Miracle-dz/UniFAR-FTUs huggingface dataset:
Daleel: Simplifying cloud instance selection using machine learning

Decision making in cloud environments is quite challenging due to the diversity in service offerings and pricing models, especially considering that the cloud market is an incredibly fast moving one. In addition, there are no hard and fast rules; each customer has a specific set of constraints (e.g. budget) and application requirements (e.g. minimum computational resources). Machine learning can help address some of the complicated decisions by carrying out customer-specific analytics to determine the most suitable instance type(s) and the most opportune time for starting or migrating instances. We employ machine learning techniques to develop an adaptive deployment policy, providing an optimal match between the customer demands and the available cloud service offerings. We provide an experimental study based on extensive set of job executions over a major public cloud infrastructure.
Draft Genome Sequence of Se(IV)-Reducing Bacterium Pseudomonas migulae ES3-33

ABSTRACT Pseudomonas migulae ES3-33 is a Gram-negative strain that strongly reduces Se(IV) and was isolated from a selenium mining area in Enshi, southwest China. Here we present the draft genome of this strain containing potential genes involved in selenite reduction and a large number of genes encoding resistances to copper and antibiotics.
Immune response genes control T killer cell response against Moloney tumor antigen cytolysis regulating reactions against the best available H-2 + viral antigen association

Cytolytic T lymphocytes (CTL) specific for the virus-induced and leukemia-associated Friend, Moloney, Rauscher (FMR) antigen are easily detected in the spleens of primary and secondary stimulated H-2b or H- 2d mice. They react, respectively, with H-2Db + FMR and H-2Kd + FMR; Dd and Kb never being involved. On the other hand, recombinant (KbDd) mice are relatively low responders that produce CTL only after secondary stimulation. Competition and blocking experiments with monospecific anti-H-2 antibodies have demonstrated that on the same H-2b tumor cells, C57BL/6 (H-2b) lymphocytes recognize Db + FMR, whereas B10.A(5R) lymphocytes recognize Kb + FMR, the restriction cannot, therefore be explained by a specific association of viral molecules with certain H-2 products. The CTL response of (B10 X 5R)F1 hybrids is (a) easily detected in primary reaction, the high responder anti-FMR phenotype being dominant and (b) directed against Db + FMR, F1 mice being low responder against Kb + FMR like the B10 parent. These results suggest that a D region-associated immune response gene controls the cell- mediated anti-FMR reaction, the best available H-2 + FMR antigenic association being chosen by CTL precursors.
Comparison of adenosine triphosphate‐ and nicotine‐activated inward currents in rat phaeochromocytoma cells.

1. The adenosine triphosphate (ATP)‐activated inward current was compared to the nicotine‐activated inward current in nerve growth factor (NGF)‐treated rat phaeochromocytoma PC12 cells. 2. Both ATP and nicotine activated an inward current at negative holding potentials. The concentration of ATP necessary to activate the inward current was about 10‐fold higher than that of nicotine; the EC50 was 20.5 microM for ATP and 2.4 microM for nicotine. The maximal responses induced by ATP and nicotine were almost identical in the same cells. The current‐voltage relationship for the ATP‐activated current was very similar to that for the nicotine‐activated current, and both currents reversed around 0 mV in a physiological saline. 3. The ATP‐activated current and the nicotine‐activated current were not additive; the current activated by a combined administration of ATP (100 microM) and nicotine (10 microM) was only about 20% larger than the current activated by either ATP or nicotine alone. Nicotine (100 microM) did not increase the current activated by 1 microM‐ATP. 4. ATP could activate an inward current in the cells even after desensitization to nicotine had developed. 5. Hexamethonium (100 microM) selectively blocked the nicotine‐activated current whereas suramin (100 microM), a purinoceptor antagonist, selectively blocked the ATP‐activated current. 6. Ionic selectivity was studied by changing compositions of extracellular solutions. When external Na+ was replaced with Cs+, both ATP and nicotine activated inward currents. However, with an extracellular solution containing Tris or glucosamine as a major cation, only ATP, not nicotine, activated an inward current. 7. ATP‐ and nicotine‐activated currents were also recorded from cells bathed in a solution containing 1.8 mM‐Ca2+ as the only external cation, suggesting that both pathways are Ca2+ permeable. 8. The results suggest that the ATP‐sensitive ionic pathway is not independent of the nicotine‐sensitive pathway in these cells. Our working hypothesis is that ATP and nicotine activate the same channels but the binding sites and the open‐states of the channels are different between these two agonists.
Recurring Retrieval Needs in Diverse and Dynamic Dataspaces: Issues and Reference Framework

