Miracle-dz/UniFAR-FTUs huggingface dataset:
Stability of networked control systems with large delays

This paper proposes stability analysis techniques for networked control systems (NCSs) with uncertain, time- varying network-induced delays. A discrete-time model, describing an NCS with delays, that can be both smaller and larger than the sampling interval, is presented. This model includes the effects of message rejection and vacancy sampling. The conditions are kept less conservative by exploiting the real Jordan form of the continuous-time model in the discretization. Based on this discrete-time NCS model sufficient LMI conditions are proposed for the stability analysis.
Remnants of adenomas in colorectal carcinomas

In consecutive large bowel resectates in patients older than age 20 years, primary colorectal cancer remnants of adenomas were histologically identified in 39 of 169 carcinomas (23%). Remnants of pure tubular adenomas were seen in 17 and of tubulovillous adenomas in 22 cases. There was no significant difference among sexes, intestinal segments, or age groups older than 55 years with the regard to the frequency of adenomas in carcinomas. A very low rate (0.05) was found in patients of both sexes younger than 55 years. The frequency with which adenomas was identified was independent of tumor size. A high rate was found in those carcinomas which were limited to the submucosal layer (0.57), were well differentiated (0.43), and had an exophytic growth (0.54). Coexisting single or multiple adenomas at a distance from the main tumor were significantly more frequent in resectates in which adenomas was detected in the carcinoma (0.51) than in resectates in which no adenoma contiguous with the carcinoma was seen (0.30). The study shows that carcinomas develop from adenomas in all parts of the large intestine, but it cannot be concluded that all carcinomas in noncolitic patients develop from adenomas.
Predictive Modeling of Surveyed Property Conditions and Vacancy

Using the results of a comprehensive in-person survey of properties in Cleveland, Ohio, we fit predictive models of vacancy and property conditions. We draw predictor variables from administrative data that is available in most jurisdictions such as deed recordings, tax assessor's property characteristics, and foreclosure filings. Using logistic regression and machine learning methods we are able to make reasonably accurate out-of-sample predictions. Our findings indicate that housing professionals could use administrative data and predictive models to identify distressed properties between surveys or among non-surveyed properties in an area subject to a random sample survey.
Improving the Soft Error Resilience of the Register Files Using SRAM Bitcells with Built-In Comparators

Soft errors caused by cosmic rays or alpha particles emitted from the packaging material around the chips are becoming an increasingly important challenge in reliable microprocessor design. Transistor density, and die size trends show that soft errors will gain even more importance in the future. Due to their significant overheads, most redundancy schemes are employed where the penalty incurred can be hidden in the pipeline. Most contemporary processors employ a large physical register file to hold the produced results which may reside there for a long time. The register file is a critical element of a microprocessor and is needed to be protected against soft errors. In this paper we propose an SRAM bitcell design with ability to hold a redundant copy of the data and compare the copies with built-in comparators to detect a possible mismatch. Our experimental results show that the proposed design has 34% area, 7.9% power 2% delay overheads which are further reducible and can protect the register file against Silent Data Corruption (SDC).
Structural Investigations of N-carbamoylputrescine Amidohydrolase from Medicago truncatula: Insights into the Ultimate Step of Putrescine Biosynthesis in Plants

