Miracle-dz/UniFAR-FTUs huggingface dataset:
A pipelined code mapping scheme for static data flow computers

Computers built on data Ilow principles promise efficient parallel computation limited in speed only by data dependencies in the calculation being performed. We demonstrate how the massive parallelism of array operations in numerical scientific computation programs can be effectively exploited by the fine-grain parallelism of static data flow architecture. The power of such fine-grain parallelism derives from machine-level programs that form large pipelines in which thousands of actors in hundreds of stages are executed concurrently. Each actor in the pipe is activated in a totally data-driven manner, and no explicit sequential control is needed. This thesis studies the principles of program mapping techniques that can be made to achieve high performance for numerical programs when executed on a computer based on data flow principles. A simple value-oriented language is specified as the source language to express user programs. The key of the program mapping techniques is to organize the data flow machine program graph such that array operations can be effectively pipelined. Program transformation can be performed on the basis of both the global and local data flow analysis to generate efficient pipelined data flow machine code. A pipelined code
A post-filter for acoustic echo cancellation in frequency domain

Most of the traditional acoustic echo cancellation algorithms are based on an adaptive filter in time domain for estimating the echo path response. Other solutions to this problem using adaptive filter in frequency domain were proposed. Impressive performances were obtained in frequency domain compared with time domain, this is due to the flexibility and low computational complexity of frequency domain techniques. In this paper, an acoustic echo canceller using frequency domain adaptive filter is combined with spectral noise suppressor technique. Results indicated that the performances of the combined scheme yielded superiority in the performances than the traditional schemes.
Feedbacks between vegetation and rainfall in the Amazon basin

The distribution of rainfall and vegetation are closely interconnected in the Amazon basin. Rainforests maintain atmospheric humidity by evapotranspiration, which eventually contributes to regional rainfall but also to rainfall over subtropical South America. A comprehensive understanding of the complex interactions between the terrestrial and atmospheric components of the hydrological cycle that occur as moist air is transported by winds over land is missing. The first aim of this thesis is to fill this gap in knowledge by means of complex network analysis of water fluxes from the sources to the sinks of rainfall on the continent. Using this novel approach, the concept of “cascading moisture recycling” is introduced, defined as moisture recycling on the continent involving “reevaporation cycles” (evaporation of precipitating moisture in the same location) along the way. A methodological framework is developed to quantify the importance of cascading moisture recycling and to identify key regions where re-evaporation cycles are taking place. Applied to several combinations of observation-based gridded climate data for South America, it reveals, for instance, that the southern part of the Amazon basin is not only a direct source of rainfall for the La Plata basin (as previously thought) but also an intermediary region that re-distributes moisture evaporating from the entire Amazon basin towards the subtropics. This new concept lays the foundation for evaluating the vulnerability of the Amazon forest to environmental perturbations, which is the second aim of this thesis. Land-use and rainfall variability are expected to be intensified at the end of the twenty-first century and may push the south-eastern part of the Amazon forest towards a grass-dominated ecosystem. Such a forest loss would reduce local dryseason evapotranspiration and the resulting moisture supply for down-wind rainfall. In turn, this might erode the resilience of the remaining forest and lead to further forest losses. Using a complex network approach, the concepts of forest resilience and cascading moisture recycling are combined in a data-driven modeling framework. Key regions are identified where deforestation would greatly destabilize the remaining forest, as well as tipping points in dry-season intensification for large-scale self-amplified Amazon forest loss. The findings highlight the need to maintain the diversity and connectivity of forest patches in order to sustain the ecological integrity of the largest remaining tropical forest on Earth.
Screening assay for dioxin-like compounds based on competitive binding to the murine hepatic Ah receptor. 2. Application to environmental samples.