Processing information requests over heterogeneous dataspaces is very challenging because aimed at guaranteeing user satisfaction with respect to conflicting requirements on result quality and response time. In [3], it has been argued that, in dynamic contexts preventing substantial user involvement in interpreting requests, information on similar requests recurring over time can be exploited during query processing. In this paper, referring to a graph-based modeling of dataspaces and requests, we propose a preliminary approach in this direction centered on the enabling concept of Profiled Graph Query Pattern (PGQP) as an aggregation of information on past evaluations of a set of previously executed queries. The information maintained in PGQP is not query results, as in materialized queries, but can include different kinds of data and metadata.
C?aSH: Structural Descriptions of Synchronous Hardware Using Haskell

CλaSH is a functional hardware description language that borrows both its syntax and semantics from the functional programming language Haskell. Polymorphism and higher-order functions provide a level of abstraction and generality that allow a circuit designer to describe circuits in a more natural way than possible with the language elements found in the traditional hardware description languages. Circuit descriptions can be translated to synthesizable VHDL using the prototype CλaSH compiler. As the circuit descriptions, simulation code, and test input are also valid Haskell, complete simulations can be done by a Haskell compiler or interpreter, allowing high-speed simulation and analysis.
Impacts of Near‐Term Climate Change on Irrigation Demands and Crop Yields in the Columbia River Basin

Adaptation to a changing climate is critical to address future global food and water security challenges. While these challenges are global, successful adaptation strategies are often generated at regional scales; therefore, regional‐scale studies are critical to inform adaptation decision making. While climate change affects both water supply and demand, water demand is relatively understudied, especially at regional scales. The goal of this work is to address this gap, and characterize the direct impacts of near‐term (for the 2030s) climate change and elevated CO2 levels on regional‐scale crop yields and irrigation demands for the Columbia River basin (CRB). This question is addressed through a coupled crop‐hydrology model that accounts for site‐specific and crop‐specific characteristics that control regional‐scale response to climate change. The overall near‐term outlook for agricultural production in the CRB is largely positive, with yield increases for most crops and small overall increases in irrigation demand. However, there are crop‐specific and location‐specific negative impacts as well, and the aggregate regional response of irrigation demands to climate change is highly sensitive to the spatial crop mix. Low‐value pasture/hay varieties of crops—typically not considered in climate change assessments—play a significant role in determining the regional response of irrigation demands to climate change, and thus cannot be overlooked. While, the overall near‐term outlook for agriculture in the region is largely positive, there may be potential for a negative outlook further into the future, and it is important to consider this in long‐term planning.
A Case for Flow-Adaptive Wireless Links

We study the performance problems that exist when loss responsive flows traverse wireless links, where losses are often unrelated to congestion. We present a novel concept - flow-adaptive wireless links - which provides service differentiation by tailoring link layer error control to the QoS requirements of each flow sharing the link. Flow-adaptive links emphasize local error control as a necessary complement to end-to-end error control, and are independent of transport (or higher) layer protocol semantics. The key idea is that applications use the IP layer as a level of indirection through which QoS requirements are communicated to each link along the path, on a per flow basis. We then demonstrate how this improves performance for the particular class of reliable loss responsive flows. We prove in general that a well engineered, fully reliable wireless link does not interfere with TCP''s end-to-end error recovery. Moreover, we propose a new error recovery algorithm (TCP-Eifel) that can optionally be implemented in TCP to further improve performance. By eliminating the retransmission ambiguity problem the algorithm detects spurious timeouts, and uses these as an implicit cross-layer signal to prevent unnecessary retransmissions in TCP.
Tools for visually exploring biological networks

