Miracle-dz/UniFAR-FTUs huggingface dataset:
Metrics for analysis and optimization of grasps and fixtures

We develop two quality measures for the analysis and optimization of grasps and fixtures. The first metric is a measure of stability and is obtained by analyzing the effect of small perturbations in the position of the grasped object or small disturbance forces on the grasped object The second metric is a measure of robustness to errors in the positions of the fixture elements. In addition, we explore the effect that the stiffness of the fixture elements has on these two quality measures and propose a design optimization approach to maximize stability and robustness to errors.
Targeted nutlin-3a loaded nanoparticles inhibiting p53-MDM2 interaction: novel strategy for breast cancer therapy.

AIM The objective of the present study is to prepare and characterize nutlin-3a loaded polymeric poly(lactide-co-glycolide) nanoparticles (NPs) surface functionalized with transferrin ligand, to deliver the encapsulated drug in a targeted manner to its site of action and to evaluate the efficacy of the nanoformulation in terms of its cellular uptake, cell cytotoxicity, cell cycle arrest, apoptosis and activation of p53 pathway at molecular level in MCF-7 breast cancer cell line. METHOD Nutlin-3a loaded poly(lactide-co-glycolide) NPs were prepared following the single oil-in-water emulsion method. Physicochemical characterization of the formulation included size and surface charge measurement, transmission electron microscopy characterization, study of surface morphology using scanning electron microscopy, Fourier-transform infrared spectral analysis and in vitro release kinetics studies. Furthermore, targeting ability of the conjugated system was assessed by cellular uptake and cell cytotoxicity studies in an in vitro cell model. Molecular basis of nutlin-3a-mediated p53 activation pathway was investigated by western blot analysis. Inhibition of cell cycle progression and apoptosis was evaluated by flow cytometry. RESULTS Physiochemical characterization of the formulations revealed that nutlin-3a was efficiently encapsulated in the nanoparticulate system, reaching an encapsulation efficiency of approximately 80% with size of approximately 220 nm and negative zeta potential of approximately -10.4 mV. Higher cellular uptake efficiency of the conjugated system proved the effectiveness of targeted therapy. IC(50) values, as determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium assay, showed superior antiproliferative activity of transferrin-conjugated NPs over unconjugated NPs and native nutlin-3a, owing to enhanced cellular uptake by cancer cells. At the molecular level the conjugated system showed enhanced activation of p53 pathway in comparison to native drug as evident from western blot analysis. Augmented cell cycle arrest and apoptosis was exhibited by the conjugated system. Thus, our results suggest that transferrin-conjugated nutlin-3a loaded NPs could be a potential drug carrier system for targeted delivery of potent anticancer drug nutlin-3a for breast cancer therapy.
Algorithm for optimal mode scheduling in switched systems

This paper considers the problem of computing the schedule of modes in an autonomous switched dynamical system, that minimizes a cost functional defined on the trajectory of the system's continuous state variable. It proposes an algorithm that modifies a finite but unbounded number of modes at each iteration, whose computational workload at the various iterations appears to be independent on the number of modes being changed. The algorithm is based on descent directions defined by Gaâteaux differentials of the performance function with respect to variations in mode-sequences , and its convergence to (local) minima is established in the framework of optimality functions and minimizing sequences, devised by Polak for infinite-dimensional optimization problems.
The Use of Clustering Techniques for Language Modeling V Application to Asian Language

Cluster-based n-gram modeling is a variant of normal word-based n-gram modeling. It attempts to make use of the similarities between words. In this paper, we present an empirical study of clustering techniques for Asian language modeling. Clustering is used to improve the performance (i.e. perplexity) of language models as well as to compress language models. Experimental tests are presented for cluster-based trigram models on a Japanese newspaper corpus and on a Chinese heterogeneous corpus. While the majority of previous research on word clustering has focused on how to get the best clusters, we have concentrated our research on the best way to use the clusters. Experimental results show that some novel techniques we present work much better than previous methods, and achieve more than 40% size reduction at the same level of perplexity.
Riemerella anatipestifer infection in domestic ducks in Japan, 2014

The outbreak of Riemerella anatipestifer (RA) infection has been confirmed in meat-type domestic ducks (Anas platyrhynchos) for the first time in 27 years in Japan. In January 2014, increased mortality in a 14- to 21-day-old duck flock was reported to veterinary officials by the owner. The affected ducks exhibited reduced movement, ataxia and dorsal recumbency with leg paddling. Pathological findings were typical for an RA infection. Fibrinous and heterophilic pericarditis, airsacculitis, perihepatitis, ventriculitis and meningitis were observed. The bacterial isolate from duck organs was identified as RA by PCR-based 16S ribosomal RNA sequencing.
Preparing Biological Samples for Analysis by High Vacuum Techniques

