Miracle-dz/UniFAR-FTUs huggingface dataset:
Geographic Variation in Host-Specificity and Parasitoid Pressure of an Herbivore (Geometridae) Associated with the Tropical Genus Piper (Piperaceae)

Abstract The extraordinary diversity of tropical herbivores may be linked to hostplant specialization driven in part by variation in pressure from natural enemies. We quantified levels of host-specificity and parasitoid attack for the specialist herbivore, Eois (Geometridae). The goals of this research were to examine: 1) whether Eois are specialized on the genus Piper (Piperaceae) and if hostplant specialization varies geographically; 2) whether Eois are equally vulnerable to parasitoid attack across different geographic regions and by the same parasitoid families; and 3) whether parasitism levels vary with precipitation and elevation. Based on over 15,000 rearings, we found Eois caterpillars feeding exclusively on Piper. However, we did not detect geographic differences in host-specificity; each Eois species fed on an average of two Piper species. Parasitism levels of Eois varied significantly with climate and topography; Eois were most vulnerable to parasitoid attack in moist versus dry and wet forests and at low versus high elevations. The diversity of parasitoid families reared from Eois was greater in Ecuador and Costa Rica than in Panama, where parasitoids were primarily in the family Braconidae. The quantitative evidence for host-specificity provides support for the hypothesis that Eois are specialized on Piper. Our results also reveal that Eois are exposed to a mosaic of potential selective pressures due to variation in parasitoid attack over a large spatial scale.
Automatic detection of melanoma using broad extraction of features from digital images

Automatic and reliable diagnosis of skin cancer, as a smartphone application, is of great interest. Among different types of skin cancers, melanoma is the most dangerous one which causes most deaths. Meanwhile, melanoma is curable if it were diagnosed in its early stages. In this paper we propose an efficient system for prescreening of pigmented skin lesions for malignancy using general-purpose digital cameras. These images can be captured by a smartphone or a digital camera. This could be beneficial in different applications, such as computer aided diagnosis and telemedicine applications. It could assist dermatologists, or smartphone users, evaluate risk of suspicious moles. The proposed method enhances borders and extracts a broad set of dermatologically important features. These discriminative features allow classification of lesions into two groups of melanoma and benign. This method is computationally appropriate as a smartphone application. Experimental results show that our proposed method is superior in diagnosis accuracy compared to state-of-the-art methods.
Functional Alteration of the DMN by Learned Regulation of the PCC Using Real-Time fMRI

The default mode network (DMN) is a network of brain regions that are active during rest and suppressed during a cognitively demanding task. Previous studies have shown that the DMN can be altered by development, aging, disorder, cognitive tasks and offline training. However, it's unclear whether activity in the DMN can be altered by real-time training. Recently, real-time functional magnetic resonance imaging (rtfMRI), as a novel neurofeedback technique, has been applied to train subjects to voluntarily control activities in specific brain regions. In the current study, it was found that by using rtfMRI to guide training, subjects were able to learn to decrease activity in the posterior cingulate cortex (PCC), which is a “key hub” in the DMN, using motor imagery strategy. After the real-time training, activity in the medial prefrontral cortex/ anterior cingulate cortex (MPFC/ACC) of the resting state DMN was decreased. By contrast, the control group without neurofeedback produced increased activity in the MPFC/ACC of the DMN during the post-training resting state. These findings suggest that this rtfMRI technique has great potential to be used in the regulation of the DMN and may be a novel approach for studying functional plasticity of the cortex.
Adaptive Phase Extraction: Incorporating the Gabor Transform in the Matching Pursuit Algorithm

