Miracle-dz/UniFAR-FTUs huggingface dataset:
A role for cytoplasmic dynein and LIS1 in directed cell movement

Cytoplasmic dynein has been implicated in numerous aspects of intracellular movement. We recently found dynein inhibitors to interfere with the reorientation of the microtubule cytoskeleton during healing of wounded NIH3T3 cell monolayers. We now find that dynein and its regulators dynactin and LIS1 localize to the leading cell cortex during this process. In the presence of serum, bright diffuse staining was observed in regions of active ruffling. This pattern was abolished by cytochalasin D, and was not observed in cells treated with lysophosphatidic acid, conditions which allow microtubule reorientation but not forward cell movement. Under the same conditions, using total internal reflection fluorescence microscopy, clear punctate dynein/dynactin containing structures were observed along the sides and at the tips of microtubules at the leading edge. Overexpression of dominant negative dynactin and LIS1 cDNAs or injection of antidynein antibody interfered with the rate of cell migration. Together, these results implicate a leading edge cortical pool of dynein in both early and persistent steps in directed cell movement.
Global Routing Paradigm for System-on-Package

The true potential of three dimensional System-OnPackage (SOP) technology lies in its capability to integrate both active and passive components into a single high speed/density multi-layer packaging substrate. We propose a new interconnect-centric SOP global routing algorithm that handles arbitrary routing topologies and produces near optimal results. The contribution of this work is threefold: (i) modeling of the SOP routing resource, (ii) formulation of the new SOP global routing problem, and (iii) development of a fast and novel algorithm that considers the various design constraints unique to SOP. Our related experimental results demonstrate the effectiveness of our algorithm.
Social Dollars: The Economic Impact of Consumer Participation in a Firm-sponsored Brand Community

Many firms operate brand-specific social networks or “communities” online. This is motivated by the belief that community members become more engaged with the brand, and as a result, increase their activity with the firm. We label the revenue generated from this activity as “social dollars. ” This research tests for the existence and magnitude of social dollars via a difference-in-differences estimator using data from a multi-channel entertainment products retailer that launched an online brand community. We find that 19% of the post-launch revenue from community customers can be attributed to their joining the community. This result is robust across a variety of tests. In addition, social dollars persist over time, arise in both online and offline channels and affect all product categories sold by the firm. Regression analysis reveals that social connections – the number and importance of friend ties – and interactions – personal page displays – are positively linked to social dollars.
4-1BB Signaling Breaks the Tolerance of Maternal CD8+ T Cells That Are Reactive with Alloantigens

4-1BB (CD137, TNFRSF9), a member of the activation-induced tumor necrosis factor receptor family, is a powerful T-cell costimulatory molecule. It generally enhances CD8+ T responses and even breaks the tolerance of CD8+ T cells in an antigen-specific manner. In the present study we found that it was expressed in the placentas of pregnant mice and that its expression coincided with that of the immunesuppressive enzyme indoleamine 2,3-dioxygenase (IDO). Therefore, we investigated whether 4-1BB signaling is involved in fetal rejection using agonistic anti-4-1BB mAb and 4-1BB-deficient mice. Treatment with agonistic anti-4-1BB mAb markedly increased the rate of rejection of allogeneic but not syngeneic fetuses, and this was primarily dependent on CD8+ T cells. Complement component 3 (C3) seemed to be the effector molecule because 4-1BB triggering resulting in accumulation of C3 in the placenta, and this accumulation was also reversed by anti-CD8 mAb treatment. These findings demonstrate that 4-1BB triggering breaks the tolerance of CD8+ T cells to alloantigens in the placenta. Moreover, triggering 4-1BB protected the pregnant mice from Listeria monocytogenes (LM) infection, but led to rejection of semi-allogeneic fetuses. Therefore, given the cross-recognition of alloantigen by pathogen-reactive CD8+ T cells, the true function of 4-1BB may be to reverse the hypo-responsiveness of pathogen-reactive CD8+ T cells in the placenta in cases of infection, even if that risks losing the fetus.
A case for redundant arrays of inexpensive disks (RAID)

