Miracle-dz/UniFAR-FTUs huggingface dataset:
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

Current practice in the normalization of microbiome count data is inefficient in the statistical sense. For apparently historical reasons, the common approach is either to use simple proportions (which does not address heteroscedasticity) or to use rarefying of counts, even though both of these approaches are inappropriate for detection of differentially abundant species. Well-established statistical theory is available that simultaneously accounts for library size differences and biological variability using an appropriate mixture model. Moreover, specific implementations for DNA sequencing read count data (based on a Negative Binomial model for instance) are already available in RNA-Seq focused R packages such as edgeR and DESeq. Here we summarize the supporting statistical theory and use simulations and empirical data to demonstrate substantial improvements provided by a relevant mixture model framework over simple proportions or rarefying. We show how both proportions and rarefied counts result in a high rate of false positives in tests for species that are differentially abundant across sample classes. Regarding microbiome sample-wise clustering, we also show that the rarefying procedure often discards samples that can be accurately clustered by alternative methods. We further compare different Negative Binomial methods with a recently-described zero-inflated Gaussian mixture, implemented in a package called metagenomeSeq. We find that metagenomeSeq performs well when there is an adequate number of biological replicates, but it nevertheless tends toward a higher false positive rate. Based on these results and well-established statistical theory, we advocate that investigators avoid rarefying altogether. We have provided microbiome-specific extensions to these tools in the R package, phyloseq.
Distributed monitoring and workflow management for goal‐oriented workflows

Business process management has often focused on business processes with a production or administrative focus, resulting in a task‐centric approach for modeling and execution of workflow based on the processes. However, the area of collaborative business processes exists, which includes important processes like research and development which have not been adequately addressed by the techniques offered for production workflows. For this, goal‐oriented processes have been proven useful to allow for a more flexible approach in modeling and executing workflow. In addition, distributed workflow management allows for a more flexible approach regarding organizational structures. However, the actual recording of action taken in a process is still relevant for workflow analysis and re‐engineering. As a result, this paper presents a distributed approach for generating, gathering, distributing, and storing events resulting from the execution of goal‐oriented workflows in a distributed workflow environment while allowing the real‐time association of occuring actions with business goals in the process using drill‐down analysis. Copyright © 2015 John Wiley & Sons, Ltd.
Implementation and Applications of Tri-State Self-Organizing Maps on FPGA

This paper introduces a tri-state logic self-organizing map (bSOM) designed and implemented on a field programmable gate array (FPGA) chip. The bSOM takes binary inputs and maintains tri-state weights. A novel training rule is presented. The bSOM is well suited to FPGA implementation, trains quicker than the original self-organizing map (SOM), and can be used in clustering and classification problems with binary input data. Two practical applications, character recognition and appearance-based object identification, are used to illustrate the performance of the implementation. The appearance-based object identification forms part of an end-to-end surveillance system implemented wholly on FPGA. In both applications, binary signatures extracted from the objects are processed by the bSOM. The system performance is compared with a traditional SOM with real-valued weights and a strictly binary weighted SOM.
An Algorithm for Coastline Extraction from Satellite Imagery

Monitoring of coastline areas facilitates landscape development, sea transport, sea-level rise, changes in coastal areas and other important activities so it is very important that coastline extraction is quick and precise. In the past coastline extraction consisted of two stages: high-resolution images were captured from airplane and then coastline was drawn based on these images. This operation was slow compared to today’s modern techniques such as satellite images and image processing. In this paper we proposed a new technique for coastline extracting from satellite images. The proposed procedure is based on algorithms for image processing and edge detection. Experimental results showed that the proposed method was fast and accurate.
A chunk-based resource allocation scheme for downlink MIMO-OFDMA channel using linear precoding