UNLABELLED Many tools exist for visually exploring biological networks including well-known examples such as Cytoscape, VisANT, Pathway Studio and Patika. These systems play a key role in the development of integrative biology, systems biology and integrative bioinformatics. The trend in the development of these tools is to go beyond 'static' representations of cellular state, towards a more dynamic model of cellular processes through the incorporation of gene expression data, subcellular localization information and time-dependent behavior. We provide a comprehensive review of the relative advantages and disadvantages of existing systems with two goals in mind: to aid researchers in efficiently identifying the appropriate existing tools for data visualization; to describe the necessary and realistic goals for the next generation of visualization tools. In view of the first goal, we provide in the Supplementary Material a systematic comparison of more than 35 existing tools in terms of over 25 different features. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Values and groundwater management in the Ogallala Aquifer region

The Ogallala Aquifer supports agricultural production and rural communities across eight US states, but the aquifer is being depleted in many areas. Depletion has continued despite numerous institutional and policy interventions, indicating that research and policy have not resulted in physical stabilization of the valuable common pool resource. We argue that explicit inquiry into the values motivating groundwater use and management is critical to conservation efforts. In this paper, we review and integrate prior social science research in the Ogallala region, drawing attention to areas where prior research considers values, implicitly or explicitly, and pointing to new or re-emerging areas for research into the relationship between human values and groundwater use, conservation, and management.
Towards guidelines for designing augmented toy environments

Combining interactive technology with traditional toys promises to significantly enhance the educational value of children's play. Designing such augmented toy environments, however, requires designers to take both the traditional, technology-less nature of the toy, and the novel interactive aspects of the newly accessible virtual environment into account. This article attempts to present a unified set of guidelines for the design and implementation of augmented toy environments, drawing upon existing literature in traditional and educational toy and game design, as well as our own experiences in building mixed reality game environments. We also offer practical advice on the use of these guidelines by reporting on our own augmented toy environment for young children, called the Augmented Knight's Castle, which encourages learning about the Middle Ages in a playful way.
Iris Recognition Based on Matching Pursuits

We propose a novel dynamic programming matching pursuit (DPMP) algorithm for iris recognition. The method modifies the matching pursuit (MP) algorithm to select the most representative atoms for the iris recognition. In the experiments, we demonstrate that our system has (1) better performance for both personal identification and verification, and (2) a better ROC curve, (3) less computation than the conventional MP-based iris recognition.
A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells

PROM1 is the gene encoding prominin-1 or CD133, an important cell surface marker for the isolation of both normal and cancer stem cells. PROM1 transcripts initiate at a range of transcription start sites (TSS) associated with distinct tissue and cancer expression profiles. Using high resolution Cap Analysis of Gene Expression (CAGE) sequencing we characterize TSS utilization across a broad range of normal and developmental tissues. We identify a novel proximal promoter (P6) within CD133+ melanoma cell lines and stem cells. Additional exon array sampling finds P6 to be active in populations enriched for mesenchyme, neural stem cells and within CD133+ enriched Ewing sarcomas. The P6 promoter is enriched with respect to previously characterized PROM1 promoters for a HMGI/Y (HMGA1) family transcription factor binding site motif and exhibits different epigenetic modifications relative to the canonical promoter region of PROM1.
A SOM Based Approach to Skin Detection with Application in Real Time Systems

A large body of human image processing techniques use skin detection as a first primitive for subsequent feature extraction. Well established methods of colour modelling, such as histograms and Gaussian mixture models have enabled the construction of suitably accurate skin detectors. However such techniques are not ideal for use in adaptive real time environments. We describe methods of skin detection using a Self-Organising Map or SOM, and show performance comparable (94% accuracy on facial images) to conventional techniques. We also introduce the AXEON Learning Processor as the basis for a hardware skin detector, and outline the potential benefits of using this system in a demanding environment, such as filtering Internet traffic, to which conventional techniques are not best suited.
Real-Time Fluorescence Measurements of ROS and [Ca2+] in Ischemic / Reperfused Rat Hearts: Detectable Increases Occur only after Mitochondrial Pore Opening and Are Attenuated by Ischemic Preconditioning

