Miracle-dz/UniFAR-FTUs huggingface dataset:
Transient Activation of Meox1 Is an Early Component of the Gene Regulatory Network Downstream of Hoxa2

ABSTRACT Hox genes encode transcription factors that regulate morphogenesis in all animals with bilateral symmetry. Although Hox genes have been extensively studied, their molecular function is not clear in vertebrates, and only a limited number of genes regulated by Hox transcription factors have been identified. Hoxa2 is required for correct development of the second branchial arch, its major domain of expression. We now show that Meox1 is genetically downstream from Hoxa2 and is a direct target. Meox1 expression is downregulated in the second arch of Hoxa2 mouse mutant embryos. In chromatin immunoprecipitation (ChIP), Hoxa2 binds to the Meox1 proximal promoter. Two highly conserved binding sites contained in this sequence are required for Hoxa2-dependent activation of the Meox1 promoter. Remarkably, in the absence of Meox1 and its close homolog Meox2, the second branchial arch develops abnormally and two of the three skeletal elements patterned by Hoxa2 are malformed. Finally, we show that Meox1 can specifically bind the DNA sequences recognized by Hoxa2 on its functional target genes. These results provide new insight into the Hoxa2 regulatory network that controls branchial arch identity.
3D beamforming for wireless data centers

Contrary to prior assumptions, recent measurements show that data center traffic is not constrained by network bisection bandwidth, but is instead prone to congestion loss caused by short traffic bursts. Compared to the cost and complexity of modifying data center architectures, a much more attractive option is to augment wired links with flexible wireless links in the 60 GHz band. Current proposals, however, are severely constrained by two factors. First, 60 GHz wireless links are limited by line-of-sight, and can be blocked by even small obstacles between the endpoints. Second, even beamforming links leak power, and potential interference will severely limit concurrent transmissions in dense data centers. In this paper, we explore the feasibility of a new wireless primitive for data centers, 3D beamforming. We explore the design space, and show how bouncing 60 GHz wireless links off reflective ceilings can address both link blockage and link interference, thus improving link range and number of current transmissions in the data center.
Multilineage differentiation potential of cells isolated from the human amniotic membrane

The human amniotic membrane (HAM) contains two cell types from different embryological origins. Human amnion epithelial cells (hAECs) are derived from the embryonic ectoderm, while human amnion mesenchymal stromal cells (hAMSCs) are derived from the embryonic mesoderm. In this study, we localized, isolated, quantified and phenotypically characterized HAM‐derived cells and analysed their in vitro differentiation potential towards mesodermal cell lineages. Human amnion‐derived cells were isolated and characterized by flow cytometry. Immunohistochemistry and quantitative real‐time reverse transcription‐polymerase chain reaction studies were performed for the analysis of multipotentiality. Immunophenotypic characterization of both cell types demonstrated the presence of the common, well‐defined human mesenchymal stem cell (MSC) markers (CD90, CD44, CD73, CD166, CD105, CD29), as well as the embryonic stem‐cell markers SSEA‐4 and STRO‐1. Phenotypes of both cell populations were maintained from passages P0 to P9. The assessment of multilineage potential demonstrated that the hAMSCs showed greater adipogenic and chondrogenic potential. Both populations had the ability to retain their capacity for differentiation during culture passages from P0 to P4. Our data demonstrate the successful localization and isolation of hAMSCs and hAECs from the HAM. Both cell populations possessed similar immunophenotype. However, they differed in cell yield and multipotential for differentiation into the major mesodermal lineages. Our functional differentiation studies demonstrated that hAMSCs possess a much greater mesodermal differentiation capacity than hAECs. These considerations will be important for use of these cells for cell therapy. J. Cell. Biochem. 111: 846–857, 2010. © 2010 Wiley‐Liss, Inc.
3D morphable face models revisited