A series of environmental samples, comprising fly ash, caustic wash water from regeneration of a petrochemical reforming catalyst, fish homogenates, soil, and pulp mill sludge, were analyzed for dioxin-like compounds by an assay involving competitive binding of a reference radioligand and an extract from the sample to mouse hepatic Ah receptor ; the results were compared with GC/MS. The bioassay generally gave higher TEQ values than GC/MS. Further analysis by GC/MS in most cases identified much of the additional Ah receptor-active material as coplanar PCBs and PAHs.
Identification of Quantitative Trait Loci Controlling Gene Expression during the Innate Immunity Response of Soybean 1 [ W ] [ OA ]

Department of Statistics (J.Q.) and Divisions of Biochemistry and Plant Sciences, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center (O.V.-L., S.T., T.H.N.N., M.L., G.S.), University of Missouri, Columbia, Missouri 65211; Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455 (W.W.X.); Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (B.H.L., R.B.G.); and United States Department of Agriculture-Agricultural Research Service (G.L.H.) and Department of Crop Sciences (C.B.H., G.L.H., B.D.), University of Illinois, Urbana, Illinois 61801
The role of the user's domain knowledge in generation

A question‐answering program that provides access to a large amount of data will be most useful if it can tailor its answers to each individual user. In particular, a user's level of knowledge about the domain of discourse is an important factor in this tailoring if the answer provided is to be both informative and understandable to the user. In this research, we address the issue of how the user's domain knowledge, or the level of expertise, might affect an answer. We present TAILOR, a flexible computer system that takes into account this knowledge to provide an answer that is appropriate for users with varying levels of expertise (including novices and experts), without requiring an a priori set of user types.
Fitness and physiology of Adelges tsugae (Hemiptera: Adelgidae) in relation to the health of the eastern hemlock

The hemlock woolly adelgid, Adelges tsugae Annand is an invasive insect that frequently causes hemlock (Tsuga spp.) mortality in the eastern United States. Studies have shown that once healthy hemlocks become infested by the adelgid, nutrients are depleted from the tree, leading to both tree decline and a reduction of the adelgid population. Since A. tsugae is dependent on hemlock for nutrients, feeding on trees in poor health may affect the ability of the insect to obtain necessary nutrients and may consequently affect their physiological and population health. Trees were categorized as lightly or moderately impacted by A. tsugae based on quantitative and qualitative tree health measurements. Population health of A. tsugae on each tree was determined by measuring insect density and peak mean fecundity; A. tsugae physiological health was determined by measuring insect biomass, total carbon, carbohydrate, total nitrogen, and amino nitrogen levels. Adelges tsugae from moderately impacted trees exhibited significantly greater fecundity than from lightly impacted trees. However, A. tsugae from lightly impacted hemlocks contained significantly greater levels of carbohydrates, total nitrogen, and amino nitrogen. While the results of the physiological analysis generally support our hypothesis that A. tsugae on lightly impacted trees are healthier than those on moderately impacted trees, this was not reflected in the population health measurements. Adelges tsugae egg health in response to tree health should be verified. This study provides the first examination of A. tsugae physiological health in relation to standard A. tsugae population health measures on hemlocks of different health levels.
Cloning and Expression of the Mycobacterium bovis BCG Gene for Extracellular oa Antigen

The gene for the extracellular a antigen of Mycobacterium bovis BCG was cloned by using a single probe restricted to G or C in the third position. This technique should have great potential for the isolation of mycobacterial antigen genes. The gene analysis revealed that the a antigen gene encoded 323 amino acid residues, including 40 amino acids for signal peptide followed by 283 amino acids for mature protein. This is the first report on the structure of the mycobacterial signal peptide. The promoter-like sequence and ribosome-binding site were observed upstream of the open reading frame. In the coding region, the third position of the codon showed high G+C content (86%). The gene was expressed as an unfused protein in Escherichia cohi by using an E. coli expression vector. This protein, which reacted with polyclonal antibody raised against a antigen from Mycobacterium tuberculosis, would be applicable to the immunodiagnosis of tuberculosis.
Dynamics of a vibrating tip near or in intermittent contact with a surface