Mitochondrial permeability transition pore (mPTP) opening is critical for ischemia / reperfusion (I/R) injury and is associated with increased [Ca2+] and reactive oxygen species (ROS). Here we employ surface fluorescence to establish the temporal sequence of these events in beating perfused hearts subject to global I/R. A bespoke fluorimeter was used to synchronously monitor surface fluorescence and reflectance of Langendorff-perfused rat hearts at multiple wavelengths, with simultaneous measurements of hemodynamic function. Potential interference by motion artefacts and internal filtering was assessed and minimised. Re-oxidation of NAD(P)H and flavoproteins on reperfusion (detected using autofluorescence) was rapid (t0.5 < 15 s) and significantly slower following ischemic preconditioning (IP). This argues against superoxide production from reduced Complex 1 being a critical mediator of initial mPTP opening during early reperfusion. Furthermore, MitoPY1 (a mitochondria-targeted H2O2-sensitive fluorescent probe) and aconitase activity measurements failed to detect matrix ROS increases during early reperfusion. However, two different fluorescent cytosolic ROS probes did detect ROS increases after 2–3 min of reperfusion, which was shown to be after initiation of mPTP opening. Cyclosporin A (CsA) and IP attenuated these responses and reduced infarct size. [Ca2+]i (monitored with Indo-1) increased progressively during ischemia, but dropped rapidly within 90 s of reperfusion when total mitochondrial [Ca2+] was shown to be increased. These early changes in [Ca2+] were not attenuated by IP, but substantial [Ca2+] increases were observed after 2–3 min reperfusion and these were prevented by both IP and CsA. Our data suggest that the major increases in ROS and [Ca2+] detected later in reperfusion are secondary to mPTP opening. If earlier IP-sensitive changes occur that might trigger initial mPTP opening they are below our limit of detection. Rather, we suggest that IP may inhibit initial mPTP opening by alternative mechanisms such as prevention of hexokinase 2 dissociation from mitochondria during ischemia.
Restoring illumination and view dependent data from sparse samples

Capturing appearance of material with respect to illumination and viewing directions is crucial to achieve realistic visual experience in virtual environments. The capturing process is time demanding or requires a specific shape of the captured material. Therefore, we propose a method of such a data reconstruction from very sparse measurements, whose placement allows for continuous and fast acquisition, from which can benefit future acquisition setups. The proposed approach was tested on a number of view- and illumination- dependent samples and showed a promising performance in terms of whole data-space reconstruction speed and visual quality.
Expression of Osteoarthritis Marker YKL-39 is Stimulated by Transforming Growth Factor Beta (TGF-beta) and IL-4 in Differentiating Macrophages

YKL-39 is a Glyco_18 domain containing chitinase-like protein which is currently recognized as a biomarker for the activation of chondrocytes and the progress of the osteoarthritis in human. YKL-39 was identified as an abundantly secreted protein in primary culture of human articular chondrocytes. Two biological activities of YKL-39 might contribute to the disease progression. One is the induction of autoimmune response and second is the participation in tissue remodeling. Other mammalian chitinase-like proteins including chitotriosidase, SI-CLP, YKL-40 and YM1 are expressed by macrophages in various pathological conditions. In contrast, YKL-39 was never reported to be produced by macrophages. We used in vitro model of human monocyte-derived macrophage differentiation to analyse regulation of YKL-39 expression. Expression of YKL-39 was examined by real-time RT-PCR. CD14+ MACS sorted human monocytes differentiated for 6 days under different stimulations including IFNγ, IL-4, dexamethasone and TGF-β. We found that both IL-4 and TGF-β have weak stimulatory effect on YKL-39 expression in all donors tested (3.2 ± 1.7 fold, p = 0.006 and 6.3 ± 3.1 fold, p = 0.014 respectively). However the combination of IL-4 and TGF-β had strong stimulatory effect on the expression of YKL-39 in all analysed individual macrophage cultures (34 ± 36 fold, p = 0.05). IFN-γ did not show statistically significant effect of YKL-39 mRNA expression. Presence of dexamethasone almost completely abolished the stimulatory effects of IL-4 and TGF-β. In summary, we show here for the first time, that human cells of monocyte origin are able to produce YKL-39. Maturation of monocyte derived macrophages in the presence of Th2 cytokine IL-4 and TGF-β leads to the strong activation of YKL-39 expression. Thus elevated levels of YKL-39 observed during chronic inflammations can not be attributed solely to the activity of chondrocytes. In perspective, YKL-39 might serve as a useful biomarker to detect macrophage-specific response in pathologies like tumour, atherosclerosis and Alzheimer disease.
Cyclostratigraphy and Magnetostratigraphy of the Middle Miocene Ashigong Formation, Guide Basin, China, and Its Implications for the Paleoclimatic Evolution of NE Tibet

