Miracle-dz/UniFAR-FTUs huggingface dataset:
Consistency Constraint Allocation in Augmented Lagrangian Coordination

Many engineering systems are too complex to design as a single entity. Decomposition-based design optimization methods partition a system design problem into subproblems, and coordinate subproblem solutions toward an optimal system design. Recent work has addressed formal methods for determining an ideal system partition and coordination strategy, but coordination decisions have been limited to subproblem sequencing. An additional element in a coordination strategy is the linking structure of the partitioned problem, i.e., the allocation of constraints that guarantee that the linking variables among subproblems are consistent. There may exist many alternative linking structures for a decomposition-based strategy that can be selected for a given partition, and this selection should be part of an optimal simultaneous partitioning and coordination scheme. This article develops a linking structure theory for a particular class of decomposition-based optimization algorithms, augmented Lagrangian coordination (ALC). A new formulation and coordination technique for parallel ALC implementations is introduced along with a specific linking structure theory, yielding a partitioning and coordination selection method for ALC that includes consistency constraint allocation. This method is demonstrated using an electric water pump design problem.
The gypsy insulator can function as a promoter‐specific silencer in the Drosophila embryo

The Drosophila gypsy retrotransposon disrupts gene activity by blocking the interactions of distal enhancers with target promoters. This enhancer‐blocking activity is mediated by a 340 bp insulator DNA within gypsy. The insulator contains a cluster of binding sites for a zinc finger protein, suppressor of Hairy wing [su(Hw)]. Recent studies have shown that a second protein, mod(mdg4), is also important for normal insulator function. Mutations in mod(mdg4) exert paradoxical effects on different gypsy‐induced phenotypes. For example, it enhances yellow2 but suppresses cut6. Here, we employ a stripe expression assay in transgenic embryos to investigate the role of mod(mdg4) in gypsy insulator activity. The insulator was inserted between defined enhancers and placed among divergently transcribed reporter genes (white and lacZ) containing distinct core promoter sequences. These assays indicate that mod(mdg4) is essential for the enhancer‐blocking activity of the insulator DNA. Moreover, reductions in mod(mdg4)+ activity cause the insulator to function as a promoter‐specific silencer that selectively represses white, but not lacZ. The repression of white does not affect the expression of the closely linked lacZ gene, suggesting that the insulator does not propagate changes in chromatin structure. These results provide an explanation for why mod(mdg4) exerts differential effects on different gypsy‐induced mutations.
Optically assisted Internet routing using arrays of novel dynamically reconfigurable FBG-based correlators

As routing tables in core Internet routers grow to exceed 100,000 entries, it is becoming essential to develop methods to reduce the lookup time required to forward packets toward their destinations. In this paper, we employ a bank of novel thermally tuned fiber-Bragg-grating-based optical correlators to construct an "optical bypass" to accelerate conventional electronic Internet routers. The correlators are configured as a routing table cache that can quickly determine the destination port for a fraction of the incoming traffic by examining only a subset of the bits in an IP packet's 32-bit destination address. We also demonstrate a novel multiwavelength correlator based on fiber Bragg grating that can simultaneously recognize the header bits on multiple wavelengths for use in wavelength-division-multiplexed (WDM) systems. Using the optical bypass, routing table lookup times are reduced by an order of magnitude from microseconds to nanoseconds and are limited only by the speed of the optical switch.
Design optimization methods for genomic DNA tiling arrays.

