Miracle-dz/UniFAR-FTUs huggingface dataset:
Inverting and Visualizing Features for Object Detection

Abstract : This paper presents methods to visualize feature spaces commonly used in object detection. The tools in this paper allow a human to put on feature space glasses and see the visual world as a computer might see it. We found that these glasses allow us to gain insight into the behavior of computer vision systems. We show a variety of experiments with our visualizations, such as examining the linear separability of recognition in HOG space, generating high scoring super objects for an object detector, and diagnosing false positives. We pose the visualization problem as one of feature inversion, i.e. recovering the natural image that generated a feature descriptor. We describe four algorithms to tackle this task, with different trade-offs in speed accuracy, and scalability. Our most successful algorithm uses ideas from sparse coding to learn a pair of dictionaries that enable regression between HOG features and natural images, and can invert features at interactive rates. We believe these visualizations are useful tools to add to an object detector researcher's toolbox, and code is available.
Entorhinal cortex structure and functional MRI response during an associative verbal memory task

Entorhinal cortex (ERC) volume in adults with mild cognitive impairment has been shown to predict prodromal Alzheimer's disease (AD). Likewise, neuronal loss in ERC has been associated with AD, but not with normal aging. Because ERC is part of a major pathway modulating input to the hippocampus, structural changes there may result in changes to cognitive performance and functional brain activity during memory tasks. In 32 cognitively intact older adults, we examined the relationship between left ERC thickness and functional magnetic resonance imaging (fMRI) activity during an associative verbal memory task. This task has been shown previously to activate regions that are sensitive to aging and AD risk. ERC was manually defined on native space, high resolution, oblique coronal MRI scans. Subjects having thicker left ERC showed greater activation in anterior cingulate and medial frontal regions during memory retrieval, but not encoding. This result was independent of hippocampal volume. Anterior cingulate cortex is directly connected to ERC, and is, along with medial frontal cortex, implicated in error detection, which is impaired in AD. Our results suggest that in healthy older adults, processes that engage frontal regions during memory retrieval are related to ERC structure. Hum Brain Mapp, 2009. © 2009 Wiley‐Liss, Inc.
Transcriptional Regulation by the Numbers 1: Models

The study of gene regulation and expression is often discussed in quantitative terms. In particular, the expression of genes is regularly characterized with respect to how much, how fast, when and where. Whether discussing the level of gene expression in a bacterium or its precise location within a developing embryo, the natural language for these experiments is that of numbers. Such quantitative data demands quantitative models. We review a class of models ("thermodynamic models") which exploit statistical mechanics to compute the probability that RNA polymerase is at the appropriate promoter. This provides a mathematically precise elaboration of the idea that activators are agents of recruitment which increase the probability that RNA polymerase will be found at the promoter of interest. We discuss a framework which describes the interactions of repressors, activators, helper molecules and RNA polymerase using the concept of effective concentrations, expressed in terms of a function we call the "regulation factor". This analysis culminates in an expression for the probability of RNA polymerase binding at the promoter of interest as a function of the number of regulatory proteins in the cell. In a companion paper [1], these ideas are applied to several case studies which illustrate the use of the general formalism.
Regional stabilization and H∞ control of time‐delay systems with saturating actuators

A linear parameter varying approach is introduced for the design of a constant state‐feedback controller that locally stabilizes linear systems with state time‐varying delays and saturating actuators and achieves a prescribed performance level for all disturbances with uniformly bounded magnitudes. A polytopic representation is used to describe the saturation behaviour. Delay‐dependent sufficient conditions in terms of linear matrix inequalities (LMIs) are obtained for the existence of such a controller. An estimate is made of the domain of attraction for the disturbance‐free system. The conditions for the stabilizability and H∞ performance of the system apply the Lyapunov–Krasovskii functional and the recent descriptor approach to the control of time‐delay systems, whereas the conditions for finding an ellipsoid that bounds the set of the states (in the Euclidean space) that are reachable from the origin in finite time are obtained via the Razumikhin approach. The resulting conditions are expressed in terms of linear matrix inequalities, with some tuning parameters, and they apply a different Lyapunov function to each of the vertex points that stem from the polytopic description of the saturation in the actuators. Copyright © 2003 John Wiley & Sons, Ltd.
Meta-IDBA: a de Novo assembler for metagenomic data