Abstract Time of flight secondary ion mass spectrometry (ToF-SIMS) and scanning electron microscopy (SEM) provide valuable complementary information about the molecular composition and morphology of biological samples, but both techniques are performed under high vacuum, which is not compatible with hydrated samples. Designing a suitable method to prepare biological (hydrated) samples for high vacuum conditions is important to obtain reliable and scientifically meaningful results from ToF-SIMS and SEM and to enable the routine use of these techniques for characterization. This article will compare freeze-drying and critical point drying for preparing adherent and nonadherent cells for ToF-SIMS and SEM analyses.
Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages

Aims In ecology and conservation biology, the number of species counted in a biodiversity study is a key metric but is usually a biased underestimate of total species richness because many rare species are not detected. Moreover, comparing species richness among sites or samples is a statistical challenge because the observed number of species is sensitive to the number of individuals counted or the area sampled. For individual-based data, we treat a single, empirical sample of species abundances from an investigator-defined species assemblage or community as a reference point for two estimation objectives under two sampling models: estimating the expected number of species (and its unconditional variance) in a random sample of (i) a smaller number of individuals (multinomial model) or a smaller area sampled (Poisson model) and (ii) a larger number of individuals or a larger area sampled. For sample-based incidence (presence–absence) data, under a Bernoulli product model, we treat a single set of species incidence frequencies as the reference point to estimate richness for smaller and larger numbers of sampling units. Methods The first objective is a problem in interpolation that we address with classical rarefaction (multinomial model) and Coleman rarefaction (Poisson model) for individual-based data and with sample-based rarefaction (Bernoulli product model) for incidence frequencies. The second is a problem in extrapolation that we address with sampling-theoretic predictors for the number of species in a larger sample (multinomial model), a larger area (Poisson model) or a larger number of sampling units (Bernoulli product model), based on an estimate of asymptotic species richness. Although published methods exist for many of these objectives, we bring them together here with some new estimators under a unified statistical and notational framework. This novel integration of mathematically distinct approaches allowed us to link interpolated (rarefaction) curves and extrapolated curves to plot a unified species accumulation curve for empirical examples. We provide new, unconditional variance estimators for classical, individual-based rarefaction and for Coleman rarefaction, long missing from the toolkit of biodiversity measurement. We illustrate these methods with datasets for tropical beetles, tropical trees and tropical ants.
Error Correcting Output Coding-Based Conditional Random Fields for Web Page Prediction

Web page prefetching has been used efficiently to reduce the access latency problem of the Internet, its success mainly relies on the accuracy of Web page prediction. As powerful sequential learning models, conditional random fields (CRFs) have been used successfully to improve the Web page prediction accuracy when the total number of unique Web pages is small. However, because the training complexity of CRFs is quadratic to the number of labels, when applied to a Web site with a large number of unique pages, the training of CRFs may become very slow and even intractable. In this paper, we decrease the training time and computational resource requirements of CRFs training by integrating error correcting output coding (ECOC) method. Moreover, since the performance of ECOC-based methods crucially depends on the ECOC code matrix in use, we employ a coding method, search coding, to design the code matrix of good quality.
Characterizing virtual memory write references for efficient page replacement in NAND flash memory

Recently, NAND flash memory is being used as the swap space of virtual memory as well as the file storage of embedded systems. Since temporal locality is dominant in page references of virtual memory, LRU and its approximated algorithms are widely used. However, we show that this is not true for write references. We analyze the characteristics of virtual memory read and write references separately, and find that the temporal locality of write references is weak and irregular. Based on this observation, we present a new page replacement algorithm that uses different strategies for read and write operations in predicting the re-reference likelihood of pages. For read operations, temporal locality alone is used, but for write operations, write frequency as well as temporal locality is used. The algorithm partitions the memory space into a read area and a write area to keep track of their reference patterns precisely, and then adjusts their sizes dynamically based on their reference patterns and I/O costs. Though the algorithm has no external parameter to tune, it performs better than CLOCK, CAR, and CFLRU by 20–66%. It also supports optimized implementations for virtual memory systems.
Tax Incidence in the Presence of Tax Evasion

This paper studies the effect of tax evasion on the economic incidence of sales taxes. We design a laboratory experiment in which buyers and sellers trade a fictitious good in double auction markets. A per-unit tax is imposed on sellers, and sellers in the treatment group are provided the opportunity to evade the tax whereas sellers in the control group are not. We find that the market equilibrium price in the treatment group is economically and statistically lower than in the control group. This result is consistent with a theoretical model in which access to evasion opportunities reduces the effective tax rate and therefore dampens real behavioral responses. Our findings suggest that the benefits of tax evasion are not limited to the side of the market with access to evasion but are partly shifted to the non-evading side of the market. We discuss the implications of our findings for the distributional and welfare effects of taxes.
Connexin 43 Expression on Peripheral Blood Eosinophils: Role of Gap Junctions in Transendothelial Migration