A recent development in microarray research entails the unbiased coverage, or tiling, of genomic DNA for the large-scale identification of transcribed sequences and regulatory elements. A central issue in designing tiling arrays is that of arriving at a single-copy tile path, as significant sequence cross-hybridization can result from the presence of non-unique probes on the array. Due to the fragmentation of genomic DNA caused by the widespread distribution of repetitive elements, the problem of obtaining adequate sequence coverage increases with the sizes of subsequence tiles that are to be included in the design. This becomes increasingly problematic when considering complex eukaryotic genomes that contain many thousands of interspersed repeats. The general problem of sequence tiling can be framed as finding an optimal partitioning of non-repetitive subsequences over a prescribed range of tile sizes, on a DNA sequence comprising repetitive and non-repetitive regions. Exact solutions to the tiling problem become computationally infeasible when applied to large genomes, but successive optimizations are developed that allow their practical implementation. These include an efficient method for determining the degree of similarity of many oligonucleotide sequences over large genomes, and two algorithms for finding an optimal tile path composed of longer sequence tiles. The first algorithm, a dynamic programming approach, finds an optimal tiling in linear time and space; the second applies a heuristic search to reduce the space complexity to a constant requirement. A Web resource has also been developed, accessible at http://tiling.gersteinlab. org, to generate optimal tile paths from user-provided DNA sequences.
Emotional Eating Is Not What You Think It Is and Emotional Eating Scales Do Not Measure What You Think They Measure

In eating research, it is common practice to group people into different eater types, such as emotional, external and restrained eaters. This categorization is generally based on scores on self-report questionnaires. However, recent studies have started to raise questions about the validity of such questionnaires. In the realm of emotional eating, a considerable number of studies, both in the lab and in naturalistic settings, fail to demonstrate increased food intake in emotional situations in self-described emotional eaters. The current paper provides a review of experimental and naturalistic studies investigating the relationships between self-reported emotional eater status, mood, and food consumption. It is concluded that emotional eating scales lack predictive and discriminative validity; they cannot be assumed to measure accurately what they intend to measure, namely increased food intake in response to negative emotions. The review is followed by a discussion of alternative interpretations of emotional eating scores that have been suggested in the past few years, i.e., concerned eating, uncontrolled eating, a tendency to attribute overeating to negative affect, and cue-reactive eating.
AGRICULTURE IN THE REPUBLIC OF KARAKALPAKSTAN AND KHOREZM OBLAST OF UZBEKISTAN

This paper describes the agricultural sector in the western region of Uzbekistan, the most populous of the former Soviet Central Asian Republics. Agriculture in this region, as in all of Uzbekistan, is entirely dependent on irrigation, as has been the case for millennia. Evidence of settlement of the desert oases and the banks of the Amu Darya River (known as the Oxus in ancient times) dates back many millennia, as does settlement of the short of the Aral Sea, largely based on fishing. However, the Aral Sea Region of Uzbekistan, including the Autonomous Republic of Karakalpakstan and Khorezm Oblast, the currently undergoing severe ecological stress, as is the entire Aral Sea Basin. Massive expansion of irrigated area starting in the 1960's has resulted in a steady shrinkage of the Aral Sea, whose shoreline is now some 100 kilometers beyond its former location. There are now problems with extreme salinization of the sea water, which supports many fewer species than previously, as well as wind-blown salt from the flats left by the retreating waters. In addition, poor irrigation management has caused severe problems with waterlogging and salinity in upstream areas.
A New Framework to Model a Secure E-Commerce System

— The existing information system (IS) developments methods are not met the requirements to resolve the security related IS problems and they fail to provide a successful integration of security and systems engineering during all development process stages. Hence, the security should be considered during the whole software development process and identified with the requirements specification. This paper aims to propose an integrated security and IS engineering approach in all software development process stages by using i* language. This proposed framework categorizes into three separate parts: modelling business environment part, modelling information technology system part and modelling IS security part. The results show that considering security IS goals in the whole system development process can have a positive influence on system implementation and better meet business expectations.
Protein decoy assembly using short fragments under geometric constraints

A small set of protein fragments can represent adequately all known local protein structure. This set of fragments, along with a construction scheme that assembles these fragments into structures, defines a discrete (relatively small) conformation space, which approximates protein structures accurately. We generate protein decoys by sampling geometrically valid structures from this conformation space, biased by the secondary structure prediction for the protein. Unlike other methods, secondary structure prediction is the only protein‐specific information used for generating the decoys. Nevertheless, these decoys are qualitatively similar to those found by others. The method works well for all‐α proteins, and shows promising results for α and β proteins. © 2003 Wiley Periodicals, Inc. Biopolymers 68: 278–285, 2003
Unsupervised Entailment Detection between Dependency Graph Fragments