Short-time Fourier transform (STFT), Gabor transform (GT), wavelet transform (WT), and the Wigner-Ville distribution (WVD) are just some examples of time-frequency analysis methods which are frequently applied in biomedical signal analysis. However, all of these methods have their individual drawbacks. The STFT, GT, and WT have a time-frequency resolution that is determined by algorithm parameters and the WVD is contaminated by cross terms. In 1993, Mallat and Zhang introduced the matching pursuit (MP) algorithm that decomposes a signal into a sum of atoms and uses a cross-term free pseudo-WVD to generate a data-adaptive power distribution in the time-frequency space. Thus, it solved some of the problems of the GT and WT but lacks phase information that is crucial e.g., for synchronization analysis. We introduce a new time-frequency analysis method that combines the MP with a pseudo-GT. Therefore, the signal is decomposed into a set of Gabor atoms. Afterward, each atom is analyzed with a Gabor analysis, where the time-domain Gaussian window of the analysis matches that of the specific atom envelope. A superposition of the single time-frequency planes gives the final result. This is the first time that a complete analysis of the complex time-frequency plane can be performed in a fully data-adaptive and frequency-selective manner. We demonstrate the capabilities of our approach on a simulation and on real-life magnetoencephalogram data.
Online Appendix Quality, Trade, and Exchange Rate Pass-Through ¤

We investigate theoretically and empirically the eects of real exchange rate changes on the behavior of …rms exporting multiple products with heterogeneous levels of quality. Our model, which features a demand elasticity that falls with quality, predicts more pricing-to-market and a smaller response of export volumes to a real depreciation for higher quality goods. We provide strong support for the model predictions using a unique data set of Argentinean …rm-level wine export values and volumes between 2002 and 2009 combined with experts wine ratings to measure quality. The heterogeneity we …nd in the response of export prices and volumes to changes in exchange rates remains robust to alternative measures of quality, samples, and speci…cations.
Dependent type theory of stateful higher-order functions

We present a dependent Hoare Type Theory (HTT) which provides support for reasoning about programs with higherorder functions and effects, including non-termination, state with aliasing and pointer arithmetic. The type structure encapsulates effectful commands using a monad indexed by preand post-conditions in the style of Hoare logic. The theory carefully distinguishes between an appropriate notion of definitional equality and propositional equality, in order to maintain the relative decidability of
Author ' s personal copy Using text to build semantic networks for pharmacogenomics

Most pharmacogenomics knowledge is contained in the text of published studies, and is thus not available for automated computation. Natural Language Processing (NLP) techniques for extracting relationships in specific domains often rely on hand-built rules and domain-specific ontologies to achieve good performance. In a new and evolving field such as pharmacogenomics (PGx), rules and ontologies may not be available. Recent progress in syntactic NLP parsing in the context of a large corpus of pharmacogenomics text provides new opportunities for automated relationship extraction. We describe an ontology of PGx relationships built starting from a lexicon of key pharmacogenomic entities and a syntactic parse of more than 87 million sentences from 17 million MEDLINE abstracts. We used the syntactic structure of PGx statements to systematically extract commonly occurring relationships and to map them to a common schema. Our extracted relationships have a 70–87.7% precision and involve not only key PGx entities such as genes, drugs, and phenotypes (e.g., VKORC1, warfarin, clotting disorder), but also critical entities that are frequently modified by these key entities (e.g., VKORC1 polymorphism, warfarin response, clotting disorder treatment). The result of our analysis is a network of 40,000 relationships between more than 200 entity types with clear semantics. This network is used to guide the curation of PGx knowledge and provide a computable resource for knowledge discovery. 2010 Elsevier Inc. All rights reserved.
Accelerated dense random projections

In dimensionality reduction, a set of points in 1Rd is mapped into III, with the target dimension k smaller than the original dimension d, while distances between all pairs of points are approximately preserved. Currently popular methods for achieving this involve random projection, or choosing a linear mapping (a k × d matrix) front a distribution that is independent of the input points. Applying the mapping (chosen according to this distribution) is shown to give the desired property with at least constant probability. The contributions in this thesis are twofold. First, we provide a framework for designing such distributions. Second, we derive efficient random projection algorithms using this framework. Our results achieve performance exceeding other existing approaches. When the target dimension is significantly smaller than the original dimension we gain significant improvement by designing efficient algorithms for applying certain linear algebraic transforms. To demonstrate practicality, we supplement the theoretical derivations with experimental results.
The correlation of insulin resistance and renal function in non diabetic chronic kidney disease patients.