Motivation: Next-generation sequencing techniques allow us to generate reads from a microbial environment in order to analyze the microbial community. However, assembling of a set of mixed reads from different species to form contigs is a bottleneck of metagenomic research. Although there are many assemblers for assembling reads from a single genome, there are no assemblers for assembling reads in metagenomic data without reference genome sequences. Moreover, the performances of these assemblers on metagenomic data are far from satisfactory, because of the existence of common regions in the genomes of subspecies and species, which make the assembly problem much more complicated. Results: We introduce the Meta-IDBA algorithm for assembling reads in metagenomic data, which contain multiple genomes from different species. There are two core steps in Meta-IDBA. It first tries to partition the de Bruijn graph into isolated components of different species based on an important observation. Then, for each component, it captures the slight variants of the genomes of subspecies from the same species by multiple alignments and represents the genome of one species, using a consensus sequence. Comparison of the performances of Meta-IDBA and existing assemblers, such as Velvet and Abyss for different metagenomic datasets shows that Meta-IDBA can reconstruct longer contigs with similar accuracy. Availability: Meta-IDBA toolkit is available at our website http://www.cs.hku.hk/~alse/metaidba. Contact: chin@cs.hku.hk
TGF-b2 Induction Regulates Invasiveness of Theileria-Transformed Leukocytes and Disease Susceptibility

Theileria parasites invade and transform bovine leukocytes causing either East Coast fever (T. parva), or tropical theileriosis (T. annulata). Susceptible animals usually die within weeks of infection, but indigenous infected cattle show markedly reduced pathology, suggesting that host genetic factors may cause disease susceptibility. Attenuated live vaccines are widely used to control tropical theileriosis and attenuation is associated with reduced invasiveness of infected macrophages in vitro. Disease pathogenesis is therefore linked to aggressive invasiveness, rather than uncontrolled proliferation of Theileria-infected leukocytes. We show that the invasive potential of Theileria-transformed leukocytes involves TGF-b signalling. Attenuated live vaccine lines express reduced TGF-b2 and their invasiveness can be rescued with exogenous TGF-b. Importantly, infected macrophages from disease susceptible Holstein-Friesian (HF) cows express more TGF-b2 and traverse Matrigel with great efficiency compared to those from disease-resistant Sahiwal cattle. Thus, TGF-b2 levels correlate with disease susceptibility. Using fluorescence and time-lapse video microscopy we show that Theileria-infected, disease-susceptible HF macrophages exhibit increased actin dynamics in their lamellipodia and podosomal adhesion structures and develop more membrane blebs. TGF-b2-associated invasiveness in HF macrophages has a transcription-independent element that relies on cytoskeleton remodelling via activation of Rho kinase (ROCK). We propose that a TGF-b autocrine loop confers an amoeboid-like motility on Theileria-infected leukocytes, which combines with MMP-dependent motility to drive invasiveness and virulence.
An efficient approach for ensemble of SVM and ANN for sentiment classification

Nowadays Opinion mining is given more important, since it provides decision makers to estimate the success of a newly proposed techniques, novel ad campaign or novel product launch. In general, supervised methods such as Support Vector Machine (SVM) and Artificial Neural Network (ANN) are used to classify the opinions. In some cases SVM performs better classification and some cases ANN performs better than SVM. To overcome this constraint, we proposed a novel ensemble classification method for opinion mining. This novel technique aims to ensemble Artificial Neural network (ANN) and Support Vector Machine (SVM) for opinion analysis. In which, weight factor of both ANN and SVM is recalibrated by comparing error value between them. The experimental results show that ensemble of ANN and SVM techniques provides high accuracy than individual.
Transcriptome Changes in Relation to Manic Episode