Entailment detection systems are generally designed to work either on single words, relations or full sentences. We propose a new task -- detecting entailment between dependency graph fragments of any type -- which relaxes these restrictions and leads to much wider entailment discovery. An unsupervised framework is described that uses intrinsic similarity, multi-level extrinsic similarity and the detection of negation and hedged language to assign a confidence score to entailment relations between two fragments. The final system achieves 84.1% average precision on a data set of entailment examples from the biomedical domain.
Chronic hepatitis C and persistent occult hepatitis C virus infection are characterized by distinct immune cell cytokine expression profiles

Summary. Hepatitis C virus (HCV) replicates in immune cells in both chronic hepatitis C (CHC) and occult HCV infection, but the extent of virus replication in this compartment in these opposing infection forms varies greatly. It was unknown whether this could be linked to HCV genotype or to differences in host gene expression shaping the immune response, and whether HCV replication in immune cells is sensitive to endogenous antiviral cytokines. In this study, we uncovered that significantly greater HCV load in peripheral blood mononuclear cells (PBMC), but not in plasma, coincided with HCV genotypes 2 and 3 in CHC, but with genotype 1 in residual occult infection after clinical resolution of hepatitis C. Moreover, PBMC from individuals with occult infection transcribed significantly greater levels of IFN‐α, IFN‐γ and TNF‐α, but less interleukin (IL)‐10 than those from CHC. In CHC, PBMC with low HCV load expressed significantly more IFN‐γ but less IL‐12 than did cells with high virus content. In occult infection, HCV RNA detection in PBMC was associated with much lower IFN‐α and IL‐12 expression. Further, HCV replication in T lymphocytes could be completely eliminated by activation of endogenous IFN‐γ in CHC, but of IFN‐α in occult infection. In conclusion, CHC and persistent occult HCV infection are characterized by clearly different profiles of antiviral cytokine response in circulating immune cells which are also different from those of healthy individuals. Higher expression of IL‐10, combined with lower transcription of IFN‐α, IFN‐γ and TNF‐α, is associated with a more robust HCV replication in immune cells.
Correlations and Population Dynamics in Cortical Networks

The function of cortical networks depends on the collective interplay between neurons and neuronal populations, which is reflected in the correlation of signals that can be recorded at different levels. To correctly interpret these observations it is important to understand the origin of neuronal correlations. Here we study how cells in large recurrent networks of excitatory and inhibitory neurons interact and how the associated correlations affect stationary states of idle network activity. We demonstrate that the structure of the connectivity matrix of such networks induces considerable correlations between synaptic currents as well as between subthreshold membrane potentials, provided Dale's principle is respected. If, in contrast, synaptic weights are randomly distributed, input correlations can vanish, even for densely connected networks. Although correlations are strongly attenuated when proceeding from membrane potentials to action potentials (spikes), the resulting weak correlations in the spike output can cause substantial fluctuations in the population activity, even in highly diluted networks. We show that simple mean-field models that take the structure of the coupling matrix into account can adequately describe the power spectra of the population activity. The consequences of Dale's principle on correlations and rate fluctuations are discussed in the light of recent experimental findings.
Learning to Combine Trained Distance Metrics for Duplicate Detection in Databases

The problem of identifying approximately duplicate records in databases has previously been studied as record linkage, the merge/purge problem, hardening soft databases, and field matching. Most existing approaches have focused on efficient algorithms for locating potential duplicates rather than precise similarity metrics for comparing records. In this paper, we present a domain-independent method for improving duplicate detection accuracy using machine learning. First, trainable distance metrics are learned for each field, adapting to the specific notion of similarity that is appropriate for the field’s domain. Second, a classifier is employed that uses several diverse metrics for each field as distance features and classifies pairs of records as duplicates or non-duplicates. We also propose an extended model of learnable string distance which improves over an existing approach. Experimental results on real and synthetic datasets show that our method outperforms traditional techniques.
Biodegradable microparticles as controlled release antigen delivery systems.

