Miracle-dz/UniFAR-FTUs huggingface dataset:
Microprogramming instruction systolic arrays

The instruction systolic array (ISA) is a programmable parallel architecture suitable for VLSI implementation. This paper presents a generalization of the ISA, called the microprogrammed ISA, which uses simple microprogramming techniques. Microprogrammed ISAs use dynamic microcodes whose length and contents are tailor made to the current program to be executed, and this can be efficiently implemented in VLSI. Here, microprogramming has the novel advantage of extending the range of algorithms that can be implemented on a given ISA. In particular, microprogramming can extend an ISA's effective communication abilities. Also, the reduction of the program input bandwidth (and pinout) afforded by microprogramming is even more important on large-scale MIMD architectures, such as the ISA. This paper also presents a weakest precondition semantics for the (microprogrammed) ISA model, which provides a means for verifying microprogrammed ISA programs. The semantics is modeled at the micro level, and has potential in the optimization of the microcodes of ISA programs.
Pathogenic Mutations in the Valosin-containing Protein/p97(VCP) N-domain Inhibit the SUMOylation of VCP and Lead to Impaired Stress Response*

Valosin-containing protein/p97(VCP) is a hexameric ATPase vital to protein degradation during endoplasmic reticulum stress. It regulates diverse cellular functions including autophagy, chromatin remodeling, and DNA repair. In addition, mutations in VCP cause inclusion body myopathy, Paget disease of the bone, and frontotemporal dementia (IBMPFD), as well as amyotrophic lateral sclerosis. Nevertheless, how the VCP activities were regulated and how the pathogenic mutations affect the function of VCP during stress are not unclear. Here we show that the small ubiquitin-like modifier (SUMO)-ylation of VCP is a normal stress response inhibited by the disease-causing mutations in the N-domain. Under oxidative and endoplasmic reticulum stress conditions, the SUMOylation of VCP facilitates the distribution of VCP to stress granules and nucleus, and promotes the VCP hexamer assembly. In contrast, pathogenic mutations in the VCP N-domain lead to reduced SUMOylation and weakened VCP hexamer formation upon stress. Defective SUMOylation of VCP also causes altered co-factor binding and attenuated endoplasmic reticulum-associated protein degradation. Furthermore, SUMO-defective VCP fails to protect against stress-induced toxicity in Drosophila. Therefore, our results have revealed SUMOylation as a molecular signaling switch to regulate the distribution and functions of VCP during stress response, and suggest that deficiency in VCP SUMOylation caused by pathogenic mutations will render cells vulnerable to stress insults.
A real time implementation and an evaluation of an optimal filtering technique for noise reduction in dual microphone hearing aids

A real time implementation and an evaluation of a singular value decomposition (SVD) based optimal filtering technique (Doclo, S. and Moonen, M., IEEE Trans. Sig. Process., vol.50, no.9, p.2230-44, 2002) for noise reduction in a dual microphone BTE (behind-the-ear) hearing aid is presented. A method to improve the performance of a voice activity detector (VAD) is described and evaluated physically. This method is used in the real time implementation of the optimal filtering technique. A perceptual evaluation by normal hearing subjects is carried out for single and multiple jammer sound sources with speech weighted noise. The SVD-based technique can perform as well as an adaptive beamformer strategy (Maj, J.B. et al., Ear and Hearing, 2003) in a single noise scenario (i.e. the ideal scenario for the latter technique), and, can outperform the beamformer technique in a multiple noise sources scenario.
Plant–insect interactions from Middle Triassic (late Ladinian) of Monte Agnello (Dolomites, N-Italy)—initial pattern and response to abiotic environmental perturbations