In the late 80s, CPU and memory performance were both increasing at exponential rates, enabled by transistor size, SRAMs and caches. In contrast, disks, as mechanical devices, were dominated by the seek times. Basic speedup equations proved that unless I/O could keep up with other system aspects, overall performance would diminish commensurately. An alternative solution was proposed that used an array of inexpensive disks, offering better read and write performance through parallelism, lower power consumption than expensive disks and long term reliability. The system would also be responsive for different applications, such as scientific processing requiring high read bandwidth and transaction processing systems that perform many small, random writes.
Yeast AEP3p Is an Accessory Factor in Initiation of Mitochondrial Translation*

Initiation of protein synthesis in mitochondria and chloroplasts normally uses a formylated initiator methionyl-tRNA (fMet-tRNAfMet). However, mitochondrial protein synthesis in Saccharomyces cerevisiae can initiate with nonformylated Met-tRNAfMet, as demonstrated in yeast mutants in which the nuclear gene encoding mitochondrial methionyl-tRNA formyltransferase (FMT1) has been deleted. The role of formylation of the initiator tRNA is not known, but in vitro formylation increases binding of Met-tRNAfMet to translation initiation factor 2 (IF2). We hypothesize the existence of an accessory factor that assists mitochondrial IF2 (mIF2) in utilizing unformylated Met-tRNAfMet. This accessory factor might be unnecessary when formylated Met-tRNAfMet is present but becomes essential when only the unformylated species are available. Using a synthetic petite genetic screen in yeast, we identified a mutation in the AEP3 gene that caused a synthetic respiratory-defective phenotype together with Δfmt1. The same aep3 mutation also caused a synthetic respiratory defect in cells lacking formylated Met-tRNAfMet due to loss of the MIS1 gene that encodes the mitochondrial C1-tetrahydrofolate synthase. The AEP3 gene encodes a peripheral mitochondrial inner membrane protein that stabilizes mitochondrially encoded ATP6/8 mRNA. Here we show that the AEP3 protein (Aep3p) physically interacts with yeast mIF2 both in vitro and in vivo and promotes the binding of unformylated initiator tRNA to yeast mIF2. We propose that Aep3p functions as an accessory initiation factor in mitochondrial protein synthesis.
A Leishmania amazonensis ZIP family iron transporter is essential for parasite replication within macrophage phagolysosomes

Infection of mammalian hosts with Leishmania amazonensis depends on the remarkable ability of these parasites to replicate within macrophage phagolysosomes. A critical adaptation for survival in this harsh environment is an efficient mechanism for gaining access to iron. In this study, we identify and characterize LIT1, a novel L. amazonensis membrane protein with extensive similarity to IRT1, a ZIP family ferrous iron transporter from Arabidopsis thaliana. The ability of LIT1 to promote iron transport was demonstrated after expression in yeast and in L. amazonensis LIT1-null amastigotes. Endogenous LIT1 was only detectable in amastigotes replicating intracellularly, and its intracellular expression was accelerated under conditions predicted to result in iron deprivation. Although L. amazonensis lacking LIT1 grew normally in axenic culture and had no defects differentiating into infective forms, replication within macrophages was abolished. Consistent with an essential role for LIT1 in intracellular growth as amastigotes, Δlit1 parasites were avirulent. After inoculation into highly susceptible mice, no lesions were detected, even after extensive periods of time. Despite the absence of pathology, viable Δlit1 parasites were recovered from the original sites of inoculation, indicating that L. amazonensis can persist in vivo independently of the ability to grow in macrophages. Our findings highlight the essential role played by intracellular iron acquisition in Leishmania virulence and identify this pathway as a promising target for therapeutic intervention.
SEARS: Space efficient and reliable storage system in the cloud

Today's cloud storage services must offer storage reliability and fast data retrieval for large amount of data without sacrificing storage cost. We present SEARS, a cloud-based storage system which integrates erasure coding and data deduplication to support efficient and reliable data storage with fast user response time. With proper association of data to storage server clusters, SEARS provides flexible mixing of different configurations, suitable for real-time and archival applications. Our prototype implementation of SEARS over Amazon EC2 shows that it outperforms existing storage systems in storage efficiency and file retrieval time. For 3 MB files, SEARS delivers retrieval time of 2.5 s compared to 7 s with existing systems.
Properties of sediments deposited in a fluid with different pH