Putrescine, 1,4-diaminobutane, is an intermediate in the biosynthesis of more complexed polyamines, spermidine and spermine. Unlike other eukaryotes, plants have evolved a multistep pathway for putrescine biosynthesis that utilizes arginine. In the final reaction, N-carbamoylputrescine is hydrolyzed to putrescine by N-carbamoylputrescine amidohydrolase (CPA, EC 3.5.1.53). During the hydrolysis, consecutive nucleophilic attacks on the substrate by Cys158 and water lead to formation of putrescine and two by-products, ammonia and carbon dioxide. CPA from the model legume plant, Medicago truncatula (MtCPA), was investigated in this work. Four crystal structures were determined: the wild-type MtCPA in complex with the reaction intermediate, N-(dihydroxymethyl)putrescine as well as with cadaverine, which is a longer analog of putrescine; and also structures of MtCPA-C158S mutant unliganded and with putrescine. MtCPA assembles into octamers, which resemble an incomplete left-handed helical twist. The active site of MtCPA is funnel-like shaped, and its entrance is walled with a contribution of the neighboring protein subunits. Deep inside the catalytic cavity, Glu48, Lys121, and Cys158 form the catalytic triad. In this studies, we have highlighted the key residues, highly conserved among the plant kingdom, responsible for the activity and selectivity of MtCPA toward N-carbamoylputrescine. Moreover, since, according to previous reports, a close MtCPA relative from Arabidopsis thaliana, along with several other nitrilase-like proteins, are subjected to allosteric regulation by substrates, we have used the structural information to indicate a putative secondary binding site. Based on the docking experiment, we postulate that this site is adjacent to the entrance to the catalytic pocket.
Audio spectrum projection based on several basis decomposition algorithms applied to general sound recognition and audio segmentation

Our challenge is to analyze/classify video sound track content for indexing purposes. To this end we compare the performance of MPEG-7 Audio Spectrum Projection (ASP) features based on basis decomposition vs. Mel-scale Frequency Cepstrum Coefficients (MFCC). For basis decomposition in the feature extraction we have three choices: Principal Component Analysis (PCA), Independent Component Analysis (ICA), and Non-negative Matrix Factorization (NMF). Audio features are computed from these reduced vectors and are fed into hidden Markov model (HMM) classifier. Experimental results show that the MFCC features yield better performance compared to MPEG-7 ASP in the sound recognition, and audio segmentation.
Dual Effect of CTCF Loss on Neuroprogenitor Differentiation and Survival

An increasing number of proteins involved in genome organization have been implicated in neurodevelopmental disorders, highlighting the importance of chromatin architecture in the developing CNS. The CCCTC-binding factor (CTCF) is a zinc finger DNA binding protein involved in higher-order chromatin organization, and mutations in the human CTCF gene cause an intellectual disability syndrome associated with microcephaly. However, information on CTCF function in vivo in the developing brain is lacking. To address this gap, we conditionally inactivated the Ctcf gene at early stages of mouse brain development. Cre-mediated Ctcf deletion in the telencephalon and anterior retina at embryonic day 8.5 triggered upregulation of the p53 effector PUMA (p53 upregulated modulator of apoptosis), resulting in massive apoptosis and profound ablation of telencephalic structures. Inactivation of Ctcf several days later at E11 also resulted in PUMA upregulation and increased apoptotic cell death, and the Ctcf-null forebrain was hypocellular and disorganized at birth. Although deletion of both Ctcf and Puma in the embryonic brain efficiently rescued Ctcf-null progenitor cell apoptosis, it failed to improve neonatal hypocellularity due to decreased proliferative capacity of rescued apical and outer radial glia progenitor cells. This was exacerbated by an independent effect of CTCF loss that resulted in depletion of the progenitor pool due to premature neurogenesis earlier in development. Our findings demonstrate that CTCF activities are required for two distinct events in early cortex formation: first, to correctly regulate the balance between neuroprogenitor cell proliferation and differentiation, and second, for the survival of neuroprogenitor cells, providing new clues regarding the contributions of CTCF in microcephaly/intellectual disability syndrome pathologies.
Cullin 5 destabilizes Cas to inhibit Src-dependent cell transformation