The Paleozoic–Mesozoic transition is characterized by the most massive extinction of the Phanerozoic. Nevertheless, an impressive adaptive radiation of herbivorous insects occurred on gymnosperm-dominated floras not earlier than during the Middle to Late Triassic, penecontemporaneous with similar events worldwide, all which exhibit parallel expansions of generalized and mostly specialized insect herbivory on plants, expressed as insect damage on a various plant organs and tissues. The flora from Monte Agnello is distinctive, due to its preservation in subaerially deposited pyroclastic layers with exceptionally preserved details. Thus, the para-autochthonous assemblage provides insights into environmental disturbances, caused by volcanic activity, and how they profoundly affected the structure and composition of herbivory patterns. These diverse Middle Triassic biota supply extensive evidence for insect herbivore colonization, resulting in specific and complex herbivory patterns involving the frequency and diversity of 20 distinctive damage types (DTs). These DT patterns show that external foliage feeders, piercer-and-suckers, leaf miners, gallers, and oviposition culprits were intricately using almost all tissue types from the dominant host plants of voltzialean conifers (e.g., Voltzia), horsetails, ferns (e.g., Neuropteridium, Phlebopteris, Cladophlebis and Thaumatopteris), seed ferns (e.g., Scytophyllum), and cycadophytes (e.g., Bjuvia and Nilssonia).
Phosphorylation of GRK1 and GRK7 by cAMP-dependent Protein Kinase Attenuates Their Enzymatic Activities*

Phosphorylation of G protein-coupled receptors is a critical step in the rapid termination of G protein signaling. In rod cells of the vertebrate retina, phosphorylation of rhodopsin is mediated by GRK1. In cone cells, either GRK1, GRK7, or both, depending on the species, are speculated to initiate signal termination by phosphorylating the cone opsins. To compare the biochemical properties of GRK1 and GRK7, we measured the Km and Vmax of these kinases for ATP and rhodopsin, a model substrate. The results demonstrated that these kinases share similar kinetic properties. We also determined that cAMP-dependent protein kinase (PKA) phosphorylates GRK1 at Ser21 and GRK7 at Ser23 and Ser36 in vitro. These sites are also phosphorylated when FLAG-tagged GRK1 and GRK7 are expressed in HEK-293 cells treated with forskolin to stimulate the endogenous production of cAMP and activation of PKA. Rod outer segments isolated from bovine retina phosphorylated the FLAG-tagged GRKs in the presence of dibutyryl-cAMP, suggesting that GRK1 and GRK7 are physiologically relevant substrates. Although both GRKs also contain putative phosphorylation sites for PKC and Ca2+/calmodulin-dependent protein kinase II, neither kinase phosphorylated GRK1 or GRK7. Phosphorylation of GRK1 and GRK7 by PKA reduces the ability of GRK1 and GRK7 to phosphorylate rhodopsin in vitro. Since exposure to light causes a decrease in cAMP levels in rod cells, we propose that phosphorylation of GRK1 and GRK7 by PKA occurs in the dark, when cAMP levels in photoreceptor cells are elevated, and represents a novel mechanism for regulating the activities of these kinases.
Ieee Transactions on Pattern Analysis and Machine Intelligence 1 3d Convolutional Neural Networks for Human Action Recognition

—We consider the automated recognition of human actions in surveillance videos. Most current methods build classifiers based on complex handcrafted features computed from the raw inputs. Convolutional neural networks (CNNs) are a type of deep models that can act directly on the raw inputs. However, such models are currently limited to handle 2D inputs. In this paper, we develop a novel 3D CNN model for action recognition. This model extracts features from both the spatial and the temporal dimensions by performing 3D convolutions, thereby capturing the motion information encoded in multiple adjacent frames. The developed model generates multiple channels of information from the input frames, and the final feature representation combines information from all channels. To further boost the performance of 3D CNN models, we propose to regularize the models with high-level features and combine the outputs of a variety of different models. We apply the developed models to recognize human actions in the real-world environment of airport surveillance videos, and it achieves superior performance in comparison to baseline methods.
Effect of Two Thermal Regimes on the Muscle Growth Dynamics of Sea Bass Larvae, Dicentrarchus labrax L.

Muscle growth was studied in larvae of sea bass, Dicentrarchus labrax L. , reared at two temperatures: real ambient temperature (≅15°C during vitelline phase and increased gradually) and 19°C from fertilization until the end of larval development. Muscle cellularity, body length and body weight were measured.
Simultaneous and proportional control of 2D wrist movements with myoelectric signals

Previous approaches for extracting real-time proportional control information simultaneously for multiple degree of Freedom(DoF) from the electromyogram (EMG) often used non-linear methods such as the multilayer perceptron (MLP). In this pilot study we show that robust control is also possible with conventional linear regression if EMG power measures are available for a large number of electrodes. In particular, we show that it is possible to linearize the problem with simple nonlinear transformations of band-pass power. Because of its simplicity the method scales well to high dimensions, is easily regularized when insufficient training data is available, and is particularly well suited for real-time control as well as on-line optimization.
Grammar Development in GF

