Miracle-dz/UniFAR-FTUs huggingface dataset:
Arginase-1–Expressing Macrophages Suppress Th2 Cytokine–Driven Inflammation and Fibrosis

Macrophage-specific expression of Arginase-1 is commonly believed to promote inflammation, fibrosis, and wound healing by enhancing L-proline, polyamine, and Th2 cytokine production. Here, however, we show that macrophage-specific Arg1 functions as an inhibitor of inflammation and fibrosis following infection with the Th2-inducing pathogen Schistosoma mansoni. Although susceptibility to infection was not affected by the conditional deletion of Arg1 in macrophages, Arg1 −/flox ;LysMcre mice died at an accelerated rate. The mortality was not due to acute Th1/NOS2-mediated hepatotoxicity or endotoxemia. Instead, granulomatous inflammation, liver fibrosis, and portal hypertension increased in infected Arg1 −/flox ;LysMcre mice. Similar findings were obtained with Arg1 flox/flox ;Tie2cre mice, which delete Arg1 in all macrophage populations. Production of Th2 cytokines increased in the infected Arg1 −/flox ;LysMcre mice, and unlike alternatively activated wild-type macrophages, Arg1 −/flox ;LysMcre macrophages failed to inhibit T cell proliferation in vitro, providing an underlying mechanism for the exacerbated Th2 pathology. The suppressive activity of Arg1-expressing macrophages was independent of IL-10 and TGF-β1. However, when exogenous L-arginine was provided, T cell proliferation was restored, suggesting that Arg1-expressing macrophages deplete arginine, which is required to sustain CD4+ T cell responses. These data identify Arg1 as the essential suppressive mediator of alternatively activated macrophages (AAM) and demonstrate that Arg1-expressing macrophages function as suppressors rather than inducers of Th2-dependent inflammation and fibrosis.
Analysing half-lives for pesticide dissipation in plants

Overall dissipation of pesticides from plants is frequently measured, but the contribution of individual loss processes is largely unknown. We use a pesticide fate model for the quantification of dissipation by processes other than degradation. The model was parameterised using field studies. Scenarios were established for Copenhagen/Denmark and Shanghai/PR China, and calibrated with measured results. The simulated dissipation rates of 42 pesticides were then compared with measured overall dissipation from field studies using tomato and wheat. The difference between measured overall dissipation and calculated dissipation by non-degradative processes should ideally be contributable to degradation in plants. In 11% of the cases, calculated dissipation was above the measured dissipation. For the remaining cases, the non-explained dissipation ranged from 30% to 83%, depending on crop type, plant part and scenario. Accordingly, degradation is the most relevant dissipation process for these 42 pesticides, followed by growth dilution. Volatilisation was less relevant, which can be explained by the design of plant protection agents. Uptake of active compound from soil into plants leads to a negative dissipation process (i.e. a gain) that is difficult to quantify because it depends largely on interception, precipitation and plant stage. This process is particularly relevant for soluble compounds.
Therapy Decision Support Based on Recommender System Methods

We present a system for data-driven therapy decision support based on techniques from the field of recommender systems. Two methods for therapy recommendation, namely, Collaborative Recommender and Demographic-based Recommender, are proposed. Both algorithms aim to predict the individual response to different therapy options using diverse patient data and recommend the therapy which is assumed to provide the best outcome for a specific patient and time, that is, consultation. The proposed methods are evaluated using a clinical database incorporating patients suffering from the autoimmune skin disease psoriasis. The Collaborative Recommender proves to generate both better outcome predictions and recommendation quality. However, due to sparsity in the data, this approach cannot provide recommendations for the entire database. In contrast, the Demographic-based Recommender performs worse on average but covers more consultations. Consequently, both methods profit from a combination into an overall recommender system.
Azotobacter Genomes: The Genome of Azotobacter chroococcum NCIMB 8003 (ATCC 4412)

