is based on parallel computation, adaptation and learning. These features cannot be easily implemented on conventional silicon devices. In order to obtain a better insight of how neurons process information, we have explored the possibility of using biological neurons as parallel and adaptable computing elements for image processing and pattern recognition. Commercially available multielectrode arrays (MEAs) were used to record and stimulate the electrical activity from neuronal cultures. By mapping digital images, i.e., arrays of pixels, into the stimulation of neuronal cultures, a low and bandpass filtering of images could be quickly and easily obtained. Responses to specific spatial patterns of stimulation were potentiated by an appropriate training (tetanization). Learning allowed pattern recognition and extraction of spatial features in processed images. Therefore, neurocomputers, (i.e., hybrid devices containing man-made elements and natural neurons) seem feasible and may become a new generation of computing devices, to be developed by a synergy of Neuroscience and Material Science.
Porcine peripheral blood dendritic cells and natural interferon‐producing cells

Peripheral blood contains two major particular infrequent dendritic cells (DC) subsets linking the innate and specific immune system, the myeloid DC and plasmacytoid DC equivalent to the natural interferon‐producing cells (NIPC). The functional characterization of these cells demands large volumes of blood, making a large animal model more appropriate and beneficial for certain studies. Here, two subsets of porcine blood mononuclear cells expressing swine workshop cluster 3 (SWC3, a SIRP family member), are described and compared to monocytes. The blood DC specialized in T‐cell stimulation were major histocompatibility complex (MHC) class II+, CD80/86+, CD1+/–, CD4−, and in contrast to monocytes CD14−. A CD16− and a CD16+ subset could be discriminated. Granulocyte–macrophage colony‐stimulating factor and interleukin‐3 were survival factors for this DC subset, and culture induced an up‐regulation of MHC class II and CD80/86. The second subset described, are porcine NIPC, typically CD4++, MHC class IIlow, CD80/86low, CD1−, CD8−/low, CD16−/low and CD45RA−/low. Porcine NIPC had high interleukin‐3 binding capacity, and survived in response to this cytokine. Their unique function was strong interferon type I secretion after virus stimulation. Both subsets were endocytically active when freshly isolated, and down‐regulated this activity after in vitro maturation. Taken together, the present report has delineated porcine blood DC and NIPC, permitting a more detailed understanding of innate immune defences, particularly in response to infections.
Effect of N-acetylcysteine on heat shock protein induction by acetaminophen in mouse liver.

It was previously shown that a necrogenic dose of acetaminophen (APAP) induced the 25- and 70-kDa heat shock proteins (hsp25 and hsp70i) in mouse liver, whereas nonnecrogenic doses failed to alter the level of either hsp. A strong correlation between the intralobular sites of APAP arylation of protein and hsp induction suggested that APAP-induced protein denaturation may play a role in triggering hsp induction. This study was conducted to determine whether APAP arylation of protein without concurrent toxicity could cause hsp induction. APAP (250 mg/kg i.p.) hepatotoxicity was eliminated using N-acetylcysteine (NAC, 300 mg/kg i.p.) or the cytochrome P-450 inhibitor diallyl sulfide (200 mg/kg p.o.). NAC did not inhibit APAP arylation of protein when administered 1 or 3 hr after the APAP dose but decreased binding by approximately 50% when administered at the same time as the APAP dose. Even though APAP hepatotoxicity was blocked by NAC administered 0 or 1 hr after the APAP dose, NAC did not inhibit the induction of hsp25 or hsp70i, indicating that APAP arylation of protein may play a key role in triggering hsp induction. Diallyl sulfide blocked APAP arylation of protein, hepatotoxicity, and induction of both hsps. These data are consistent with the hypothesis that toxicant adduction of protein triggers hsp induction.
The Study of the Frequency Effect of Dynamic Compressive Loading on Primary Articular Chondrocyte Functions Using a Microcell Culture System

Compressive stimulation can modulate articular chondrocyte functions. Nevertheless, the relevant studies are not comprehensive. This is primarily due to the lack of cell culture apparatuses capable of conducting the experiments in a high throughput, precise, and cost-effective manner. To address the issue, we demonstrated the use of a perfusion microcell culture system to investigate the stimulating frequency (0.5, 1.0, and 2.0 Hz) effect of compressive loading (20% and 40% strain) on the functions of articular chondrocytes. The system mainly integrates the functions of continuous culture medium perfusion and the generation of pneumatically-driven compressive stimulation in a high-throughput micro cell culture system. Results showed that the compressive stimulations explored did not have a significant impact on chondrocyte viability and proliferation. However, the metabolic activity of chondrocytes was significantly affected by the stimulating frequency at the higher compressive strain of 40% (2 Hz, 40% strain). Under the two compressive strains studied, the glycosaminoglycans (GAGs) synthesis was upregulated when the stimulating frequency was set at 1 Hz and 2 Hz. However, the stimulating frequencies explored had no influence on the collagen production. The results of this study provide useful fundamental insights that will be helpful for cartilage tissue engineering and cartilage rehabilitation.
Impact of Mobile Intervention in Indian Agriculture

The major challenge in India’s agricultural sector is to create and improve the existing agriculture infrastructure which can improve the livelihood of rural masses. Penetration of mobile phones in India in the last 10 years has grown tremendously. Many service providers have emerged as players in this market providing a portfolio of services to consumers. Mobile-enabled information services have been introduced in agri-business to empower farmers with updated information related to farming and marketing of agricultural produce. The objective of this paper is to explore the potential of mobile phones and mobile-enabled agricultural services in improving the agricultural performance of farmers. Farmers are benefiting from better access to information through mobile phones on seed variety selection, weather update, crop diseases and getting a better market price for their produce. Farmers equipped with information have a stronger bargaining position within existing trade relationships. The study adopted the constructs of Technology Acceptance Model (TAM) such as perceived usefulness, ease of use, self-efficacy, attitude of the respondent (farmer) and behavioural intention to measure mobile adoption behaviour of farmers in agriculture. Factor analysis and regression analysis are used to identify factors significantly affecting behavioural intention of adopting mobile technology and reach an effective conclusion.
Variations in anuran embryogenesis: yolk‐rich embryos of Hyperolius puncticulatus (Hyperoliidae)

Anuran development is usually described using model species, most notably Xenopus laevis and Rana pipiens. We describe the development of the East African Reed Frog, Hyperolius puncticulatus, a species displaying development that is highly divergent from the "classic" anuran developmental pattern. Although having small eggs, the eggs of H. puncticulatus are characterized by a large amount of yolk, and embryonic development is reminiscent of species with large eggs. The eggs are teleolecithal and the cleavage is holoblastic, with a "pseudo-meroblastic" pattern. Gastrulation proceeds primarily at the dorsal lip and is characterized by reduced embryonic cavities. Gastrulation ends with a thickened "embryonic mantle" that sits upon a large yolk mass and forms most of the tissues of the embryo. The embryonic axis curves across the yolk mass, instead of the typical lengthening of anuran embryos. The tadpole hatches with a large ventral yolk mass which is gradually absorbed. We hypothesize about the developmental mechanisms that underlie this unusual development, based on comparisons with other anuran and fish species. We suggest that this type of development is not unique to this species, but can be found in many species of different anuran taxonomic groups. Comparing the development of H. puncticulatus and similar species to what is known about the development of model species, such as X. laevis, shows us the variation in early anuran embryogenesis. Knowing the existing diversity is a prerequisite to understanding the evolution of early anuran development and the changes in patterning mechanisms in different lineages.