We discuss the stability of the tip motion in dynamic atomic force microscopy. A nonlinear dynamics analysis shows that the tip’s phase space is divided in two basins of attraction. A phase space diagram dominated by either basin of attraction implies a stable motion while a substantial contribution from both basins is associated with instabilities. Because the dominance of a given basin of attraction depends on the tip-surface interaction potential and separation, stable and unstable motions are intrinsic features of an oscillating tip near or in intermittent contact with a surface.
USP22 Induces Cisplatin Resistance in Lung Adenocarcinoma by Regulating γH2AX-Mediated DNA Damage Repair and Ku70/Bax-Mediated Apoptosis

Resistance to platinum-based chemotherapy is one of the most important reasons for treatment failure in advanced non-small cell lung cancer, but the underlying mechanism is extremely complex and unclear. The present study aimed to investigate the correlation of ubiquitin-specific peptidase 22 (USP22) with acquired resistance to cisplatin in lung adenocarcinoma. In this study, we found that overexpression of USP22 could lead to cisplatin resistance in A549 cells. USP22 and its downstream proteins γH2AX and Sirt1 levels are upregulated in the cisplatin- resistant A549/CDDP cell line. USP22 enhances DNA damage repair and induce cisplatin resistance by promoting the phosphorylation of histone H2AX via deubiquitinating histone H2A. In addition, USP22 decreases the acetylation of Ku70 by stabilizing Sirt1, thus inhibiting Bax-mediated apoptosis and inducing cisplatin resistance. The cisplatin sensitivity in cisplatin-resistant A549/CDDP cells was restored by USP22 inhibition in vivo and vitro. In summary, our findings reveal the dual mechanism of USP22 involvement in cisplatin resistance that USP22 can regulate γH2AX-mediated DNA damage repair and Ku70/Bax-mediated apoptosis. USP22 is a potential target in cisplatin-resistant lung adenocarcinoma and should be considered in future therapeutic practice.
Focal Local Field Potential Signature of the Single-Axon Monosynaptic Thalamocortical Connection

A resurgence has taken place in recent years in the use of the extracellularly recorded local field potential (LFP) to investigate neural network activity. To probe monosynaptic thalamic activation of cortical postsynaptic target cells, so called spike-trigger-averaged LFP (stLFP) signatures have been measured. In these experiments, the cortical LFP is measured by multielectrodes covering several cortical lamina and averaged on spontaneous spikes of thalamocortical (TC) cells. Using a well established forward-modeling scheme, we investigated the biophysical origin of this stLFP signature with simultaneous synaptic activation of cortical layer-4 neurons, mimicking the effect of a single afferent spike from a single TC neuron. Constrained by previously measured intracellular responses of the main postsynaptic target cell types and with biologically plausible assumptions regarding the spatial distribution of thalamic synaptic inputs into layer 4, the model predicted characteristic contributions to monosynaptic stLFP signatures both for the regular-spiking (RS) excitatory neurons and the fast-spiking (FS) inhibitory interneurons. In particular, the FS cells generated stLFP signatures of shorter temporal duration than the RS cells. Added together, a sum of the stLFP signatures of these two principal synaptic targets of TC cells were observed to resemble experimentally measured stLFP signatures. Outside the volume targeted by TC afferents, the resulting postsynaptic LFP signals were found to be sharply attenuated. This implies that such stLFP signatures provide a very local measure of TC synaptic activation, and that newly developed inverse current-source density (CSD)-estimation methods are needed for precise assessment of the underlying spatiotemporal CSD profiles. SIGNIFICANCE STATEMENT Despite its long history and prevalent use, the proper interpretation of the extracellularly recorded local field potential (LFP) is still not fully established. Here we investigate by biophysical modeling the origin of the focal LFP signature of the single-axon monosynaptic thalamocortical connection as measured by spike-trigger-averaging of cortical LFPs on spontaneous spikes of thalamocortical neurons. We find that this LFP signature is well accounted for by a model assuming thalamic projections to two cortical layer-4 cell populations: one excitatory (putatively regular-spiking cells) and one inhibitory (putatively fast-spiking cells). The LFP signature is observed to decay sharply outside the cortical region receiving the thalamocortical projection, implying that it indeed provides a very local measure of thalamocortical synaptic activation.
A 19-mode 8.29mm2 52-mW LDPC Decoder Chipp for IEEE 802.16e System