Bipolar disorder (BD) is highly heritable and well known for its recurrent manic and depressive episodes. The present study focused on manic episode in BD patients and aimed to investigate state-specific transcriptome alterations between acute episode and remission, including messenger RNAs (mRNAs), long noncoding RNAs (lncRNAs), and micro-RNAs (miRNAs), using microarray and RNA sequencing (RNA-Seq) platforms. BD patients were enrolled with clinical information, and peripheral blood samples collected at both acute and remission status spanning for at least 2 months were confirmed by follow-ups. Symptom severity was assessed by Young Mania Rating Scale. We enrolled six BD patients as the discovery samples and used the Affymetrix Human Transcriptome Array 2.0 to capture transcriptome data at the two time points. For replication, expression data from Gene Expression Omnibus that consisted of 11 BD patients were downloaded, and we performed a mega-analysis for microarray data of 17 patients. Moreover, we conducted RNA sequencing (RNA-Seq) in additional samples of 7 BD patients. To identify intraindividual differentially expressed genes (DEGs), we analyzed data using a linear model controlling for symptom severity. We found that noncoding genes were of majority among the top DEGs in microarray data. The expression fold change of coding genes among DEGs showed moderate to high correlations (∼0.5) across platforms. A number of lncRNAs and two miRNAs (MIR181B1 and MIR103A1) exhibited high levels of gene expression in the manic state. For coding genes, we reported that the taste function-related genes, including TAS2R5 and TAS2R3, may be mania state-specific markers. Additionally, four genes showed a nominal p-value of less than 0.05 in all our microarray data, mega-analysis, and RNA-Seq analysis. They were upregulated in the manic state and consisted of MS4A14, PYHIN1, UTRN, and DMXL2, and their gene expression patterns were further validated by quantitative real-time polymerase chain reaction (PCR) (qRT-PCR). We also performed weight gene coexpression network analysis to identify gene modules for manic episode. Genes in the mania-related modules were different from the susceptible loci of BD obtained from genome-wide association studies, and biological pathways in relation to these modules were mainly related to immune function, especially cytokine–cytokine receptor interaction. Results of the present study elucidated potential molecular targets and genomic networks that are involved in manic episode. Future studies are needed to further validate these biomarkers for their roles in the etiology of bipolar illness.
Responses of Ornithonyssus sylviarum (Acari: Macronyssidae) and Menacanthus stramineus (Phthiraptera: Menoponidae) to Gradients of Temperature, Light, and Humidity, with Comments on Microhabitat Selection on Chickens

ABSTRACT Responses of the northern fowl mite (NFM), Ornithonyssus sylviarum (Canestrini & Fanzago) (Acari: Macronyssidae), and the chicken body louse (CBL), Menacanthus stramineus (Nitzsch) (Phthiraptera: Menoponidae), to variation in temperature, light, and humidity were assessed in bioassays. The location on a continuous thermal gradient at which each ectoparasite arrested was recorded and analyzed. NFM adults arrested at an average temperature of 30.09 ± 0.34°C. Adult CBL and first-instar CBL nymphs arrested at 33.69 ± 0.20°C and 34.99 ± 0.26°C, respectively. Groups of each ectoparasite were placed into clear glass vials (n = 10/vial) with one half shaded, and vials were exposed to three light levels, as follows: high (200 µmolm -2s-1) , low (4 µmolm -2s-1), and nearly no light (0 µmolm -2s-1). The vial cap edges provided an opportunity to assess the interactive effect of light with harborage. NFM avoided light and sought harborage. In low light, the harborage preference overrode the tendency to avoid light. CBL avoided the harborage and showed a minimal preference for light. A four-level humidity gradient was established in two separate experimental arenas for NFM and CBL. Trials were run in ambient light (4 µmolm -2s-1) for the NFM and in nearly no light for the CBL. The NFM gradient used 38 ± 2%, 54 ± 7%, 73 ± 3%, and 90 ± 4% RH, whereas the CBL gradient used 42 ± 5%, 48 ± 7%, 63 ± 4%, and 73 ± 5% RH. NFM showed no humidity response in the walking bioassay, but the CBL settled at the lowest humidity level. Temperature and humidity on different hen body regions were related to the bioassay results and observed on-host ectoparasite distributions.
Antigen-Specific IFN-γ Responses Correlate with the Activity of M. tuberculosis Infection but Are Not Associated with the Severity of Tuberculosis Disease