The genome of the soil-dwelling heterotrophic N2-fixing Gram-negative bacterium Azotobacter chroococcum NCIMB 8003 (ATCC 4412) (Ac-8003) has been determined. It consists of 7 circular replicons totalling 5,192,291 bp comprising a circular chromosome of 4,591,803 bp and six plasmids pAcX50a, b, c, d, e, f of 10,435 bp, 13,852, 62,783, 69,713, 132,724, and 311,724 bp respectively. The chromosome has a G+C content of 66.27% and the six plasmids have G+C contents of 58.1, 55.3, 56.7, 59.2, 61.9, and 62.6% respectively. The methylome has also been determined and 5 methylation motifs have been identified. The genome also contains a very high number of transposase/inactivated transposase genes from at least 12 of the 17 recognised insertion sequence families. The Ac-8003 genome has been compared with that of Azotobacter vinelandii ATCC BAA-1303 (Av-DJ), a derivative of strain O, the only other member of the Azotobacteraceae determined so far which has a single chromosome of 5,365,318 bp and no plasmids. The chromosomes show significant stretches of synteny throughout but also reveal a history of many deletion/insertion events. The Ac-8003 genome encodes 4628 predicted protein-encoding genes of which 568 (12.2%) are plasmid borne. 3048 (65%) of these show > 85% identity to the 5050 protein-encoding genes identified in Av-DJ, and of these 99 are plasmid-borne. The core biosynthetic and metabolic pathways and macromolecular architectures and machineries of these organisms appear largely conserved including genes for CO-dehydrogenase, formate dehydrogenase and a soluble NiFe-hydrogenase. The genetic bases for many of the detailed phenotypic differences reported for these organisms have also been identified. Also many other potential phenotypic differences have been uncovered. Properties endowed by the plasmids are described including the presence of an entire aerobic corrin synthesis pathway in pAcX50f and the presence of genes for retro-conjugation in pAcX50c. All these findings are related to the potentially different environmental niches from which these organisms were isolated and to emerging theories about how microbes contribute to their communities.
Moving Volume KinectFusion

Newcombe and Izadi et al’s KinectFusion [5] is an impressive new algorithm for real-time dense 3D mapping using the Kinect. It is geared towards games and augmented reality, but could also be of great use for robot perception. However, the algorithm is currently limited to a relatively small volume fixed in the world at start up (typically a ∼ 3m cube). This limits applications for perception. Here we report moving volume KinectFusion with additional algorithms that allow the camera to roam freely. We are interested in perception in rough terrain, but the system would also be useful in other applications including free-roaming games and awareness aids for hazardous environments or the visually impaired. Our approach allows the algorithm to handle a volume that moves arbitrarily on-line (Figure 1).
New Technique for Synthesizing Concurrent Dual-Band Impedance-Matching Filtering Networks and ${\hbox{0.18-}}\mu{\hbox {m}}$  SiGe BiCMOS 25.5/37-GHz Concurrent Dual-Band Power Amplifier

New technique for synthesizing concurrent dual-band impedance-matching filtering networks is presented. The technique enables the design of concurrent dual-band impedance-matching filtering networks that provide not only simultaneous matching of two arbitrary loads to two arbitrary sources at two different frequencies, but also dual-bandpass filtering response capable of suppressing unwanted signals like the harmonics and inter-modulation products in nonlinear circuits, such as power amplifiers (PAs). A new 0.18-μm SiGe BiCMOS concurrent dual-band PA was designed based on the developed dual-band matching filtering technique around 25.5 and 37 GHz, which works in the concurrent dual-band mode (25.5 and 37 GHz), as well as single-band mode (25.5 or 37 GHz). The measured results show that, in the single-band mode, the dual-band PA exhibits gain of 21.4 and 17 dB, maximum output power of 16 and 13 dBm, and maximum power-added efficiency (PAE) of 10.6% and 4.9% at 25.5 and 37 GHz, respectively. In the dual-band mode, the maximum output power is 13 and 9.5 dBm at 25.5 and 37 GHz, respectively, and the total maximum PAE is 7.1%. The designed concurrent dual-band PA has a chip size of 1.3×0.68 mm2 and consumes a dc current of 120 mA from a 3-V supply voltage.
Generator Based On Deep Neural Networks