A model but poor immunogen, ovalbumin (OVA), was entrapped in a novel antigen delivery system comprising poly (D,L-lactide-co-glycolide) (PLGA) microparticles. Both the primary and the secondary IgG antibody responses obtained with OVA in microparticles were compared to those obtained with OVA emulsified in Freunds' adjuvants by two routes of immunization, intraperitoneal (i.p.) and subcutaneous (s.c.) injection. Following single i.p. or s.c. injections, the IgG serum antibody responses to OVA in microparticles were significantly greater than the responses to OVA in Freunds' complete adjuvant (FCA) for up to 10 weeks. After s.c. booster doses of OVA, the secondary IgG antibody responses to OVA in microparticles remained greater than the secondary responses to OVA in Freunds', but not significantly so. Furthermore, the primary IgG responses to OVA in microparticles obtained 8-12 weeks after a single i.p. injection were greater than the secondary responses to OVA in Freunds' obtained by repeat s.c. injections at Weeks 0 and 6. These results demonstrate that microparticles can function as potent antigen delivery systems for an entrapped antigen. Due to their ability to degrade slowly in vivo and to release entrapped antigens, microparticles have considerable potential as controlled release antigen delivery systems for the induction of long-term immune responses.
A fast and accurate algorithm for copy-move forgery detection

In recent years, and with the presence of many efficient image processing tools, digital image forgery has become a serious social issue. Copy-move forgery is one of the most widely used methods for image forgeries in which a part of the image is copied and then pasted to another location in the same image. This procedure is usually used to add or cover a critical part of the image. In this paper, we propose a new fast and accurate algorithm for copy-move forgery detection in digital images. In the proposed algorithm, the image to analyze is segmented into overlapping square blocks with a predefined side length, each one of the blocks is split into equally spaced k sub-blocks. The sum of pixel intensities of each sub-block is used to form a k-dimensional vector with the help of sliding window and such vector is used as a feature for each block. The resulting features of all blocks are stored in a KD-tree. The block corresponding to each node in the KD-tree is checked with the block corresponding to the nearest neighbor of this node. If the correlation between such blocks is above a prespecified threshold, the two blocks are considered as clones. Experimental results and comparisons with a state of the art method show that the proposed algorithm is fast and accurate.
Wintertime air‐sea interaction processes across the Gulf Stream

Aircraft, buoy and satellite measurements have been used to study the wintertime air-sea interaction processes across the Gulf Stream during January 25–30, 1986. The turbulent flux regime in the marine atmospheric boundary layer exhibited considerable spatial and temporal variability during this 6-day period, which was related to both the evolution of the synoptic scale atmospheric conditions and the sea surface temperature (SST) field. During the pre-storm conditions prior to January 25, the spatial structure of the SST field played an important role in generating a shallow atmospheric frontal zone along the Gulf Stream front by causing differential heating of the marine atmospheric boundary layer over the stream versus over the cooler shelf waters. As this front moved shoreward on January 25, the warm, moist, maritime air flowing northwestward behind the front induced moderate ocean-to-atmosphere heat fluxes (∼300 W m−2 total heat flux measured over the core of the Gulf Stream). The subsequent outbreak of eastward flowing cold, dry, continental air over the ocean on January 27 and 28 generated high total heat fluxes (∼1060 W m−2 over the core of the Stream), as did a second, somewhat weaker outbreak which followed on January 30 (∼680 W2 over the core of the Stream). During each of these outbreaks, with air flowing from land out over the continental shelf, Gulf Stream and Sargasso Sea waters, the SST field again affected the spatial structure of the flux fields. The near-surface fluxes of both sensible and latent heat were found to be relatively low over the cool continental shelf waters, while higher fluxes were seen over the Gulf Stream and Sargasso Sea. Similar spatial structure was seen in the near-surface momentum flux values, but relative changes were typically smaller from one location to another on a particular day. The most noticeable responses of the Gulf Stream to these surface fluxes were the deepening of its mixed layer and a loss of upper layer heat; however, no direct current observations were made in the stream, so velocity changes may not be assessed. An average mixed layer deepening of about 35 m was observed in the stream, and the upper layer heat loss was estimated to be 3.2×1013 J m−1 alongstream, an amount sufficient to decrease the average mixed layer temperature by 0.62°C. No path changes in the stream could be attributed to the atmospheric forcing of this period, since there was a large offshore movement of the stream in the region of the Charleston bump at this time due to other processes. Any path changes that may have been associated with the atmospheric forcing would have been masked by that offshore movement.
Actin associated with membranes from 3T3 mouse fibroblast and HeLa cells