IFN-γ is a key cytokine in antituberculosis (TB) defense. However, how the levels of its secretion affect M. tuberculosis (Mtb) infection is not clear. We have analyzed associations between IFN-γ responses measured in QuantiFERON®-TB Gold In-tube (QFT) assay, TB disease severity, and Mtb infection activity. TB severity was evaluated based on the results of radiological, microbiological, and clinical examinations. Antigen-driven IFN-γ secretion did not correlate with TB severity. Mitogen-induced IFN-γ secretion correlated inversely with the form of pulmonary pathology and the area of affected pulmonary tissue; the levels of spontaneous IFN-γ secretion correlated with patients' age (r = 0.395, p = 0.001). Mtb infection activity was evaluated based on radiological data of lung tissue infiltration, destruction, dissemination or calcification, and condensation. The rate of positive QFT results and the levels of antigen-driven IFN-γ secretion increased in a row: patients with residual TB lesions < patients with low TB activity < patients with high TB activity. Thus, antigen-driven IFN-γ secretion and QFT results did not associate with TB severity but associated with the infection activity. The results suggest that quantitative parameters of IFN-γ secretion play a minor role in determining the course of TB disease but mirror the activity of the infectious process.
A “Buttressed Mesh” Technique for Fascial Closure in Complex Abdominal Wall Reconstruction

Today, plastic surgeons are increasingly faced with the problem of complex abdominal wall reconstruction. Obesity, bariatric surgery, and failed prior herniorrhaphy contribute to high rates of hernia recurrence in these difficult tertiary cases. We reviewed 50 consecutive complex abdominal wall reconstructions to identify the roles of 3 technical variables in successful outcomes: use of mesh, use of a flap buttress to reinforce the fascial repair, and the use of concomitant body-contouring techniques. Six groups were identified based on the presence or absence of each of these variables. Incidence of hernia recurrence and incidence of complications were compared for each group. Patient satisfaction with reconstructive outcome was assessed at follow-up using a 5-point scale. At a mean follow-up of 24 months, we observed an overall hernia recurrence rate of 4.0%, and an overall complication rate of 34%. Tension-free primary fascial repair and mesh repair of tension defects had equivalent recurrence rates (3.3% vs. 5%) and complication rates (40% vs. 25%). Repairs buttressed with flaps and repairs without buttressing had equivalent recurrence rates (3% vs. 6%) and complication rates (38% vs 28%). Repairs with and without body contouring techniques as part of the reconstructive plan had equivalent recurrence rates (7.7% vs. 0%) and complication rates (31.7% vs. 53%). Mean patient satisfaction was 4.8 of 5. Reconstruction of complex and recurrent hernias can be successfully performed. When tension-free primary fascial closure is not possible, an inlay mesh with a soft-tissue buttress leads to a 10-fold reduction in hernia recurrence as compared to historical norms. Concomitant body contouring surgery does not impact recurrence or complication rates and may contribute to reconstructive success.
WHAT DO UNIONS DO (TO NONUNION WORKERS)

This paper develops a model of wage and employment determination under the threat of unionization. The model shows that this threat generally leads nonunion firms to pay higher than competitive wages and to set a level of employment equal to or higher than the competitive employment level. This result holds independently of the model used to represent union-management bargaining, as long as it exhibits an intuitively appealing trade-off between wages and employment (monotonicity). The right-to-manage and the Nash-bargaining models are shown to be monotone, so the result extends to the most commonly used models of unionmanagement bargaining.
Accuracy of intra-articular injections in peripheral joints performed blindly in patients with rheumatoid arthritis.

OBJECTIVES To assess the accuracy of blind IA injections (IAIs) in patients with RA and determine their effectiveness. METHODS A controlled prospective study including 96 RA patients undergoing blind IAIs in peripheral joints was carried out. Clinical evaluation was performed at baseline (T(0)), 1 (T(1)) and 4 (T(4)) weeks after IAI using the following instruments: visual analogue scale (VAS) for pain at rest and movement, VAS for oedema (range 0-10 cm) and morning stiffness. Following IAI, radiographic exam was performed in all joints for further analysis by two 'blinded' radiologists. The kappa-statistic, chi-square and analysis of variance tests were performed to determine potential differences between time-points of evaluation. Significance level was set as P < 0.05. RESULTS A total of 232 injections were performed. Accuracy observed for the shoulder, elbow, wrist, MCP joints, knee and ankle were 82, 100, 97, 97, 100 and 77%, respectively. A statistically significant improvement was observed for all variables at both T(1) and T(4) when compared with T(0). CONCLUSIONS Blind IAI proved safe and accurate when performed by a trained professional. Significant improvement was seen in the VAS for pain at rest and during movement, VAS for oedema and morning stiffness.
Model and simulation study of a peer-to-peer game with a reputation-based incentive mechanism