In this paper we revisit the process of constructing a high resolution 3D morphable model of face shape variation. We demonstrate how the statistical tools of thin-plate splines and Procrustes analysis can be used to construct a morphable model that is both more efficient and generalises to novel face surfaces more accurately than previous models. We also reformulate the probabilistic prior that the model provides on the distribution of parameter vector lengths. This distribution is determined solely by the number of model dimensions and can be used as a regularisation constraint in fitting the model to data without the need to empirically choose a parameter controlling the trade off between plausibility and quality of fit. As an example application of this improved model, we show how it may be fitted to a sparse set of 2D feature points (approximately 100). This provides a rapid means to estimate high resolution 3D face shape for a face in any pose given only a single face image. We present experimental results using ground truth data and hence provide absolute reconstruction errors. On average, the per vertex error of the reconstructed faces is less than 3.6 mm.
Reassembly of Anthramycin Biosynthetic Gene Cluster by Using Recombinogenic Cassettes

The reassembly and heterologous expression of complete gene clusters in shuttle vectors has enabled investigations of several large biosynthetic pathways in recent years. With a gene cluster in a mobile construct, the interrogation of gene functions from both culturable and nonculturable organisms is greatly accelerated and large pathway engineering efforts can be executed to produce “new” natural products. However, the genetic manipulation of complete natural product biosynthetic gene clusters is often complicated by their sheer size (10–200 kbp), which makes standard restriction/ligation‐based methods impracticable. To circumvent these problems, alternative recombinogenic methods, which depend on engineered homology‐based recombination have recently arisen as a powerful alternative. Here, we describe a new general technique that can be used to reconstruct large biosynthetic pathways from overlapping cosmids by retrofitting each cosmid with a “recombinogenic cassette” that contains a shared homologous element and orthogonal antibiotic markers. We employed this technique to reconstruct the anthramycin biosynthetic gene cluster of the thermotolerant actinomycete Streptomyces refuineus, from two >30 kbp cosmids into a single cosmid and integrate it into the genome of Streptomyces lividans. Anthramycin production in the heterologous Streptomyces host confirmed the integrity of the reconstructed pathway and validated the proposed boundaries of the gene cluster. Notably, anthramycin production by recombinant S. lividans was seen only during growth at high temperature—a property also shown by the natural host. This work provides tools to engineer the anthramycin biosynthetic pathway and to explore the connection between anthramycin production and growth at elevated temperatures.
Cache locality is not enough: High-Performance Nearest Neighbor Search with Product Quantization Fast Scan

Nearest Neighbor (NN) search in high dimension is an important feature in many applications (e.g., image retrieval, multimedia databases). Product Quantization (PQ) is a widely used solution which offers high performance, i.e., low response time while preserving a high accuracy. PQ represents high-dimensional vectors (e.g., image descriptors) by compact codes. Hence, very large databases can be stored in memory, allowing NN queries without resorting to slow I/O operations. PQ computes distances to neighbors using cache-resident lookup tables, thus its performance remains limited by (i) the many cache accesses that the algorithm requires, and (ii) its inability to leverage SIMD instructions available on modern CPUs.In this paper, we advocate that cache locality is not sufficient for efficiency. To address these limitations, we design a novel algorithm, PQ Fast Scan, that transforms the cache-resident lookup tables into small tables, sized to fit SIMD registers. This transformation allows (i) in-register lookups in place of cache accesses and (ii) an efficient SIMD implementation. PQ Fast Scan has the exact same accuracy as PQ, while having 4 to 6 times lower response time (e.g., for 25 million vectors, scan time is reduced from 74ms to 13ms).
A comparison of the circulation patterns over the Southwestern Atlantic Shelf driven by different wind stress climatologies

We compare the oceanic circulation patterns over the Southwestern Atlantic Shelf (SWAS) forced by nine different wind stress climatologies. The largest differences are observed in experiments forced with the Hellerman and Rosenstein [1983, hereafter HR83] and Trenberth et al. [1990, hereafter TR90] winds. HR83 shows a general northeastward flow near the shelf break. The TR90 results shows a bifurcating path south of ∼40°S and a poleward flow north of 35°S. The most robust circulation patterns are a broad northward flow and the generation of coastal re‐circulation cells in southern Patagonia and the development of a southward jet in the inner portion of the South Brazil Bight.
First Order vs. Higher Order Modification in Distributional Semantics