INTRODUCTION A greater degree of insulin resistance may predispose to renal injury by worsening renal hemodynamics through the elevation of glomerular filtration fraction. However, there are sparse data on the relationship between insulin resistance, glomerular filtration rate (GFR) and body composition in chronic kidney disease (CKD) without diabetes. OBJECTIVES To evaluate the relationship between insulin resistance, total body fat and GFR in CKD without diabetes. MATERIAL AND METHOD The authors screened 84 non-diabetic CKD patients according to the K/DOQI definitions and only 78 patients were enrolled into the study (CKD stages 2-4, GFR between 15 and 90 ml/min/ 1.73 m2). Insulin resistance was evaluated by homeostasis model assessment (HOMA-IR). Bioelectrical impedance analysis was performed to determine the percentage of total body fat. GFR was calculated by the average of creatinine and urea clearances. RESULTS The correlation analysis showed that HOMA-IR was positively correlated with percent body fat (r = 0.32, P<0.05), BMI (r = 0.46, P<0.01), serum triglyceride (TG) (r =0.29, P<0.01), and mean arterial pressure (r =0.25, P<0.05), but not significantly correlated with GFR, age, cholesterol, HDL, uric acid and 24-hr urinary protein. CONCLUSION In non-diabetic CKD patients, the independent factor for insulin resistance was the amount of total body fat. The insulin level and HOMA-IR were not dependent on the GFR in the present study.
Focal C4d+ in Renal Allografts Is Associated with the Presence of Donor‐Specific Antibodies and Decreased Allograft Survival

Diffuse peritubular capillary C4d deposition in renal allograft biopsies is associated with donor‐specific antibodies (DSA) and graft failure. The significance of focal C4d+ is unclear. We reviewed 368 biopsies from 301 patients performed for renal dysfunction or proteinuria over 5 years. Diffuse C4d+, focal C4d+ and C4d‐ detected by immunofluorescence occurred in 9.5%, 20.9% and 69.4% of biopsies, respectively. Patients were similar in gender, age, cause of renal disease, donor source, HLA mismatch, serum creatinine at baseline and interval from transplantation to biopsy. Diffuse and focal C4d+ were associated with acute cellular rejection (p < 0.001). Transplant glomerulopathy was associated with diffuse C4d+. DSA at the time of biopsy, were positive in 79.3% of diffusely C4d+ patients, 68.8% of those with focal C4d+ (p = 0.27) and 9.9% of patients with C4d‐ (p < 0.001, compared to either the focal or diffuse groups, respectively). Allograft survival at 40 months was lower in diffuse C4d+ compared to the C4d‐ group (p = 0.014), but not when compared to the focal C4d+ group. There was a clear trend toward worse graft survival in patients with focal C4d+ in this time interval, but focal C4d+ compared to both diffuse C4d+ and C4d‐groups was not statistically significant (p = 0.08).
A Model for Large Deflections of Nanobeams and Experimental Comparison

Bending tests are commonly used for characterization of materials at the nanoscale. Beams are also key elements of nanomechanical and nanoelectromechanical devices. This paper is motivated by recent experiments of large deflections of chromium cantilevers and modeling based on the classical large deflection beam theory to simulate experiments. A review of nanobeam experiments shows complex size dependency of elastic modulus that is influenced by beam thickness (or diameter) and end boundary conditions. A new large deflection beam model that accounts for surface energy effects is presented. It is shown that the model is capable of simulating experiments by using size-independent properties such as bulk elastic modulus and surface residual stress. The model is then used to explain the softening or stiffening behavior observed experimentally in nanocantilevers and relative size independence of clamped-clamped beams. Size dependence of elastic modulus (or stiffening/softening) is a modeling artifact introduced due to the use of classical elasticity theory for nanostructures and the current model shows that simulations based on classical beam theory require careful interpretation.
ABCG5 gene responses to treadmill running with or without administration of Pistachio atlantica in female rats