In this project, we systematically analyze a deep neural networks based image caption generation method. With an image as the input, the method can output an English sentence describing the content in the image. We analyze three components of the method: convolutional neural network (CNN), recurrent neural network (RNN) and sentence generation. By replacing the CNN part with three state-of-the-art architectures, we find the VGGNet performs best according to the BLEU score. We also propose a simplified version the Gated Recurrent Units (GRU) as a new recurrent layer, implementing by both MATLAB and C++ in Caffe. The simplified GRU achieves comparable result when it is compared with the long short-term memory (LSTM) method. But it has few parameters which saves memory and is faster in training. Finally, we generate multiple sentences using Beam Search. The experiments show that the modified method can generate captions comparable to the-state-of-the-art methods with less training memory.
Speckle Reduction by Optimized Multimode Fiber Combined With Dielectric Elastomer Actuator and Lightpipe Homogenizer

Speckle, due to the interference of coherent light having random phases, can seriously degrade image quality in a laser based projection system. The speckle is even worse when the diode pumped solid state (DPSS) lasers are used as light sources since the laser linewidth from the DPSS lasers is usually very narrow. In this paper, a de-speckle system consisting of a multimode fiber (MMF), a dielectric elastomer actuator (DEA) and a lightpipe is proposed and demonstrated, which can reduce speckle significantly. The speckle reduction components used in the system are optimized, taking into account speckle reduction ability and optical efficiency. The proposed de-speckle system is low in cost and easy to set up. It features a low optical power penalty and is compatible with large venue laser projection for applications such as digital cinema. In the proposed de-speckle system, test images captured by a camera with a setup following the recently proposed speckle measurement standard can achieve a speckle contrast ratio as low as 4.7%. By adding a voice coil motor (VCM) to vibrate the MMF to generate temporal diversity, the speckle contrast ratio can be further reduced to 3.7%.
Comparing Model-Based Predictive Approaches to Self-Adaptation: CobRA and PLA

Modern software-intensive systems must often guarantee certain quality requirements under changing run-time conditions and high levels of uncertainty. Self-adaptation has proven to be an effective way to engineer systems that can address such challenges, but many of these approaches are purely reactive and adapt only after a failure has taken place. To overcome some of the limitations of reactive approaches (e.g., lagging behind environment changes and favoring short-term improvements), recent proactive self-adaptation mechanisms apply ideas from control theory, such as model predictive control (MPC), to improve adaptation. When selecting which MPC approach to apply, the improvement that can be obtained with each approach is scenario-dependent, and so guidance is needed to better understand how to choose an approach for a givensituation. In this paper, we compare CobRA and PLA, two approaches that are inspired by MPC. CobRA is a requirements-based approach that applies control theory, whereas PLA is architecture-based and applies stochastic analysis. We compare the two approaches applied to RUBiS, a benchmark system for web and cloud application performance, discussing the required expertise needed to use both approaches and comparing their run-time performance with respect to different metrics.
The recursive grid layout scheme for VLSI layout of hierarchical networks

We propose the recursive grid layout scheme for deriving efficient layouts of a variety of hierarchical networks and computing upper bounds on the VLSI area of general hierarchical networks. In particular we construct optimal VLSI layouts for butterfly networks, generalized hypercubes, and star graphs that have areas within a factor of 1+o(1) from their lower bounds. We also derive efficient layouts for a number of other important networks, such as cube-connected cycles (CCC) and hypernets, which are the best results reported for these networks thus far.
Enhanced diversity and aflatoxigenicity in interspecific hybrids of Aspergillus flavus and Aspergillus parasiticus