Adjectival modification, particularly by expressions that have been treated as higher-order modifiers in the formal semantics tradition, raises interesting challenges for semantic composition in distributional semantic models. We contrast three types of adjectival modifiers -- intersectively used color terms (as in white towel, clearly first-order), subsectively used color terms (white wine, which have been modeled as both first- and higher-order), and intensional adjectives (former bassist, clearly higher-order) -- and test the ability of different composition strategies to model their behavior. In addition to opening up a new empirical domain for research on distributional semantics, our observations concerning the attested vectors for the different types of adjectives, the nouns they modify, and the resulting noun phrases yield insights into modification that have been little evident in the formal semantics literature to date.
Characterization and Modeling of Subfemtofarad Nanowire Capacitance Using the CBCM Technique

The experimental characterization of gate capacitance in nanoscale devices is challenging. We report an application of the charge-based capacitance measurement (CBCM) technique to measure the gate capacitance of a single-channel nanowire transistor. The measurement results are validated by 3-D electrostatic computations for parasitic estimation and 2-D self-consistent sp3s* d5 tight-binding computations for intrinsic gate capacitance calculations. The device simulation domains were constructed based on SEM and TEM images of the experimental device. The carefully designed CBCM technique thus emerges as a useful technique for measuring the capacitance and characterizing the transport in nanoscale devices.
Reactive Power Sharing and Voltage Harmonic Distortion Compensation of Droop Controlled Single Phase Islanded Microgrids

When paralleling multiple inverters that are capable of operating as an island, the inverters typically employ the droop control scheme. Traditional droop control enables the decentralized regulation of the local voltage and frequency of the microgrid by the inverters. The droop method also enables the inverters to share the real and reactive power required by the loads. This paper focuses on some of the limitations of parallel islanded single phase inverters using droop control. Algorithms with the aim to address the following limitations in islanded operation were proposed: reactive power sharing and reduction of the voltage harmonic distortion at the point of common coupling (PCC). Experimental results were then presented to show the suitability of the proposed algorithms in achieving reactive power sharing and in improving the voltage harmonic distortion at the PCC.
Psychological Distress Increases Perceived Stigma Toward Attempted Suicide Among Those With a History of Past Attempted Suicide

Abstract People who suffer from mental illness have high self-stigmatizing attitudes. This study aims to test the effect of psychopathological distress on stigma toward attempted suicide in a population of suicide attempters. Data were collected through an interview and 2 questionnaires (90-item Symptom Checklist; Stigma of Suicide Attempt scale) administered to 67 patients hospitalized after an attempted suicide. Participants with a history of past attempted suicide had higher scores on the Stigma of Suicide Attempt scale (t58.9 = −2.51, p = 0.014). Higher levels of psychological distress were related to greater perceived stigma only in individuals with a history of past attempted suicide (standardized coefficient = 0.37; t = 2.36; p = 0.024; R2 = 14%; adjusted R2 = 11.5%). A previous experience of attempted suicide is related to greater self-stigmatizing attitudes toward suicidal behavior. Among those who have previously attempted suicide in particular, psychopathological distress may significantly contribute to increase the perception of stigma.
Distinction between signaling mechanisms in lipid rafts vs. caveolae

The relative importance of lipid rafts vs. specialized rafts termed caveolae to influence signal transduction is not known. Here we show that in cells lacking caveolae, the dually acylated protein, endothelial nitric oxide synthase (eNOS), localizes to cholesterol-rich lipid raft domains of the plasma membrane. In these cells, expression of caveolin-1 (cav-1) stimulates caveolae biogenesis, promotes the interaction of cav-1 with eNOS, and the inhibition of NO release from cells. Interestingly, in cells where cav-1 does not drive caveolae assembly, despite equal levels of cav-1 and eNOS and localization of both proteins to raft domains of the plasmalemma, the physical interaction of eNOS with cav-1 is dramatically less resulting in less inhibition of NO release. Thus, cav-1 concentrated in caveolae, not in rafts, is in closer proximity to eNOS and is necessary for negative regulation of eNOS function, thereby providing the first clear example of spatial regulation of signaling in this organelle that is distinct from raft domains.
Are wildlife-caused losses of agriculture increasing?