This paper presents a novel chunk-based resource allocation scheme for MIMO-OFDMA multiuser downlink channel. In chunk-based resource allocation, a number of contiguous subcarriers of each OFDM symbol are considered as a chunk and resource allocation is performed on chunk-by-chunk basis. Herein, an optimization problem is formulated that aims to maximize system sum rate under an average power constraint per chunk when Zero Forcing Beamforming (ZFB) is used for inter-user interference elimination within chunks. Under this framework, a low-complexity resource allocation algorithm is presented that exploits frequency and space correlation of wireless channels and jointly solves the problems of chunk allocation and power allocation. Simulation results show that the proposed algorithm performs closely to the optimal solution of the examined problem.
Efficacy of Trans-Mastoidal Vestibular Galvanic Stimulation in Improvement of Gait Performance and Upright Postural Stability in Hemiplegic C.P. Children

Objectives: This work was carried out to investigate the efficacy of galvanic vestibular stimulation in improving of gait performance and upright postural stability in hemiplegic cerebral palsy children. Method: Thirty children were enrolled in this study and randomly assigned into two groups; group A (galvanic vestibular stimulation plus vestibular training program), and group B (vestibular training program only). Stride length and time, walking speed tests and modified Ashworth, pediatric balance scales were used to detect and follow the walking performance and upright postural stability. This measurement was taken before initial treatment and after 12 weeks of treatment. The children parents in both groups A and B were instructed to complete 3 hours of the home routine program. Results: Data analysis was available on the 30 hemiplegic cerebral palsied children participated in the study. The difference between pre and post-treatment results was significant representative in stride length , time and walking velocity, spasticity changes and pediatric balance scores in study groups while insignificant improvement in control groups. Conclusion: The combined vestibular training program and trans-mastoidal vestibular galvanic stimulation are suggested in improving walking performance and upright postural stability in a static and dynamic situation. So this selective physiotherapy approach may be used as a strong choice for improving walking and balance abilities in hemiplegic C.P children.
Speech Recognition using Neural Networks

Speech is the most common way for humans to interact. Since it is the most effective method for communication, it can be also extended further to interact with the system. As a result, it has become extremely popular in no time. The speech recognition allows system to interact and process the data provided verbally by the user. Ever since the user can interact with the help of voice the user is not confined to the alphanumeric keys. Speech recognition can be defined as a process of recognizing the human voice to generate commands or word strings. It is also popularly known as ASR (Automatic speech recognition), computer speech recognition or speech to text (STT). Speech recognition activity can be performed after having a knowledge of diverse fields like linguistic and computer science. It is not an isolated activity. Various techniques available for speech recognition are HMM (Hidden Markov model)[1], DTW(Dynamic time warping)based speech recognition[2], Neural Networks[3], Deep feedforward and recurrent neural networks[4] and End-to-end automatic speech recognition[5]. This paper mainly focusses on Different Neural networks used for Automatic speech recognition. This research paper primarily focusses on different types of neural networks used for speech recognition. In addition to this paper also consist of work done on speech recognition using this neural networks. Keywords— Speech recognition; Recurrent Neural network; Hidden Markov Model; Long Short term memory network
Glutamate receptors mediate dynamic regulation of nitric oxide synthase expression in cerebellar granule cells

Nitric oxide (NO) is a multifaceted messenger molecule believed to be involved in neural plasticity and development. Within the cerebellum, the NO synthesizing enzyme, NO synthase (NOS), is expressed exclusively by granule cells and stellate/basket neurons. In the adult cerebellum, levels of NOS expression can be used to define discrete clusters of granule cell populations. Differential expression of NOS by granule cells temporally coincides with the establishment of afferent innervation of granule cells. In primary cerebellar cultures that comprise a functional network of glutamatergic and GABAergic cerebellar neurons, blockade of electrical activity by tetrodotoxin induced the expression of the neuronal isoform of NOS (nNOS) in granule cells. Conversely, direct depolarization of cultured neurons with K+ completely downregulated nNOS expression. Suppression of NMDA receptor- and AMPA receptor-mediated spontaneous synaptic signaling in cultured cells resulted in a drastic upregulation of nNOS expression in granule neurons. In contrast, blockade of GABAA receptor-mediated intercellular communication did not affect nNOS expression by granule cells. Blocking N-, P-, and Q-type voltage-dependent Ca2+ channels resulted in a graded upregulation of NOS expression, whereas manipulations of the cAMP- dependent signal transduction pathway induced no changes. We conclude that nNOS expression in developing cerebellar granule cells is regulated by excitatory neurotransmission and that calcium is an important signal transduction molecule involved in this regulatory process.
An Open-Source, Efficient, and Parameterizable Hardware Implementation of the AES Algorithm