Eosinophils circulate in the blood and are recruited in tissues during allergic inflammation. Gap junctions mediate direct communication between adjacent cells and may represent a new way of communication between immune cells distinct from communication through cytokines and chemokines. We characterized the expression of connexin (Cx)43 by eosinophils isolated from atopic individuals using RT-PCR, Western blotting, and confocal microscopy and studied the biological functions of gap junctions on eosinophils. The formation of functional gap junctions was evaluated measuring dye transfer using flow cytometry. The role of gap junctions on eosinophil transendothelial migration was studied using the inhibitor 18-a-glycyrrhetinic acid. Peripheral blood eosinophils express Cx43 mRNA and protein. Cx43 is localized not only in the cytoplasm but also on the plasma membrane. The membrane impermeable dye BCECF transferred from eosinophils to epithelial or endothelial cells following coculture in a dose and time dependent fashion. The gap junction inhibitors 18-a-glycyrrhetinic acid and octanol did not have a significant effect on dye transfer but reduced dye exit from eosinophils. The gap junction inhibitor 18-a-glycyrrhetinic acid inhibited eosinophil transendothelial migration in a dose dependent manner. Thus, eosinophils from atopic individuals express Cx43 constitutively and Cx43 may play an important role in eosinophil transendothelial migration and function in sites of inflammation.
Disruption of the FATB Gene in Arabidopsis Demonstrates an Essential Role of Saturated Fatty Acids in Plant Growth Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.008946.

Acyl-acyl carrier protein thioesterases determine the amount and type of fatty acids that are exported from the plastids. To better understand the role of the FATB class of acyl-acyl carrier protein thioesterases, we identified an Arabidopsis mutant with a T-DNA insertion in the FATB gene. Palmitate (16:0) content of glycerolipids of the mutant was reduced by 42% in leaves, by 56% in flowers, by 48% in roots, and by 56% in seeds. In addition, stearate (18:0) was reduced by 50% in leaves and by 30% in seeds. The growth rate was reduced in the mutant, resulting in 50% less fresh weight at 4 weeks compared with wild-type plants. Furthermore, mutant plants produced seeds with low viability and altered morphology. Analysis of individual glycerolipids revealed that the fatty acid composition of prokaryotic plastid lipids was largely unaltered, whereas the impact on eukaryotic lipids varied but was particularly severe for phosphatidylcholine, with a >4-fold reduction of 16:0 and a 10-fold reduction of 18:0 levels. The total wax load of fatb-ko plants was reduced by 20% in leaves and by 50% in stems, implicating FATB in the supply of saturated fatty acids for wax biosynthesis. Analysis of C18 sphingoid bases derived from 16:0 indicated that, despite a 50% reduction in exported 16:0, the mutant cells maintained wild-type levels of sphingoid bases, presumably at the expense of other cell components. The growth retardation caused by the fatb mutation was enhanced in a fatb-ko act1 double mutant in which saturated fatty acid content was reduced further. Together, these results demonstrate the in vivo role of FATB as a major determinant of saturated fatty acid synthesis and the essential role of saturates for the biosynthesis and/or regulation of cellular components critical for plant growth and seed development.
Hrs1/Med3 Is a Cyc8-Tup1 Corepressor Target in the RNA Polymerase II Holoenzyme*

The Srb/Mediator, a multisubunit subcomplex of the RNA polymerase II (RNA pol II) holoenzyme has been proposed to function as a control panel regulating transcription in response to gene-specific activator proteins. In this report, we identify the Mediator subunit Hrs1/Med3 as a physical target for Cyc8-Tup1, a yeast transcriptional corepressor. Two-hybrid and glutathioneS-transferase interaction assays show that Hrs1 can associate directly with Cyc8-Tup1. Moreover, affinity chromatography experiments, using yeast protein extracts, reveal that Cyc8-Tup1 co-purifies with Hrs1 and with additional Mediator subunits in a Hrs1-dependent manner. These observations suggest that Cyc8-Tup1 contacts the Mediator complex via its interaction with the Hrs1 subunit. Further on, genetic analysis indicates that increased Hrs1 dosage can alleviate Cyc8-Tup1-mediated repression, suggesting that Hrs1/Mediator's function is inhibited upon its interaction with Cyc8-Tup1. Finally, artificial holoenzyme recruitment assays support a model by which the contact between the corepressor and the Hrs1/Mediator may prevent pol II holoenzyme recruitment to the core promoter. These data, together with previous genetic evidence, establish a functional and physical interaction between the Cyc8-Tup1 corepressor and the RNA pol II holoenzyme and support a central role of the Mediator complex in transcriptional repression.
Computational Modeling of Nanoparticle Coalescence