Author(s): Wywialowski, Alice P. | Abstract: Both the percent of producers reporting and the value of wildlife-caused losses increased from 1989 to 1994. In 1994, 58% of respondents reported wildlife-caused losses of their agricultural commodities, an increase from the 55% of respondents who reported losses in 1989. Based on the median value of producer-estimated loss, wildlife-caused losses cost producers approximately $591 million in 1994, $130 million more than in 1989. Losses based on producer estimates have been consistent with field-measured estimates of damage. While these losses represent 1% of the value of agricultural production, losses were not evenly distributed and 23% of producers estimated losses of g$500, an amount that is psychologically significant if not also economically significant. While catfish losses to wildlife were 4% of the total sale value of catfish in 1996, the losses were equivalent to one-sixth to one-third of the average catfish producers’ profit. Producers’ ability to predict the location of their crop losses as well as consistent patterns of losses based on field assessments suggests that wildlife managers may be able to develop models of wildlife damage that would allow them to better assist producers in planning agricultural production so that wildlife-caused losses are reduced. Given the increasing populations of many wildlife species and the declining habitat base for supporting those populations, wildlife managers will need to increasingly rely on cooperative relationships with agricultural producers. Management of wildlife damage relative to agricultural needs will increasingly challenge the wildlife profession in the coming years. Wildlife managers must recognize the magnitude and distribution of wildlife-caused damage to agriculture and consider both perceptions and damage in their decisions about wildlife management.
Adaptive feature set updating algorithm for multimodal biometrics

Multimodal Biometrics is an emerging domain in biometric technology where we combine more than one biometric trait to improve the performance. Here we propose a new concept that can be used in designing future multimodal biometrics systems which can adapt to the change in the biometrics features like face, voice, signature, and gait over the time or any other factor without compromising the security. We adapt to the change in biometric features by updating feature set without re-enrollment of entire set. This technique requires use of at least one biometric feature which has very low variance or high degree of permanence, like Fingerprint, Iris, Retina etc. This algorithm can address the problem of false rejection caused by sustained change in biometric features due to aging or any other factor without the need of re-enrollment of feature set. We suggest architecture of Multimodal biometric system implementing this algorithm.
A Fast Online Gait Planning with Boundary Condition Relaxation for Humanoid Robots

A fast online gait planning method is proposed. Based on an approximate dynamical biped model whose mass is concentrated to COG, general solution of the equation of motion is analytically obtained. Dynamical constraint on the external reaction force due to the underactuation is resolved by boundary condition relaxation, namely, by admitting some error between the desired and actually reached state. It potentially creates responsive motion which requires strong instantaneous acceleration by accepting discontinuity of ZMP trajectory, which is designed as an exponential function. A semi-automatic continuous gait planning is also presented. It generates physically feasible referential trajectory of the whole-body only from the next desired foot placement. The validity of proposed is ensured through both simulations and experiments with a small anthropomorphic robot.
Prediction of Heme Binding Sites in Heme Proteins Using an Integrative Sequence Profile Coupling Evolutionary Information with Physicochemical Properties

Heme-protein interactions are essential for various biological processes such as electron transfer, catalysis, signal transduction and the control of gene expression. The knowledge of heme binding residues can provide crucial clues to understand the mechanism of heme-protein interactions and aid in functional annotation. In the present work, we propose a sequence-based approach for the accurate prediction of heme binding residues by a novel integrative sequence profile coupling position specific scoring matrices with heme specific physicochemical properties. Particularly, we design an intuitive feature selection scheme for informative physicochemical properties. As shown in the primary results, our integrative sequence profile approach for prediction of heme binding residues outperforms the conventional methods using amino acid and evolutionary information on the 5-fold cross validation and the independent test.
A simple 2d pore-scale network model for the transport of water vapor and oxygen in polymeric films