Recent tectonostratigraphy studies have shown that Northeast Tibet underwent significant tectonic uplift and basin partitioning at 13–8 Ma. This time window is also a period of significant changes in Asian monsoonal intensity, mechanisms of which remain poorly understood. Though many studies have tried to decipher paleoclimatic trends from sedimentary archives in Northeast Tibetan basins, it is often hard to distinguish local orographic effects from regional climate changes in such a tectonically active context. Here we investigated the sedimentary record of the Ashigong Formation, Guide Basin, in order to better constrain the Tibetan paleoenvironmental evolution and link it to uplift episodes and monsoonal evolution. By studying the lithology, magnetostratigraphy, redness, magnetic susceptibility, and elemental content of a ~500‐m section, we show that the Ashigong Formation was deposited in a saline paleolake between 14.4 and 10 Ma. Lake expansion displayed cyclic variations following ~100‐kyr cycles and weaker ~41‐kyr cycles, reaching its maximum between ~11.4 and 10.5 Ma. Our results show that the Guide Basin was hydrologically closed from most of the middle Miocene, confirming previous studies that proposed an early Miocene partitioning of this basin. The maximum lake expansion between 11.4 and 10.5 Ma is coeval to a known peak of monsoonal intensity. This, and the evidence for a strong orbital control on lake expansion, supports a strong monsoonal control on the expansion of middle Miocene Tibet paleolakes. The origin of the ~100‐kyr forcing on monsoonal moisture supply—different from Quaternary forcing—questions the climatic mechanism of these middle Miocene monsoons and suggests that westerly derived moisture might have also significantly contributed to the regional hydrological budget.
Climate resilience in rural Zambia: evaluating farmers’ response to El Niño-induced drought

Abstract This paper aims at identifying whether and how sustainable land management practices and livelihood diversification strategies have contributed to moderating the impacts of the El Niño-related drought in Zambia. This is done using a specifically designed survey called the El Niño Impact Assessment Survey, which is combined with the Rural Agricultural Livelihoods Surveys, as well as high resolution rainfall data at the ward level over 34 years. This unique panel data set allows us to control for the time-invariant unobserved heterogeneity to understand the impacts of shocks like El Niño, which are expected to become more frequent and severe as a result of climate change. We find that maize yields were substantially reduced and that household incomes were only partially protected from the shock thanks to diversification strategies. Mechanical erosion control measures and livestock diversification emerge as the only strategies that provided yield and income benefits under weather shock.
Relativistic Second-Harmonic Gyrotron With a Selective Quasi-Regular Cavity

A typical problem of gyrotrons operating at the second harmonic of the electron cyclotron frequency is the suppression of parasitic near-cutoff waves excited at the fundamental harmonic. In this paper, we discuss the possibility for the selective excitation of two different second-harmonic waves in a relativistic millimeter-wavelength gyrotron by means of the use of a method for a significant improvement of the selectivity of this system. This method is based on the use of a quasi-regular cavity with a short irregularity providing different effects on the interaction of the electron beam with the operating second-harmonic wave and the spurious fundamental-harmonic wave.