Abstract The effect of pH on the physical and mechanical properties of a sediment was investigated through a set of experimental tests. The sediment was formed from deposition of suspended particles in a fluid. Two different types of clay soil were suspended in fluids with different pH (2, 4, 7, 9 and 11) in cylindrical tubes with volume of 1 liter and also in special cylindrical reservoirs. The height of the sediment was measured in the cylindrical tube until equilibrium was achieved. The sediment deposited in the reservoirs was dried in air and then Atterberg limit, compaction and unconfined compressive strength (UCS) tests were conducted on samples prepared from each sediment. The results showed that the final height of the settled sediment is a function of pH; the height of sediment is increased with increasing the pH. Also, the Atterberg limits increased with increasing the pH. The maximum dry unit weight and optimum water content decreased and increased with increasing the pH. The final strength of the sediment decreased with increasing pH. Based on the SEM analysis, it was found that the values of pH influence the properties of the formed sediments.
Bias Current Generators with Wide Dynamic Range

Mixed-signal or analog chips often require a wide range of biasing currents that are independent of process and supply voltage and that are proportional to absolute temperature. This paper describes CMOS circuits that we use to generate a set of fixed bias currents typically spanning six decades at room temperature down to a few times the transistor off-current. A bootstrapped current reference with a new startup and power-control mechanism generates a master current, which is successively divided by a current splitter to generate the desired reference currents. These references are nondestructively copied to form the chip’s biases. Measurements of behavior, including temperature effects from 1.6 and 0.35 μ implementations, are presented and nonidealities are investigated. Temperature dependence of the transistor off-current is investigated because it determines the lower limit for generated currents. Readers are directed to a design kit that allows easy generation of the complete layout for a bias generator with a set of desired currents for scalable MOSIS CMOS processes.
Multiscale computations for flow and transport in porous media

Many problems of fundamental and practical importance have multiple scale solutions. The direct numerical solution of multiple scale problems is difficult to obtain even with modern supercomputers. The major difficulty of direct solutions is the scale of computation. The ratio between the largest scale and the smallest scale could be as large as 10^5 in each space dimension. From an engineering perspective, it is often sufficient to predict the macroscopic properties of the multiple-scale systems, such as the effective conductivity, elastic moduli, permeability, and eddy diffusivity. Therefore, it is desirable to develop a method that captures the small scale features. This paper reviews some of the recent advances in developing systematic multiscale methods with particular emphasis on multiscale finite element methods with applications to flow and transport in heterogeneous porous media. This manuscript is not intended to be a general survey paper on this topic. The discussion is limited by the scope of the lectures and expertise of the author.
A book chapter template < 1 Shape Matching for Foliage Database Retrieval

Short overview of the Chapter—Computer-aided foliage image retrieval systems have the potential to dramatically speed up the process of plant species identification. Despite previous research, this problem remains challenging due to the large intra-class variability and inter-class similarity of leaves. This is particularly true when a large number of species are involved. In this chapter, we present a shape-based approach, the inner-distance shape context, as a robust and reliable solution. We show that this approach naturally captures part structures and is appropriate to the shape of leaves. Furthermore, we show that this approach can be easily extended to include texture information arising from the veins of leaves. We also describe a real electronic field guide system that uses our approach. The effectiveness of the proposed method is demonstrated in experiments on two leaf databases involving more than 100 species and 1000 leaves.
Effect of venous shear stress on CD18-mediated neutrophil adhesion to cultured endothelium.