A protein component of membranes isolated from 3T3 mouse fibroblasts and HeLa cells has been identified as actin by peptide mapping. Extensive but apparently not total coincidence was found between the peptide maps of these two nonmuscle membrane-associated actins compared to chick skeletal muscle actin. Between 2 and 4 percent of the total membrane protein appears in the actin band on sodium dodecyl sulfate polyacrylamide gels of 3T3 membranes while about 4 percent of the membrane protein appears as the actin band from HeLa membranes. These values represent approximately the same proportion of actin to total protein found in the cell homogenates. Treatment of intact cells with levels of cytochalasin B sufficient to cause pronounced morphological changes did not change the amount of actin associated with the membrane in either 3T3 or HeLa cells. However, incubation of isolated membranes under conditions favoring conversion of actin from filamentous to monomeric form resulted in dissociation of approximately 80 and 60 percent of the actin from 3T3 and HeLa membranes, respectively. Thus, approximately 20 percent of 3T3 membrane actin and 40 percent of HeLa membrane actin remained associated with the membrane even under actin depolymerizing conditions.
Embedded MDS codes for multicast streaming

We study low-delay streaming codes for erasure channels in point-to-point and multicast scenarios. We consider a sliding window erasure channel which captures the temporal correlation in packet losses observed in real channels. This correlation is often modelled using statistical channels such as Gilbert-Elliott channel. In the point-to-point case, we provide a new class of codes, Embedded Maximum Distance Separable (EMDS) codes, which recovers from channels introducing a mixture of burst and isolated erasures. Moreover, we propose a technique that extends point-to-point codes for the multicast scenario with two receivers that tolerate different delays, T1 and T2. The multicast codes opportunistically decode packets with short delay T1 when the channel is relatively better and with long delay T2 when the channel is worse. Simulations over multicast Gilbert-Elliott channels show that EMDS codes outperform other streaming codes for both users.
Pre-clinical study of BK-UM, a novel inhibitor of HB-EGF, for ovarian cancer therapy.

BACKGROUND/AIM Heparin-binding epidermal growth factor-like growth factor (HB-EGF), a member of the epidermal growth factor family, is a target for ovarian cancer therapy. The present study investigated the administration schedule of BK-UM, an anticancer agent targeting HB-EGF. MATERIALS AND METHODS The ovarian cancer cell line, RMG-I, was injected subcutaneously into five-week-old female nude mice. The BK-UM was administered intraperitoneally, using three administration schedules with different doses. The tumor volume was calculated every week. Statistical significance was assessed using the Mann-Whitney U-test. RESULTS At doses >0.1 mg/kg, BK-UM displayed significant antitumor effects, although the antitumor effects and body weights of mice did not significantly differ by dose or by three different administration schedules. At a dose <0.1 mg/kg, however, BK-UM had little inhibitory effect on tumor growth. CONCLUSION Daily administration of BK-UM, which has a potentially dose-dependent antitumor effect, may be the optimal schedule for clinical application.