A distributed, cumulative reputation system is used to encourage resource sharing and cooperation among partic ipants in a peer-to-peer system, specifically a content distr ibution (file-swapping) network. The reputation system that is empl oyed is a variation of one that was shown to be able to reveal true prop ensities to cooperate of the peer nodes. The actions of peer nod es are herein modeled with a game in which users modify the amount of uplink bandwidth they allocate to the network. In principle , increasing uplink bandwidth will result in improved reputati on that will, in turn, result in improved downloading performance. This was demonstrated by our simulation results.
Galectin-3-positive cell infiltration in human diabetic nephropathy.

BACKGROUND Galectin-3 has several functions, such as cell proliferation, regulation of apoptosis and interaction of cell adhesion, and has a high binding affinity for advanced glycation end products. In animal models with diabetic nephropathy (DMN) or acute renal failure, galectin-3 is known to be upregulated. However, galectin-3 expression has not been investigated in human kidney diseases. METHODS Using immunohistochemistry we examined galectin-3 expression in renal biopsy specimens obtained from 37 patients with nephropathy: DMN (n = 9), IgA nephropathy (n = 9), crescentic glomerulonephritis (n = 8), membranous nephropathy (n = 6) and minimal change nephrotic syndrome (n = 5). RESULTS In normal human kidney, galectin-3 was found in distal tubuli, but not in glomeruli. However, galectin-3-positive cell infiltration was observed in glomeruli of 12 patients. Galectin-3-positive cells, also stained with CD68, were significantly more numerous in glomeruli of DMN than in glomeruli of other nephropathies. The ratio of galectin-3-positive cells to the total number of macrophages in tubules was also significantly increased in DMN. There was a significant correlation between the number of galectin-3-positive cells in glomeruli and urinary protein excretion in all patients (r = 0.616, P<0.001). In diabetic patients, the number of galectin-3-positive cells in glomeruli closely correlated with the regression rate of renal function (r = -0.930, P<0.005). CONCLUSION These findings suggest that galectin-3-positive cell infiltration may play an important role in the progression of DMN, and the degree of its expression may be predictive of poor prognosis of DMN.
Interdependence of Muscle Atrophy and Bone Loss Induced by Mechanical Unloading

Mechanical unloading induces muscle atrophy and bone loss; however, the time course and interdependence of these effects is not well defined. We subjected 4‐month‐old C57BL/6J mice to hindlimb suspension (HLS) for 3 weeks, euthanizing 12 to 16 mice on day (D) 0, 7, 14, and 21. Lean mass was 7% to 9% lower for HLS versus control from D7–21. Absolute mass of the gastrocnemius (gastroc) decreased 8% by D7, and was maximally decreased 16% by D14 of HLS. mRNA levels of Atrogin‐1 in the gastroc and quadriceps (quad) were increased 99% and 122%, respectively, at D7 of HLS. Similar increases in MuRF1 mRNA levels occurred at D7. Both atrogenes returned to baseline by D14. Protein synthesis in gastroc and quad was reduced 30% from D7–14 of HLS, returning to baseline by D21. HLS decreased phosphorylation of SK61, a substrate of mammalian target of rapamycin (mTOR), on D7–21, whereas 4E‐BP1 was not lower until D21. Cortical thickness of the femur and tibia did not decrease until D14 of HLS. Cortical bone of controls did not change over time. HLS mice had lower distal femur bone volume fraction (−22%) by D14; however, the effects of HLS were eliminated by D21 because of the decline of trabecular bone mass of controls. Femur strength was decreased approximately 13% by D14 of HLS, with no change in tibia mechanical properties at any time point. This investigation reveals that muscle atrophy precedes bone loss during unloading and may contribute to subsequent skeletal deficits. Countermeasures that preserve muscle may reduce bone loss induced by mechanical unloading or prolonged disuse. Trabecular bone loss with age, similar to that which occurs in mature astronauts, is superimposed on unloading. Preservation of muscle mass, cortical structure, and bone strength during the experiment suggests muscle may have a greater effect on cortical than trabecular bone. © 2014 American Society for Bone and Mineral Research.