The CD11/CD18 family of glycoproteins has been identified as a mediator of a number of adhesive interactions crucial to inflammatory responses. Using a monoclonal antibody (MoAb) against CD18 (TS1/18), the role of these molecules in polymorphonuclear neutrophil (PMNL) adhesion to cultured primary human umbilical vein endothelial cells (HUVEC) was examined under venous flow conditions. Incubation of PMNL with TS1/18 (anti-CD18) did not inhibit PMNL adhesion to interleukin-1 (IL-1)-treated HUVEC at 2.0 dynes/cm2 (TS1/18-treated 305 +/- 58 PMNL/mm2 v 334 +/- 63 PMNL/mm2 on control). Furthermore, incubation of HUVEC with R6.5. D6, an MoAb against intercellular adhesion molecule-1 (ICAM-1) did not significantly inhibit PMNL adhesion to IL-1-treated HUVEC at 2.0 dynes/cm2 (P greater than .3). In contrast to the lack of inhibition of adhesion under conditions of flow, incubation of PMNL with TS1/18 reduced PMNL adherence in static adhesion assays. PMNL migration beneath HUVEC monolayers has been shown to be stimulated by 4-hour IL-1 treatment. TS1/18 and R6.5. D6 significantly inhibited migration of PMNL beneath IL-1-treated HUVEC monolayers under flow conditions by slightly more than 80% (P less than .005). In flow experiments with CD18-deficient PMNL, virtually no transendothelial migration was observed. The effect of FMLP (10(-8) mol/L) on PMNL adhesion to untreated HUVEC at wall shear stresses ranging from 0.25 to 2.0 dynes/cm2 was also investigated. FMLP had little effect on PMNL adherence at shear stresses above 0.5 dynes/cm2 (P greater than .45). In response to FMLP exposure at lower wall shear stresses, PMNL adherence to untreated HUVEC increased 6.9-fold at 0.5 dynes/cm2 (P less than .001). At 0.25 dynes/cm2, FMLP stimulation increased PMNL adherence to untreated HUVEC 6.5-fold compared with controls (P less than .005), and FMLP failed to make CD18-deficient PMNL more adherent. In experiments with PMNL pretreated with TS1/18 (anti-CD18), there was a 67% inhibition of FMLP-stimulated adhesion at 0.5 dynes/cm2 (P less than .025). The upper threshold of CD18-mediated PMNL adhesion appears to be between 0.5 and 1.0 dyne/cm2. Above these wall shear stresses, the initial attachment of PMNL to cultured endothelium was mediated almost exclusively by CD18-independent mechanisms. By simulating some of the flow parameters in the microcirculation with well-characterized shear forces, PMNL adhesion by CD18-independent and dependent mechanisms can be differentiated. These data also indicate that CD18 is an important mediator of transendothelial migration by PMNL, which have attached to the endothelium by a CD18-independent mechanism.
Toxoplasma gondii Uses Sulfated Proteoglycans for Substrate and Host Cell Attachment

ABSTRACT Toxoplasma gondii is an obligate intracellular parasite that actively invades a wide variety of vertebrate cells, although the basis of this pervasive cell recognition is not understood. We demonstrate here that binding to the substratum and to host cells is partially mediated by interaction with sulfated glycosaminoglycans (GAGs). Addition of excess soluble GAGs blocked parasite attachment to serum-coated glass, thereby preventing gliding motility of extracellular parasites. Similarly, excess soluble GAGs decreased the attachment of parasites to human host cells from a variety of lineages, including monocytic, fibroblast, endothelial, epithelial, and macrophage cells. The inhibition of parasite attachment by GAGs was observed with heparin and heparan sulfate and also with chondroitin sulfates, indicating that the ligands for attachment are capable of recognizing a broad range of GAGs. The importance of sulfated proteoglycan recognition was further supported by the demonstration that GAG-deficient mutant host cells, and wild-type cells treated enzymatically to remove GAGs, were partially resistant to parasite invasion. Collectively, these studies reveal that sulfated proteoglycans are one determinant used for substrate and cell recognition by Toxoplasma. The widespread distribution of these receptors may contribute to the broad host and tissue ranges of this highly successful intracellular parasite.
Robust , Bistable , BMP-Dependent Patterning of the Drosophila Blastoderm Embryo