ABSTRACT Phosphorylation-dependent protein ubiquitylation and degradation provides an irreversible mechanism to terminate protein kinase signaling. Here, we report that mammary epithelial cells require cullin-5–RING–E3-ubiquitin-ligase complexes (Cul5-CRLs) to prevent transformation by a Src–Cas signaling pathway. Removal of Cul5 stimulates growth-factor-independent growth and migration, membrane dynamics and colony dysmorphogenesis, which are all dependent on the endogenous tyrosine kinase Src. Src is activated in Cul5-deficient cells, but Src activation alone is not sufficient to cause transformation. We found that Cul5 and Src together stimulate degradation of the Src substrate p130Cas (Crk-associated substrate). Phosphorylation stimulates Cas binding to the Cul5-CRL adaptor protein SOCS6 and consequent proteasome-dependent degradation. Cas is necessary for the transformation of Cul5-deficient cells. Either knockdown of SOCS6 or use of a degradation-resistant Cas mutant stimulates membrane ruffling, but not other aspects of transformation. Our results show that endogenous Cul5 suppresses epithelial cell transformation by several pathways, including inhibition of Src–Cas-induced ruffling through SOCS6.
Power allocation for joint estimation with energy harvesting constraints

This paper considers joint estimation with multiple sensors powered by energy harvesters in wireless sensor networks. In particular, we focus on a network with K sensor nodes, which communicate with a fusion center via K orthogonal channels and power themselves by harvesting energy from the environment. Assuming a deterministic energy-harvesting model under which the harvested energy profile is known prior to transmission, the worst-case mean-square error (MSE) minimization problem over a finite horizon of T estimation periods is investigated. We consider the cases that the sensors have either infinite or finite battery capacity, and develop efficient iterative algorithms to compute the optimal power allocation strategy, with numerical results presented to validate our analysis.
Raf-1 Antagonizes Erythroid Differentiation by Restraining Caspase Activation

The Raf kinases are key signal transducers activated by mitogens or oncogenes. The best studied Raf isoform, Raf-1, was identified as an inhibitor of apoptosis by conventional and conditional gene ablation in mice. c-raf-1 − / − embryos are growth retarded and anemic, and die at midgestation with anomalies in the placenta and fetal liver. Here, we show that Raf-1–deficient primary erythroblasts cannot be expanded in culture due to their accelerated differentiation into mature erythrocytes. In addition, Raf-1 expression is down-regulated in differentiating wild-type cells, whereas overexpression of activated Raf-1 delays differentiation. As recently described for human erythroid precursors, we find that caspase activation is necessary for the differentiation of murine fetal liver erythroblasts. Differentiation-associated caspase activation is accelerated in erythroid progenitors lacking Raf-1 and delayed by overexpression of the activated kinase. These results reveal an essential function of Raf-1 in erythropoiesis and demonstrate that the ability of Raf-1 to restrict caspase activation is biologically relevant in a context distinct from apoptosis.
Hammamet -tunisia " Evaluation and Optimization of Innovative Production Systems of Goods and Services " Heuristics for the Multi-item Capacitated Lot-sizing Problem with Lost Sales

This paper deals with the multi-item capacitated lot-sizing problem with setup times and lost sales. Because lost sales, demands can be partially or totally lost. To find a good lower bound, we use a Lagrangian relaxation of the capacity constraints, when single-item uncapacitated lot-sizing problems with lost sales have to be solved. Each subproblem is solved using an adaptation of the O(T 2) dynamic programming algorithm of (Aksen et al., 2003). To find feasible solutions, we propose a non-myopic heuristic based on a probing strategy and a refining procedure. We propose also some metaheuristic principles to improve solutions. Some computational experiments showing the effectiveness and limit of each approach are presented.
Scheduling and route selection for military land moves using genetic algorithms

We investigate the problem of scheduling the move of a large amount of military equipment from a fort or depot to a port. This problem differs from traditional distribution scheduling problems in a number of ways including: (i) the trucks need to be grouped into convoys, (ii) there is a single source location and a single destination, and (iii) there are potentially so many trucks traveling the same set of roads that the effects on other traffic must be considered. We have divided the problem into two parts: (i) selecting a fixed set of routes and (ii) forming the trucks into convoys and selecting routes and departure times for each convoy. We describe how we have used genetic algorithms to solve each of these problems. We emphasize how the ability to incorporate domain knowledge into the genetic algorithms has allowed us to easily create algorithms well suited to the particular constraints of the problems.
Allocating online advertisement space with unreliable estimates