Aspergillus flavus and A. parasiticus are the two most important aflatoxin‐producing fungi responsible for the contamination of agricultural commodities worldwide. Both species are heterothallic and undergo sexual reproduction in laboratory crosses. Here we examine the possibility of interspecific matings between A. flavus and A. parasiticus. These species can be distinguished morphologically and genetically, as well as by their mycotoxin profiles. Aspergillus flavus produces both B aflatoxins and cyclopiazonic acid (CPA), B aflatoxins or CPA alone, or neither mycotoxin; Aspergillus parasiticus produces B and G aflatoxins or the aflatoxin precursor O‐methylsterigmatocystin, but not CPA. Only four of forty‐five attempted interspecific crosses between opposite mating types of A. flavus and A. parasiticus were fertile and produced viable ascospores. Single ascospore strains from each cross were shown to be recombinant hybrids using multilocus genotyping and array comparative genome hybridization. Conidia of parents and their hybrid progeny were haploid and predominantly monokaryons and dikaryons based on flow cytometry. Multilocus phylogenetic inference showed that experimental hybrid progeny were grouped with naturally occurring A. flavus L strain and A. parasiticus. Higher total aflatoxin concentrations in some F1 progeny strains compared to midpoint parent aflatoxin levels indicate synergism in aflatoxin production; moreover, three progeny strains synthesized G aflatoxins that were not produced by the parents, and there was evidence of allopolyploidization in one strain. These results suggest that hybridization is an important diversifying force resulting in the genesis of novel toxin profiles in these agriculturally important fungi.
Inducing a Discriminative Parser to Optimize Machine Translation Reordering

This paper proposes a method for learning a discriminative parser for machine translation reordering using only aligned parallel text. This is done by treating the parser's derivation tree as a latent variable in a model that is trained to maximize reordering accuracy. We demonstrate that efficient large-margin training is possible by showing that two measures of reordering accuracy can be factored over the parse tree. Using this model in the pre-ordering framework results in significant gains in translation accuracy over standard phrase-based SMT and previously proposed unsupervised syntax induction methods.
Stakeholders' Perceptions of the Value of Elementary School Counselor Roles

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Intrasarcoplasmic Amyloidosis Impairs Proteolytic Function of Proteasomes in Cardiomyocytes by Compromising Substrate Uptake

The presence of increased ubiquitinated proteins and amyloid oligomers in failing human hearts strikingly resembles the characteristic pathology in the brain of many neurodegenerative diseases. The ubiquitin–proteasome system (UPS) is responsible for degradation of most cellular proteins and plays essential roles in virtually all cellular processes. UPS impairment by aberrant protein aggregation was previously shown in cell culture but remains to be demonstrated in intact animals. Mechanisms underlying the impairment are poorly understood. We report here that UPS proteolytic function is severely impaired in the heart of a mouse model of intrasarcoplasmic amyloidosis caused by cardiac-restricted expression of a human desmin–related myopathy-linked missense mutation of &agr;B-crystallin (CryABR120G). The UPS impairment was detected before cardiac hypertrophy, and failure became discernible, suggesting that defective protein turnover likely contributes to cardiac remodeling and failure in this model. Further analyses reveal that the impairment is likely attributable to insufficient delivery of substrate proteins into the 20S proteasomes, and depletion of key components of the 19S subcomplex may be responsible. The derangement is likely caused by aberrant protein aggregation rather than loss of function of the CryAB gene because UPS malfunction was not evident in CryAB-null hearts and inhibition of aberrant protein aggregation by Congo red or a heat shock protein significantly attenuated CryABR120G-induced UPS malfunction in cultured cardiomyocytes. Because of the central role of the UPS in cell regulation and the high intrasarcoplasmic amyloidosis prevalence in failing human hearts, our data suggest a novel pathogenic process in cardiac disorders with abnormal protein aggregation.
Population stratification in epidemiologic studies of common genetic variants and cancer: quantification of bias.