Supporting online material (SOM) 2 SUMMARY In many developing systems, the developmental fate of a cell is determined by its position in a time-independent spatial distribution of a morphogen. However, during dorsal-ventral patterning in the Drosophila embryo, signaling begins broad and low, and refines to a narrow, high intensity band. This suggests that cells respond to the local transient morphogen distribution that results from interactions between bone morphogenetic proteins (BMPs), their receptors, the BMP binding proteins Sog and Tsg, the metalloprotease Tld, and a putative positively-regulated component that locally enhances surface binding of BMPs within the region of high pMad signaling. We develop a computational model for dorsal surface patterning and show that when positive feedback of a cell surface BMP binding protein is incorporated, a bistability in the kinetic interactions transduces the transient BMP distribution into a switch-like distribution of BMP-bound receptor. We also show that positive feedback leads to the observed contraction of the signaling because cells near the dorsal midline out-compete adjacent lateral cells for limited amounts of BMP. In the model, cells interpret the morphogen distribution by differentiating according to the history of their exposure, rather than to a threshold concentration in a static spatial gradient of the morphogen.
Altered osmotic swelling behavior of proteoglycan-depleted bovine articular cartilage using high frequency ultrasound

Swelling behavior is an electrochemical mechanical property of articular cartilage. It plays an important role in weight bearing and joint lubrication. In this study, the altered transient and inhomogeneous swelling behavior of the degenerated articular cartilage was observed and quantified in situ using ultrasound. Three groups of bovine patellar articular cartilage samples (n = 10 × 3) were obtained and digested by trypsin for 10, 20 and 30 min respectively to mimic different levels of degeneration. The osmotic-free shrinkage and swelling behavior induced by changing the concentration of the bathing saline solution from 0.15 M to 2 M and then back to 0.15 M were characterized using high-frequency ultrasound (central frequency = 35 MHz) before and after digestion. It was found that the degenerated cartilage specimens showed a weaker shrinkage–swelling behavior compared with the normal cartilage samples. However, no significant differences in the peak shrinkage or swelling strains were observed between different groups. The absolute values of the peak shrinkage strain significantly (p < 0.05) decreased by 45.4%, 42.1% and 50.6% respectively after the trypsin digestion for 10, 20 and 30 min, but such significance was not demonstrated for the peak swelling strains. Due to the potential alterations in the collagen-PG matrix during trypsin digestion, the correlation between the swelling strain and the shrinkage strain of the degenerated samples changed slightly in comparison with the normal samples. The proposed ultrasound method has been successfully used to measure the transient and inhomogeneous swelling behavior of the degenerated articular cartilage and has the potential for the characterization of osteoarthritis.
Similarity Ratio Based Adaptive Mahalanobis Distance Algorithm to Generate SAR Superpixels

ABSTRACT Superpixel algorithms are aimed to partition an image into multiple similar sized segments based on similarity and proximity of pixels. In the heterogeneous regions, the boundaries of the objects should adhere well to the superpixels, and in the homogeneous parts, the pixels should be clustered so that compact superpixels are generated. Since speckle noise inherently exists in synthetic aperture radar (SAR) images their segmentation is considerably more difficult. In this article, the first contribution is the use of Mahalanobis distance instead of Euclidian, so that the superpixels can have elongated shapes to fit the complex structure of the real world better. Secondly, this geometric distance term is combined with similarity ratio term, which leads to even better performance on SAR images. Finally, the global constant that determines the relative importance of geometric proximity and pixel intensity similarity terms, whose best value should be chosen for each image, is considered. Instead of a global constant, its value is determined individually for each superpixel pair as a function of the average values of the superpixels. Experimental results with synthetic and real images demonstrate that the proposed approach has better segmentation performance than many of the existing state-of-the-art algorithms.
ACTIVE AND ASSISTED LIVING: A COMPREHENSIVE REVIEW OF ENABLING TECHNOLOGIES AND SCENARIOS

From the past few decades entire world is witnessing the phenomenon of population ageing as a result of life longevity and declining birth rate of modern society. India is also not immune to this demographic change and will have major socio-economic consequences over the period of time. Information and Communication Technologies (ICT) will make the targeted interventions to provide assistance to the older adults to improve their quality of life, stay healthier and live independently for a time. Active and Assisted Living (AAL) is one such innovative targeted technology to provide quality healthcare and rehabilitation services to the impaired seniors. In this paper we present comprehensive survey to monitor the recent trends in the realm of AAL. First we discuss about the generic overview of AAL and Ambient Intelligence (AmI). Next, we highlight the relevance of enabling technologies for AAL. Then we review the various trending scenarios of AAL and major research projects being carried out across the world. Finally, we conclude by proposing some possible directions for the future work in the area of AAL.