This paper presents a LDPC decoder chip supporting all 19 modes in IEEE 802.16e system. An efficient design strategy is proposed to reduce 31.25% decoding latency, and enhance hardware utilization ratio from 50% to 75%. Besides, we propose an early termination scheme that can dynamically adjust the number of iterations. The multi-mode chip can be maximally measured at 83.3 MHz with only 52 mW power consumption. The core area is 4.45 mm2 and the die area is 8.29 mm2.
Estimating Number of Clusters Based on a General Similarity Matrix with Application to Microarray Data

Many clustering methods require that the number of clusters believed present in a given data set be specified a priori, and a number of methods for estimating the number of clusters have been developed. However, the selection of the number of clusters is well recognized as a difficult and open problem and there is a need for methods which can shed light on specific aspects of the data. This paper adopts a model for clustering based on a specific structure for a similarity matrix. Publicly available gene expression data sets are analyzed to illustrate the method and the performance of our method is assessed by simulation.
A new evolutionary approach to decision-making in autonomic systems

Increasingly, autonomic systems are present in our lives. For this kind of systems the ability to self-reconfigure and adapt in response to changes in users requirements and environmental conditions is primordial. Several approaches have been proposed in the literature to achieve self-reconfiguration, however, as the complexity of the adaptive system grows, designing and managing the set of reconfiguration rules becomes difficult and error-prone. To tackle this limitation, we propose a new approach that uses a search-based evolutionary algorithm that explores valid configurations to find the most relevant one given a specific running context. Another salient advantage of our approach is the re-exploitation, in the context of adaptability, of the design knowledge and existing model-based technologies through the reuse of the feature model of the system.
Object-oriented construction handbook - developing application-oriented software with the tools and materials approach

Preface Introduction The T&M Object Metamodel Guiding Metaphors and Design Metaphors Patterns, Frameworks, and Components Application-Oriented Software Development Software Development as a Modeling Process T&M Conceptual Patterns T&M Design Patterns T&M Model Architecture Supporting Cooperative Work Interactive Application Systems and Persistence The Development Process T&M Document Types.
Engaging Teachers’ Pedagogical Content Knowledge: Adopting a Nine-Step Problem-Based Learning Model

Engaging primary and elementary students in meaningful, relevant science learning is challenging. PBL is an instructional approach that provides a means to foster meaningful science learning while enhancing teachers’ pedagogical content knowledge (PCK). This paper reports on the experiences of a teacher inquiry group consisting of fi ve teachers (K-5) and a university researcher as they adopted a nine-step problem design model to develop PBL experiences. The objectives of the study were to examine how various facets of teachers’ pedagogical content knowledge are engaged as they design PBL modules; describe how teachers engage with a nine-step problem design model; and document teachers’ perceptions of the strengths and limitations of the nine-step problem design model.
A preference of histone H1 for methylated DNA.

We have identified a clear preference of histone H1 for CpG‐methylated DNA, irrespective of DNA sequence. The conditions under which this preference is observed allowed cooperative binding of H1; the H1‐DNA complexes formed were shown earlier to be ‘tramlines’ of two DNA duplexes bridged by an array of H1 molecules, and multiples of these. The preference for methylated DNA is clear in sedimentation assays, which also show that the preference is greater with increased methylation level, and in gel retardation assays with an oligonucleotide containing a single methyl‐CpG pair; it is shared by the globular domain which also binds cooperatively to DNA. A small intrinsic preference of H1 for methylated DNA is also apparent in Southwestern assays where the immobilized H1 presumably cannot bind cooperatively. Methylated DNA in H1‐DNA complexes was partially protected (relative to unmethylated DNA) against digestion by MspI but not by enzymes whose cutting sites were not methylated, consistent with a direct interaction of H1 with methylated nucleotides; this was also true of GH1‐DNA complexes. H1 variants (spH1 and H5) from transcriptionally repressed nuclei have a stronger preference than H1 for methylated DNA, suggesting that this may be relevant to the stabilization of chromatin higher order structure and transcriptional repression.
Numerical analysis of aerodynamic characteristics of a bumped leading edge turbine blade