We study the problem of optimally allocating online advertisement space to budget-constrained advertisers. This problem was defined and studied from the perspective of worst-case online competitive analysis by Mehta et al. Our objective is to find an algorithm that takes advantage of the given estimates of the frequencies of keywords to compute a near optimal solution when the estimates are accurate, while at the same time maintaining a good worst-case competitive ratio in case the estimates are totally incorrect. This is motivated by real-world situations where search engines have stochastic information that provide reasonably accurate estimates of the frequency of search queries except in certain highly unpredictable yet economically valuable spikes in the search pattern. Our approach is a black-box approach: we assume we have access to an oracle that uses the given estimates to recommend an advertiser everytime a query arrives. We use this oracle to design an algorithm that provides two performance guarantees: the performance guarantee in the case that the oracle gives an accurate estimate, and its worst-case performance guarantee. Our algorithm can be fine tuned by adjusting a parameter α, giving a tradeoff curve between the two performance measures with the best competitive ratio for the worst-case scenario at one end of the curve and the optimal solution for the scenario where estimates are accurate at the other en. Finally, we demonstrate the applicability of our framework by applying it to two classical online problems, namely the lost cow and the ski rental problems.
Accounting for missing data in monthly temperature series: Testing rule‐of‐thumb omission of months with missing values

The “3/5 rule” is a commonly used rule‐of‐thumb for dealing with missing data when calculating monthly climate normals. The rule states that any month that is missing more than three consecutive daily values, or more than five daily values in total, should not be included in calculated monthly climate normals. We quantify the impact of missing data in a given year–month for between 1 and 25 missing values. As such, we describe the error the “3/5 rule” (and a related rule that we have dubbed the “4/10 rule”) permits. We tested the statistical robustness of these rules using observed temperature data from a temperate station and a tropical station. We show that, for observed data, the “3/5 rule” permits an average of between 0.06 and 0.07 standard deviations of error in the calculated monthly mean (ɛ) when three consecutive or five random values are missing. For its part, the “4/10 rule” permits a maximum ɛ of between 0.07 and 0.09 when four consecutive values are missing, or up to 0.10 when 10 random values are missing. The proportional impact of missing values was similar across variables. We performed a correlation analysis and show that each additional missing value from a year–month of data increases ɛ by between 0.008 and 0.018 for up to 19 missing values. There is a significant relationship between the lag‐1 autocorrelation of a year–month, and ɛ. ɛ can be reduced by simple linear interpolation when values are missing at random and the year–month exhibits lag‐1 autocorrelation. Overall, we find that the application of any “rule‐of‐thumb” should be based on the particular characteristics of the source data and the goals of the research project.
Analysis of within Subjects Variability in Mouse Ultrasonic Vocalization: Pups Exhibit Inconsistent, State-Like Patterns of Call Production