GF is a grammar formalism that has a powerful type system and module system, permitting a high level of abstraction and division of labour in grammar writing. GF is suited both for expert linguists, who appreciate its capacity of generalizations and conciseness, and for beginners, who benefit from its static type checker and, in particular, the GF Resource Grammar Library, which currently covers 12 languages. GF has a notion of multilingual grammars, enabling code sharing, linguistic generalizations, rapid development of translation systems, and painless porting of applications to new languages.
Incorporating biology into discrete event simulation models of organ allocation

We describe a discrete event simulation model of the national liver allocation system. This model differs from previous modeling efforts in that it considers the natural history of the disease independently of any particular patient priority scheme, thus allowing an unbiased appraisal of various allocation schemes. We provide the basic structure of the model, which consists of patient and organ generators, a survival module, and a disease progression module. The model provides various outputs such as patient survival, financial cost, and the number of wasted organs. We describe our model of patient survival with and without a transplant. We discuss some difficulties estimating model parameters due to a lack of appropriate medical data, and how these difficulties were overcome. We close with conclusions and directions for further research.
Determining Lightness from an Image

A 111ct11od l i ~ r t h e tic-termination ol' liglntness t'rom image intensity is prcscwtc~l . 1;or certain classes ot' images, l i g l ~ t r ~ e s s corresponds to rcflrctancc, whilc~ irni~ge intc*nsity is the product ol' rcflcctance :und illr~mination intensity. T l ~ e mct l~ot l is twot l i~nc~ls io~ni~ l :und clcpends o n t l ~ c liffercwt spntid tlistril)r~tion of tllesctwo cornp)nrn ts ol' innage illtensity. SIICII i~ ligl1t1less-jl1dgi11g process is r e q ~ ~ i r e d for L m d ' s r ~ t i n e x t l ~ c w y 01' color vision. A numl)er of p11ysic;d models a r c tlcwelopetl and connputer silnr~lation ol' t h e process is tle~iionstratcd. T l ~ i s work s h o r ~ l d I I ~ of interest to tlesigncrs 01' imagc* proccwing Ili~rd\wircI, cognitive psycl~ologists cl( : i~l i~~g wit11 the humiun visr~nl system ~ I I I C I n e ~ ~ r o ~ ) l ~ y s i o l o g i s t s concerned with the l'unction of s t r u c t ~ ~ r c s in t l ~ c primates re tin;^.
LGR5 is Expressed by Ewing Sarcoma and Potentiates Wnt/β-Catenin Signaling

Ewing sarcoma (ES) is an aggressive bone and soft tissue tumor of putative stem cell origin that predominantly occurs in children and young adults. Although most patients with localized ES can be cured with intensive therapy, the clinical course is variable and up to one third of patients relapse following initial remission. Unfortunately, little is yet known about the biologic features that distinguish low-risk from high-risk disease or the mechanisms of ES disease progression. Recent reports have suggested that putative cancer stem cells exist in ES and may contribute to an aggressive phenotype. The cell surface receptor leucine-rich repeat-containing G-protein coupled receptor 5 (LGR5) is a somatic stem cell marker that functions as an oncogene in several human cancers, most notably colorectal carcinoma. LGR5 is a receptor for the R-spondin (RSPO) family of ligands and RSPO-mediated activation of LGR5 potentiates Wnt/β-catenin signaling, contributing to stem cell proliferation and self-renewal. Given its presumed stem cell origin, we investigated whether LGR5 contributes to ES pathogenesis. We found that LGR5 is expressed by ES and that its expression is relatively increased in cells and tumors that display a more aggressive phenotype. In particular, LGR5 expression was increased in putative cancer stem cells. We also found that neural crest-derived stem cells express LGR5, raising the possibility that expression of LGR5 may be a feature of ES cells of origin. LGR5-high ES cells showed nuclear localization of β-catenin and robust activation of TCF reporter activity when exposed to Wnt ligand and this was potentiated by RSPO. However, modulation of LGR5 or exposure to RSPO had no impact on proliferation confirming that Wnt/β-catenin signaling in ES cells does not recapitulate signaling in epithelial cells. Together these studies show that the RSPO-LGR5-Wnt-β-catenin axis is present and active in ES and may contribute to tumor pathogenesis.
Capacity of multi-channel wireless networks with random (c, f) assignment