This paper investigates the aerodynamic effects of waving bumps inspired by a humpback whale fin on the leading edge of a turbine blade. A comparison was made between performances of two isolated blades: a blade with a sinusoidally shaped bumped leading edge (LE) and one with a straight leading edge; both based on the same NACA0012 cross section profile. The simulations used a Reynolds number of 1.8·10^5 for a range of angles of attack from 0o to 30o. The results for the bumped blade have shown a substantial gain in aerodynamic characteristics for certain angles of attack (AoA). At AoA larger than 10o, the bumped blade has shown an increase in lift (3%-9.5%) and decreased drag, while negligible differences in lift and a smaller drag were exhibited for AoA smaller than 10o. Overall, the bumped blade provided greater advantage in lift to drag ratio (approximately 50%) over the AoA range from 0o to 20o. The sinusoidal leading edge also delayed the stall crisis, increasing the critical angle of attack by approximately 5o over the one for the blade with a straight leading edge.
Vitamin A Affects Flatfish Development in a Thyroid Hormone Signaling and Metamorphic Stage Dependent Manner

Vitamin A (VA) and retinoid derivatives are known morphogens controlling vertebrate development. Despite the research effort conducted during the last decade, the precise mechanism of how VA induces post-natal bone changes, and particularly those operating through crosstalk with the thyroid hormones (THs) remain to be fully understood. Since effects and mechanisms seem to be dose and time-dependent, flatfish are an interesting study model as they undergo a characteristic process of metamorphosis driven by THs that can be followed by external appearance. Here, we studied the effects of VA imbalance that might determine Senegalese sole (Solea senegalensis) skeletogenetic phenotype through development of thyroid follicles, THs homeostasis and signaling when a dietary VA excess was specifically provided during pre-, pro- or post-metamorphic stages using enriched rotifers and Artemia as carriers. The increased VA content in enriched live prey was associated to a higher VA content in fish at all developmental stages. Dietary VA content clearly affected thyroid follicle development, T3 and T4 immunoreactive staining, skeletogenesis and mineralization in a dose and time-dependent fashion. Gene expression analysis showed that VA levels modified the mRNA abundance of VA- and TH-specific nuclear receptors at specific developmental stages. Present results provide new and key knowledge to better understand how VA and TH pathways interact at tissue, cellular and nuclear level at different developmental periods in Senegalese sole, unveiling how dietary modulation might determine juvenile phenotype and physiology.
Progressive nonfluent aphasia: A rare clinical subtype of FTLD‐TDP in Japan

Progressive nonfluent aphasia (PNFA) is a clinical subtype of frontotemporal lobar degeneration (FTLD). FTLD with tau accumulation (FTLD‐tau) and FTLD with TDP‐43 accumulation (FTLD‐TDP) both cause PNFA. We reviewed clinical records of 29 FTLD‐TDP cases in the brain archive of our institute and found only one case of PNFA. The patient was an 81‐year‐old male at death. There was no family history of dementia or aphasia. He presented with slow, labored and nonfluent speech at age 75. Behavioral abnormality and movement disorders were absent. MRI at age 76 demonstrated atrophy of the perisylvian regions, including the inferior frontal gyrus, insular gyrus and superior temporal gyrus. The atrophy was more severe in the left hemisphere than the right. On post mortem examinations, neuronal loss was evident in these regions as well as in the substantia nigra. There were abundant TDP‐43‐immunoreactive neuronal cytoplasmic inclusions and round or irregular‐shaped structures in the affected cerebral cortices. A few dystrophic neurites and neuronal intranuclear inclusions were also seen. FTLD‐TDP showing PNFA seems to be rare but does exist in Japan, similar to that in other countries.