The coalescence of nanoclusters fabricated in the gas phase is a fundamental growth mechanism determining cluster shapes, sizes, compositions, and structures, with resultant effects on practically all of their physical and chemical properties. Furthermore, coalescence can affect properties of larger structures that consist of nanoparticles as their elementary building blocks, such as the fractal dimension of cluster aggregates and the porosity and conductance of thin films. Therefore, it comes as no surprise that a great body of research, both experimental and theoretical, has focused on nanoparticle coalescence over the course of the past few decades. This review attempts to summarize the most important recent results from computational studies on nanoparticle coalescence and draw parallels between theoretical and experimental findings. The approach used here aspires to explain nanoparticle coalescence within the framework of a single intuitive narrative by integrating previous results obtained using various methods by the authors and others. Simultaneously, it is discussed where understanding and controlling (i.e., enhancing or inhibiting) nanoparticle coalescence can have great technological interest.
On Reducing the Number of Visual Words in the Bag-of-Features Representation

A new class of applications based on visual search engines are emerging, especially on smart-phones that have evolved into powerful tools for processing images and videos. The state-of-the-art algorithms for large visual content recognition and content based similarity search today use the "Bag of Features" (BoF) or "Bag of Words" (BoW) approach. The idea, borrowed from text retrieval, enables the use of inverted files. A very well known issue with this approach is that the query images, as well as the stored data, are described with thousands of words. This poses obvious efficiency problems when using inverted files to perform efficient image matching. In this paper, we propose and compare various techniques to reduce the number of words describing an image to improve efficiency and we study the effects of this reduction on effectiveness in landmark recognition and retrieval scenarios. We show that very relevant improvement in performance are achievable still preserving the advantages of the BoF base approach.
Verb-centered Sentiment Inference with Description Logics

We introduce description logics as a means to carry out sentiment inferences triggered by some verbs on their seman- tic roles. Verbs might impose polar effects on some roles, but also have polar expectations on other roles. For instance, an entity inherits a positive polarity just by being actor of some verb (“she succeeds”). More complicated scenarios arise if we take subclause embeddings, negation and polarity conflicts into consideration. Polarity propagation and effect inversion need to be coped with, then. We have implemented a prototype in OWL covering a substantial subset of our verb lexicon covering about 140 German verbs.
Biomarkers in Lung Diseases : from Pathogenesis to Prediction to New Therapies A genetic variant of cortactin linked to acute lung injury impairs lamellipodia dynamics and endothelial wound healing

Sangwook Choi, Sara M. Camp, Arkaprava Dan, Joe G. N. Garcia, Steven M. Dudek, and Deborah E. Leckband Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, Illinois; Department of Medicine, University of Arizona, Tucson, Arizona; Division of Pulmonary, Critical Care, Sleep, and Allergy, University of Illinois Hospital and Health Sciences System, Chicago, Illinois; and Department of Chemistry, University of Illinois, Urbana, Illinois
Diagnosing Common Carotid Artery Agenesis Using Duplex Ultrasound

The complete absence of a common carotid artery, also known as common carotid artery (CCA) agenesis, is a well-described yet extremely rare congenital anomaly. Most carotid system anomalies are related to origins of the external or internal carotid arteries. All such anomalies are typically asymptomatic unless associated with a concomitant arterial lesion that results in a workup for symptomatic intracerebral pathology or a focal neurological deficit. The literature is scant on the topic, being limited to singular case reports. We report 3 cases of CCA agenesis and provide the readers with insightful data on the available literature.
Maintaining Performance while Saving Energy on Wireless LANs

Minimizing the energy consumption of wireless network interfaces is crucial in the design of battery-powered mobile computing devices. The IEEE 802.11 wireless LAN specification describes a power-saving mode which allows the network interface on the mobile device to enter a sleep mode when the link is idle; periodically, the mobile device must wake up to listen to beacons from the access point which indicate if it has any buffered data. This work first presents detailed measurements which show that when TCP is run over existing implementations of the 802.11 power-saving mode, performance suffers because otherwise fast round-trip-times are rounded up to 100 ms. The proposed solution is the Stay-Awake scheme which delays entering sleep mode for a short period of time after the link is active. This work also determines that in typical web browsing traffic scenarios existing 802.11 power-saving mode implementations will spend most of their energy sleeping and listening to beacons during relatively long idle periods. The proposed improvement is ListenInterval-Backoff which allows the network interface to sleep for longer periods of time when the link remains idle. The combination of these proposed power-saving enhancements is shown to reduce the additional per-page delay incurred by the power-saving mode from a mean of around 70% to 3% with negligible change in the overall energy consumption, or to reduce the per-page delay to 10% while reducing the overall energy by 20%.