With the availability of multiple unlicensed spectral bands, and potential cost-based limitations on the capabilities of individual nodes, it is increasingly relevant to study the performance of multi-channel wireless networks with channel switching constraints. To this effect, some constraint models have been recently proposed, and connectivity and capacity results have been formulated for networks of randomly deployed single-interface nodes subject to these constraints. One of these constraint models is termed random (<i>c</i>, <i>f</i>) assignment, wherein each node is pre-assigned a random subset of <i>f</i> channels out of <i>c</i> (each having bandwidth <i>W</i><over><i>c</i>), and may only switch on these. Previous results for this model established bounds on network capacity, and proved that when <i>c</i>=<i>O</i>(log<i>n</i>), the <i>per-flow</i> capacity is <i>O</i>(<i>W</i>√<i>p</i><sub><i>rnd</i></sub><over><i>n</i>log<i>n</i>) and Ω(<i>W</i>√<i>f</i><over><i>cn</i>log<i>n</i>) (where <i>p</i><sub><i>rnd</i></sub> = 1 - (1-<i>f</i><over><i>c</i>)(1-<i>f</i><over><i>c</i>-1). (1-<i>f</i><over><i>c-f</i>+1) ≥ 1-ε<sup>-<i>f</i><sup>2</sup><over><i>c</i></sup>). In this paper we present a lower bound construction that matches the previous upper bound. This establishes the capacity as Θ(<i>W</i>√<i>p</i><sub><i>rnd</i></sub><over><i>n</i>log<i>n</i>). The surprising implication of this result is that when <i>f</i>=Ω(√<i>c</i>), random (<i>c</i>, <i>f</i>) assignment yields capacity of the same order as attainable via unconstrained switching. The routing/scheduling procedure used by us to achieve capacity requires synchronized route-construction for all flows in the network, leading to the open question of whether it is possible to achieve capacity using asynchronous procedures.
The catalysis of the SARS 3C‐like protease is under extensive regulation by its extra domain

The 3C‐like protease of the severe acute respiratory syndrome (SARS) coronavirus has a C‐terminal extra domain in addition to the chymotrypsin‐fold adopted by piconavirus 3C proteases hosting the complete catalytic machinery. Previously we identified the extra domain to be involved in enzyme dimerization which has been considered essential for the catalytic activity. In an initial attempt to map out the extra‐domain residues critical for dimerization, we have systematically generated 15 point mutations, five deletions and one triple mutation and subsequently characterized them by enzymatic assay, dynamic light scattering, CD and NMR spectroscopy. The results led to identification of four regions critical for enzyme dimerization. Interestingly, Asn214Ala mutant with a significant tendency to form a monomer still retained ≈ 30% activity, indicating that the relationship between the activity and dimerization might be very complex. Very surprisingly, two regions (one over Ser284–Thr285–Ile286 and another around Phe291) were discovered on which Ala‐mutations significantly increased the enzymatic activities. Based on this, a super‐active triple‐mutant STI/A with a 3.7‐fold activity enhancement was thus engineered by mutating residues Ser284, Thr285 and Ile286 to Ala. The dynamic light scattering, CD and NMR characterizations indicate that the wild‐type (WT) and STI/A mutant share similar structural and dimerization properties, thus implying that in addition to dimerization, the extra domain might have other mechanisms to regulate the catalytic machinery. We rationalized these results based on the enzyme structure and consequently observed an interesting picture: the majority of the dimerization‐critical residues plus Ser284–Thr285–Ile286 and Phe291 are clustered together to form a nano‐scale channel passing through the central region of the enzyme. We therefore speculate that this channel might play a role in relaying regulatory effects from the extra domain to the catalytic machinery.
Slotted Microstrip Antennas for Circular Polarization with Compact Size