A mathematical model was developed to describe mass transport in polymeric films based on modifications of Fick's law in a continuous mac- roscopic approach. The purpose of this work was specifically to model the transport of water vapor and oxygen in polymeric films at the pore level, based on physical aspects of the condensation pro- cess and the morphology and connectivity of the po- rous medium, with two-dimensional pore networks representing pore spaces. Using a Pore scale discrete model, we found that the pore-level distributions of liquid (condensate) and vapor as transport phenom- ena occurred. The vapor and oxygen diffusivities ranged from 4.22×10 -6 to 3.16×10 -7 cm 2 /s and from 3.66×10 -6 to 2.86×10 -7 cm 2 /s, respectively. Also, the vapor and oxygen permeabilities ranged from 2.61×10 -3 to 3.83×10 -4 nD (1nD=10 -21 m 2 ) and from 6.77×10 -3 to 1.35×10 -3 nD, respectively. The transport properties obtained by the model were compared with the corresponding results for chitosan films ob- tained in previous experimental studies, showing a partial agreement.
Volumetric Flow Estimation for Incompressible Fluids Using the Stationary Stokes Equations

In experimental fluid dynamics, the flow in a volume of fluid is observed by injecting high-contrast tracer particles and tracking them in multi-view video. Fluid dynamics researchers have developed variants of space-carving to reconstruct the 3D particle distribution at a given time-step, and then use relatively simple local matching to recover the motion over time. On the contrary, estimating the optical flow between two consecutive images is a long-standing standard problem in computer vision, but only little work exists about volumetric 3D flow. Here, we propose a variational method for 3D fluid flow estimation from multi-view data. We start from a 3D version of the standard variational flow model, and investigate different regularization schemes that ensure divergence-free flow fields, to account for the physics of incompressible fluids. Moreover, we propose a semi-dense formulation, to cope with the computational demands of large volumetric datasets. Flow is estimated and regularized at a lower spatial resolution, while the data term is evaluated at full resolution to preserve the discriminative power and geometric precision of the local particle distribution. Extensive experiments reveal that a simple sum of squared differences (SSD) is the most suitable data term for our application. For regularization, an energy whose Euler-Lagrange equations correspond to the stationary Stokes equations leads to the best results. This strictly enforces a divergence-free flow and additionally penalizes the squared gradient of the flow.
Buffer effects of streamside native forests on water provision in watersheds dominated by exotic forest plantations

The Valdivian rainforest ecoregion in Chile (35°–48°S) has a high conservation priority worldwide. These forests are also keys for social welfare as a result of their supply of timber as well as ecosystem services. Forests in the ecoregion have been extensively converted to fast growing Pinus radiata and Eucalyptus spp. plantations for timber production promoted by public policies and timber companies. This study describes the results of detailed measurements of hydrology and stream water chemistry in eight small watersheds in south central Chile, subjected to replacement of native temperate rainforest by exotic Eucalyptus plantations. In this system, watersheds have streamside buffers of native forest (SNFW) with varying widths. Results indicate that retention of SNFW counteracts hydrologic effects of Eucalyptus plantations, which are widely known to reduce water yields. A 1.4% rate of increase of the run‐off coefficient for each metre of increase of SNFW was observed. In addition, a decrease in the concentrations of total nitrogen, dissolved inorganic nitrogen (DIN), nitrate‐N, and different sized fractions of particulate organic matter were found in streams draining these plantations as a function of increasing SNFW. Streamside buffer widths of 17–22 m for total nitrogen and DIN concentrations and ≥36 m for sediments were required to provide comparable values to reference watersheds (100% native forest). The findings from this study suggest that SNFW may significantly reduce adverse effects from exotic species forestry plantations on water provision in an area of south central Chile where exotic forest plantations are rapidly expanding. Copyright © 2014 John Wiley & Sons, Ltd.