BACKGROUND Some critics argue that bias from population stratification (the mixture of individuals from heterogeneous genetic backgrounds) undermines the credibility of epidemiologic studies designed to estimate the association between a genotype and the risk of disease. We investigated the degree of bias likely from population stratification in U.S. studies of cancer among non-Hispanic Caucasians of European origin. METHODS An expression of the confounding risk ratio-the ratio of the effect of the genetic factor on risk of disease with and without adjustment for ethnicity-is used to measure the potential relative bias from population stratification. We first use empirical data on the frequency of the N-acetyltransferase (NAT2) slow acetylation genotype and incidence rates of male bladder cancer and female breast cancer in non-Hispanic U.S. Caucasians with ancestries from eight European countries to assess the bias in a hypothetical population-based U.S. study that does not take ethnicity into consideration. Then, we provide theoretical calculations of the bias over a large range of allele frequencies and disease rates. RESULTS Ignoring ethnicity leads to a bias of 1% or less in our empirical studies of NAT2. Furthermore, evaluation of a wide range of allele frequencies and representative ranges of cancer rates that exist across European populations shows that the risk ratio is biased by less than 10% in U.S. studies except under extreme conditions. We note that the bias decreases as the number of ethnic strata increases. CONCLUSIONS There will be only a small bias from population stratification in a well-designed case-control study of genetic factors that ignores ethnicity among non-Hispanic U.S. Caucasians of European origin. Further work is needed to estimate the effect of population stratification within other populations.
Sites of Belonging, Sites of Empowerment: How Asian American Girls Construct "Home" in a Borderland World

Title of Dissertation: SITES OF BELONGING, SITES OF EMPOWERMENT: HOW ASIAN AMERICAN GIRLS CONSTRUCT “HOME” IN A BORDERLAND WORLD Tomoko Tokunaga, Doctor of Philosophy, 2012 Directed By: Professor Barbara Finkelstein Department of Teaching and Learning, and Policy and Leadership This ethnographic study explores the ways in which nine first, 1.5, and second generation Asian American high school girls imagine, search for, and construct homelike sites. The study revealed that “home” for the girls was not only the place where the girls sleep, their families reside, or the country from where they came. Instead, “home,” was multiple, literal, and imagined spaces, places, and communities where the girls felt a sense of belonging, empowerment, community, ownership, safety, and opportunity. In order to examine the behaviors, meaning, and perspectives of these girls, I conducted participant observations, interviews, and focus groups at an Asian American youth organization as well as in the girls’ homes, schools, and neighborhoods. I also had online communication with the girls and collected supplementary materials and sources. The study revealed that the girls had creativity and improvisational skills to invent various “homes” as they linked the many worlds in which they lived. The girls carved out multiple “homes”—through imagining belonging globally while building belonging locally. They imagined an expansive understanding of “home” in the deterritorialized world. They idealized their countries of origin, acknowledged the United States as a possible “home,” portrayed a third possible homeland where they had never lived, and fashioned a pan-Asian consciousness. The girls not only imagined “homes” outside of their immediate view but also co-constructed a home-like community in their everyday lives. They named it the Basement Group, after the place where they hang out in school. They developed a group identity which honored five characteristics: 1) expansion of who is family to include friends, 2) pride in diversity and inclusivity, 3) celebrations of cultural fusion, 4) value of “natural” girlhood beauty, and 5) shared interest in Asian popular culture. They constructed a borderland community in which they could collectively celebrate and nurture their in-between lives. This study illuminated the power and complexity of their lives in-between as well as expanded the terrains of agency that the girls possessed. The study also revealed intersectional differences among the girls. It provided lessons for youth organizations and schools to create spaces where immigrant youth can thrive. SITES OF BELONGING, SITES OF EMPOWERMENT: HOW ASIAN AMERICAN GIRLS CONSTRUCT “HOME” IN A BORDERLAND WORLD
PEX11 promotes peroxisome division independently of peroxisome metabolism

The PEX11 peroxisomal membrane proteins are the only factors known to promote peroxisome division in multiple species. It has been proposed that PEX11 proteins have a direct role in peroxisomal fatty acid oxidation, and that they only affect peroxisome abundance indirectly. Here we show that PEX11 proteins are unique in their ability to promote peroxisome division, and that PEX11 overexpression promotes peroxisome division in the absence of peroxisomal metabolic activity. We also observed that mouse cells lacking PEX11β display reduced peroxisome abundance, even in the absence of peroxisomal metabolic substrates, and that PEX11β− / − mice are partially deficient in two distinct peroxisomal metabolic pathways, ether lipid synthesis and very long chain fatty acid oxidation. Based on these and other observations, we propose that PEX11 proteins act directly in peroxisome division, and that their loss has indirect effects on peroxisome metabolism.