Objective(s): ABC transporters comprise a large family of transmembrane proteins that use the energy provided by ATP hydrolysis to translocate a variety of substrates across biological membranes. All members of the human ABCG subfamily, except for ABCG2, are cholesterol-transporter. The aim of this study was to determine the liver, the small intestine and kidney ABCG5 relative gene expression in response to treadmill-running training in female rats. Materials and Methods: Twenty Wistar rats (6-8 weeks old and 125-135 g weight) were used. Animals were randomly assigned to saline-control (SC), saline-training (ST), and Baneh-control (BC), and Baneh-training (BT) groups. Training groups did the exercise on a motor-driven treadmill at 25 m/min (0% grade) for 60 min/day for eight weeks (5 days/week). Rats were fed orally, with Baneh extraction and saline for six weeks. The two-way ANOVA was employed for statistical analysis. ABCG5 relative gene expression was detected by Real-time PCR method. Results: The current findings indicate that the Baneh-treated tissues had significantly lower levels of ABCG5 gene expression in the liver, small intestine, and kidneys (P< 0.001, P< 0.003, P< 0.001, respectively), when compared with saline-treated tissues. However, a higher level of gene expression was observed in exercise groups. A lower level of HDL-c but not triglyceride (TG) and total cholesterol (TC) levels were found in Baneh-treated animals at rest. Conclusion: Exercise training increases ABCG5 relative gene expression in the liver, small intestine and kidney tissues; therefore exercise training may adjust the reduction of ABCG5 relative gene expression in Baneh-training group.
Developing a Tourism Innovation Typology

Innovation has become a buzzword, regularly cited to convey any improvement made, regardless of the extent of newness. Tourism innovation has historically been viewed as either incremental or radical, a binary developed within manufacturing. However, given that incremental improvements are the norm in the tourism sector and that radical innovation is an abnormality, the binary is not representative of tourism innovation. We suggest a three-level typology, based on field research in Europe and Australia, and informed by Rogers’s innovation diffusion model; the concept of liminality and its role in the search for tacit knowledge through weak network ties; and the need to ask ultimate (why) rather than proximate (what, how) questions. Since the term innovation is overused, we introduce three alternate concepts: the “artist,” who is comparable to the innovator; the “artisan,” who represents early innovation adopters; and the “painter,” who epitomizes the early and late majority.
The Effects of Repeated Readings and Attentional Cues on Reading Fluency and Comprehension

The failure of some researchers to find improved reading comprehension with increased fluency may result from the assumption that readers automatically shift attention to comprehension when fluency is established. Research on cuing readers to a purpose in reading suggests that a simple cue about comprehension may be sufficient to prompt this attentional shift. In this study, the effects of repeated readings and attentional cues on measures of reading fluency and comprehension were examined. Thirty third graders read separate passages one, three, and seven times following cues to attend to either reading rate or meaning. After the final reading of each passage, the students retold as much of the story as they could. Fluency and proportion of story propositions retold were analyzed in repeated measures analyses of variance. Significant main effects for both repeated readings and attentional cues were obtained on both dependent measures. Thus, both fluency and comprehension increased as the number of repeated readings increased. In addition, readers cued to fluency read faster but comprehended less than those cued to comprehension. These results suggest that increasing fluency is a less efficient means of improving comprehension than presenting cues about comprehension.
Novel performance optimization of large-scale discrete-event simulation on the Cell Broadband Engine

This paper presents a computing technique for efficient parallel simulation of large-scale discrete-event models on the IBM Cell Broadband Engine (CBE), which has one Power Processor Element (PPE) and eight Synergistic Processing Elements (SPE). Based on the general-purpose Discrete Event System Specification (DEVS), the technique tackles all performance bottlenecks, combining multi-dimensional parallelism and various optimizations. Preliminary experiments have produced very promising results, attaining speedups up to 134.34 and 41.23 over the baseline implementation on PPE and on Intel Core2 Duo E6400 processor respectively. The methods can also be applied to other multicore and shared-memory architectures. We conclude that the technique not only allows discrete-event simulation users to tap CBE potential without being distracted by multicore programming, but also provides insight on migration of legacy software to current and future multicore platforms.
"Search-and-capture" of microtubules through plus-end-binding proteins (+TIPs).