Circularly polarized diagonally symmetric slotted microstrip-patch antennas are proposed with compact size. The compact circularly polarized (CP) diagonally symmetric slotted microstrip-patch (DSSMP) antenna design rules are also summarized. Circularly polarized radiation can be achieved using any arbitrarily shaped slots in diagonal directions on the square microstrip-patch antenna. Different shapes for the slots are studied and compared, based on the fixed overall volume of the antenna for circularly polarized diagonally symmetric slotted microstrip-patch antennas. The cross-shaped-slot diagonally symmetric slotted microstrip-patch antenna is compact when compared with the circular-, square-, and circular-ring-shaped diagonally symmetric slotted microstrip-patch antennas. A measured 3 dB axial-ratio (AR) bandwidth of around 0.7% (6.0 MHz) with 2.0% (18.0 MHz) impedance bandwidth was achieved. The measured boresight gain was more than 3.3 dBic over the operating band, while the overall antenna size was 0. 272λ0 × 0. 272λ0 × 0. 0138λ0 at 0.905 GHz.
Development and application of a loop-mediated isothermal amplification assay for rapid detection of Pythium helicoides.

Root rot of poinsettia, caused by Pythium helicoides at high temperatures in hydroponic cultures, has become a serious problem in many parts of the world. We have developed a species-specific, loop-mediated isothermal amplification (LAMP) assay for the rapid diagnosis of this pathogen. The primers were designed using the ribosomal DNA internal transcribed spacer sequence. Primer specificity was established using 40 Pythium species including P. helicoides, 11 Phytophthora species, and eight other soil-borne pathogens. A sensitivity test was carried out using genomic DNA extracted from P. helicoides, and the detection limit was c. 100 fg which is comparable to that of the polymerase chain reaction (PCR). In addition, we tested the ease of pathogen detection in poinsettia roots. The LAMP results were consistent with those from the conventional plating method and showed more sensitivity than the PCR results. Consequently, the LAMP method developed in this study is effective for the rapid and easy detection of P. helicoides.
Metagenomic analysis reveals microbial diversity and function in the rhizosphere soil of a constructed wetland

Microbial communities play a critical role in the degradation of effluent contaminants in constructed wetlands. Many questions remain, however, regarding the role of microbial communities in rhizospheric soil. In this study, we used metagenomic analysis to assess microbial community composition and function in a constructed wetland receiving surface water. The diversity of the microbial community of rhizosphere soil was found to be significantly greater than that of the wetland influent water. This enhancement is likely due to the availability of diverse habitats and nutrients provided by the wetland plants. From function annotation of metagenomic data, a number of biodegradation pathways associated with 14 xenobiotic compounds were identified in soil. Nitrogen fixation, nitrification and denitrification genes were semi-quantitatively analysed. By screening of manganese transformation genes, we found that the biological oxidation of Mn2+ (mainly catalysed by multicopper oxidase) in the influent water yielded insoluble Mn4+, which subsequently precipitated and were incorporated into the wetland soil. These data show that the use of metagenomic analysis can provide important new insights for the study of wetland ecosystems and, in particular, how biologically mediated transformation or degradation can be used to reduce contamination of point and non-point source wastewater.
Magnetic Resonance Imaging and Graph Theoretical Analysis of Complex Brain Networks in Neuropsychiatric Disorders

Neurological and psychiatric disorders disturb higher cognitive functions and are accompanied by aberrant cortico-cortical axonal pathways or synchronizations of neural activity. A large proportion of neuroimaging studies have focused on examining the focal morphological abnormalities of various gray and white matter structures or the functional activities of brain areas during goal-directed tasks or the resting state, which provides vast quantities of information on both the structural and functional alterations in the patients' brain. However, these studies often ignore the interactions among multiple brain regions that constitute complex brain networks underlying higher cognitive function. Information derived from recent advances of noninvasive magnetic resonance imaging (MRI) techniques and computational methodologies such as graph theory have allowed researchers to explore the patterns of structural and functional connectivity of healthy and diseased brains in vivo. In this article, we summarize the recent advances made in the studies of both structural (gray matter morphology and white matter fibers) and functional (synchronized neural activity) brain networks based on human MRI data pertaining to neuropsychiatric disorders. These studies bring a systems-level perspective to the alterations of the topological organization of complex brain networks and the underlying pathophysiological mechanisms. Specifically, noninvasive imaging of structural and functional brain networks and follow-up graph-theoretical analyses demonstrate the potential to establish systems-level biomarkers for clinical diagnosis, progression monitoring, and treatment effects evaluation for neuropsychiatric disorders.