Mice produce ultrasonic vocalizations (USV) in multiple communicative contexts, including adult social interaction (e.g., male to female courtship), as well as pup calls when separated from the dam. Assessment of pup USV has been widely applied in models of social and communicative disorders, dozens of which have shown alterations to this conserved behavior. However, features such as call production rate can vary substantially even within experimental groups and it is unclear to what extent aspects of USV represent stable trait-like influences or are vulnerable to an animal's state. To address this question, we have employed a mixed modeling approach to describe consistency in USV features across time, leveraging multiple large cohorts recorded from two strains, and across ages/times. We find that most features of pup USV show consistent patterns within a recording session, but inconsistent patterns across postnatal development. This supports the conclusion that pup USV is most strongly influenced by “state”-like variables. In contrast, adult USV call rate and call duration show higher consistency across sessions and may reflect a stable “trait. ” However, spectral features of adult song such as the presence of pitch jumps do not show this level of consistency, suggesting that pitch modulation is more susceptible to factors affecting the animal's state at the time of recording. Overall, the utility of this work is three-fold. First, as variability necessarily affects the sensitivity of the assay to detect experimental perturbation, we hope the information provided here will be used to help researchers plan sufficiently powered experiments, as well as prioritize specific ages to study USV behavior and to decide which features to consider most strongly in analysis. Second, via the mouseTube platform, we have provided these hundreds of recordings and associated data to serve as a shared resource for other researchers interested in either benchmark data for these strains or in developing algorithms for studying features of mouse song. Finally, we hope that this work informs both interpretation of USV studies in models of developmental disorder, and helps to further research into understanding the neural processes that contribute to the production and predictability of USV behavior.
CoG Kits: Enabling Middleware for Designing Science Applications, Web Portals, and Problem Solving Environments

This report summarizes this quarters accomplishments of the SciDAC CoG Kit project funded through the Department of Energy MICS program under grant number FWP #56825. The highlights of this semester include the collaboration with other SciDAC projects such as the DOE Science Grid, CMCS, and OGSA. All of these projects reuse components developed and designed by the CoG Kit project. Additionally, we have published several papers, and improved the software Kits with several new features. We have made major progress in supporting the GridFTP protocol in the Java CoG Kit.
Comparing Repetition Priming Effects in Words and Arithmetic Equations: Robust Priming Regardless of Color or Response Hand Change

Previous studies have shown that stimulus repetition can lead to reliable behavioral improvements. Although this repetition priming (RP) effect has been reported in a number of paradigms using a variety of stimuli including words, objects, and faces, only a few studies have investigated mathematical cognition involving arithmetic computation, and no prior research has directly compared RP effects in a linguistic task with an arithmetic task. In two experiments, we used a within-subjects design to investigate and compare the magnitude of RP, and the effects of changing the color or the response hand for repeated, otherwise identical, stimuli in a word and an arithmetic categorization task. The results show that the magnitude of RP was comparable between the two tasks and that changing the color or the response hand had a negligible effect on priming in either task. These results extended previous findings in mathematical cognition. They also indicate that priming does not vary with stimulus domain. The implications of the results were discussed with reference to both facilitation of component processes and episodic memory retrieval of stimulus–response binding.
Bounds on the outage constrained capacity of the single-antenna Gaussian relay channel

We study the probabilistically constrained capacity of a Gaussian relay channel in terms of the corresponding outage constrained decode-and-forward (DF) achievable rate and the cut-set bound (CSB). The probabilistic outage constraint is necessary due to Rayleigh fading and the absence of channel state information (CSI) at the transmitting nodes. The DF outage probability can be calculated in closed form, which allows a direct optimization of the joint source and relay transmit strategy. In contrast, the CSB probability can only be calculated in closed form for noncoherent transmission from the source and relay to the destination. For coherent transmission, we propose two upper bounds based on a genie-aided transmission and Markov's inequality. The numerical results verify the quality of the bounds.
BrainQuest: Perception-Guided Brain Network Comparison

Why are some people more creative than others? How do human brain networks evolve over time? A key stepping stone to both mysteries and many more is to compare weighted brain networks. In contrast to networks arising from other application domains, the brain network exhibits its own characteristics (e.g., high density, indistinguishability), which makes any off-the-shelf data mining algorithm as well as visualization tool sub-optimal or even mis-leading. In this paper, we propose a shift from the current mining-then-visualization paradigm, to jointly model these two core building blocks (i.e., mining and visualization) for brain network comparisons. The key idea is to integrate the human perception constraint into the mining block earlier so as to guide the analysis process. We formulate this as a multi-objective feature selection problem, and propose an integrated framework, BrainQuest, to solve it. We perform extensive empirical evaluations, both quantitatively and qualitatively, to demonstrate the effectiveness and efficiency of our approach.