The generation of a polarized microtubule organization is critically important for proper cellular functions, such as cell division, differentiation and migration. Microtubules themselves are highly dynamic structures, and this dynamic property is temporally and spatially regulated within cells, especially at their plus ends. To explain how microtubules set up and make contacts with cellular structures, a "search-and-capture" mechanism has been proposed, in which the microtubule plus ends dynamically search for and capture specific sites, such as mitotic kinetochores and cell cortex. To date, several classes of proteins have been shown to be associated with microtubule plus ends in a wide range of organisms from fungi to humans and to play critical roles in the "search-and-capture" mechanism. In this review, we overview our current understanding of the "plus-end-binding proteins" (+TIPs), including APC (adenomatous polyposis coli) tumor suppressor protein, cytoplasmic linker proteins (CLIPs), CLIP-associating proteins (CLASPs), cytoplasmic dynein/dynactin, and EB1, an APC-interacting protein.
Chapter 13 In Silico Control of Biomolecular Processes

By implementing an external feedback loop one can tightly control the expression of a gene over many cell generations with quantitative accuracy. Controlling precisely the level of a protein of interest will be useful to probe quantitatively the dynamical properties of cellular processes and to drive complex, syntheticallyengineered networks. In this chapter we describe a platform for real-time closed-loop control of gene expression in yeast that integrates microscopy for monitoring gene expression at the cell level, microfluidics to manipulate the cells environment, and original software for automated imaging, quantification, and model predictive control. By using an endogenous osmo-stress responsive promoter and playing with the osmolarity of the cells environment, we demonstrate that long-term control can indeed be achieved for both time-constant and time-varying target profiles, at the population level, and even at the single-cell level.
Solids-Liquid Separation of Swine Manure with Polymer Treatment and Sand Filtration

Small particles typical of liquid swine manure often clog sand filter beds and fine filters. We evaluated the effectiveness of polymer flocculants to improve drainage and filtration performance of sand filter beds by increasing the effective particle size. A pilot unit was evaluated at the Swine Unit of the NCSU Lake Wheeler Rd. Laboratory in Raleigh, N.C. , in 35 consecutive cycles during a 19-month period. The unit consisted of a homogenization tank that mixed the flushed manure, an inline polymer mixer, and two sand filter beds (29.7 m2) for dewatering designed to receive 30.5 cm (1- ft) depth of the polymer treated liquid. Flocculation improved drainage characteristics of the sand filter and prevented clogging and surface sealing. The treatment removed 98% of total suspended solids (TSS) and volatile suspended solids (VSS), 87% of BOD, and 84% of COD from the flushed manure. Along with the solids, there was a capture of 62% TKN and 76%TP. Most of the nutrients removed in the solids were organic forms. Drying time to produce removable cakes varied with the loading rate of solids applied to the sand filter bed. A load of 2 kg TSS/m2 per drying cycle provides a balance between bed size and drying time.
Multi-person activity recognition through hierarchical and observation decomposed HMM

Multi-person activity recognition is a challenging task due to the complex interactions between people and the multi-dimensionality of features. This paper proposes a hierarchical and observation decomposed hidden Markov model to classify multi-person activities. In order to give detailed descriptions of people's interactions by different feature scale, states of individual persons and states of interactions between people are separated. In addition, observations are decomposed into groups of subobservations to handle high dimensionality problem of feature space. This decomposition enhances the flexibility in feature selection which enables the combination of discrete and continuous features. Besides, this model has no limitations in terms of the number of persons. Experiments are successfully conducted with encouraging results. Activities of two persons and three persons are classified with good accuracies.