Although the reliability and robustness of the AES protocol have been deeply proved through the years, recent research results and technology advancements are rising serious concerns about its solidity in the (quite near) future. In this context, we are proposing an extension of the AES algorithm in order to support longer encryption keys (thus increasing the security of the algorithm itself). In addition to this, we are proposing a set of parametric implementations of this novel extended protocols. These architectures can be optimized either to minimize the area usage or to maximize their performance. Experimental results show that, while the proposed implementations achieve a throughput higher than most of the state-of-the-art approaches and the highest value of the Performance/Area metric when working with 128-bit encryption keys, they can achieve a 84× throughput speed-up when compared to the approaches that can be found in literature working with 512-bit encryption keys.
Complete mitochondrial genome of the silkworm strain, Hukpyobeom Bombyx mori (Lepidoptera: Bombycidae), that has a unique larval body marking

Abstract In Korea, a new Bombyx mori (Lepidoptera: Bombycidae) strain, which has a peculiar larval body marking was bred to draw public attention to the importance of national resources. We sequenced the complete mitochondrial genome (mitogenome) of the strain “Hukpyobeom” and phylogenetic relationships of the strain were analyzed. The complete genome of the strain comprised 15,671 bp, contained a typical set of genes of animals, and had a gene arrangement and composition typical in Lepidoptera. The newly bred “Hukpyobeom” strain had a 20-50 bp longer whole genome size, 39 bp longer protein-coding genes, and 5-23 bp shorter intergenic spacer regions compared to the other strains. Phylogenetic analyses showed the “Hukpyobeom” to form a strong subgroup together with each one Japan- and China-originated strain. A strain originating from Russia (strain name Soviet_Union_No.1) was placed as the most basal lineage, forming a sister to the remaining strains, indicating genetic divergence within B. mori.
Symbolic quasi-static scheduling of actor-oriented SystemC models

In this paper, we propose a quasi-static scheduling (QSS) method applicable to actor-oriented SystemC designs. QSS determines a schedule where several static schedules are combined in a dynamic schedule to reduce runtime overhead. This is done by performing as much static scheduling as possible at compile time, and only treating data-dependent control flow as runtime decision. Our approach improves known quasi-static approaches in a way that it is directly applicable to real world designs, and has less restrictions on the underlying model. The effectiveness of the approach based on symbolic computation is demonstrated by scheduling a SystemC design of a network packet filter.
Parallel path planning with multiple evasion strategies

Probabilistic path planning driven by a potential field is a well established technique and has been successfully exploited to solve complex problems arising in a variety of domains. However, planners implementing this approach are rather inefficient in dealing with certain types of local minima occurring in the potential field, especially those characterized by deep or large attraction basins. In this paper, we present a potential field planner combining "smart" escape motions from local minima with parallel computation to improve overall performance. The results obtained show significant improvement in planning time, along with remarkable reduction in standard deviation. A performance comparison on a benchmark problem of the potential field planner and an existing, state-of-the-art planner is also included. Our investigation confirms the effectiveness of potential field as heuristic to solve difficult path planning problems.
A Phase I Dose-Escalation Study Evaluating the Safety Tolerability and Pharmacokinetics of CUDC-427, a Potent, Oral, Monovalent IAP Antagonist, in Patients with Refractory Solid Tumors

Purpose: To determine the dose-limiting toxicities (DLT), adverse events (AE), pharmacokinetics, and preliminary evidence of antitumor activity of CUDC-427 (formerly GDC-0917), a selective antagonist of inhibitor of apoptosis (IAP) proteins. Experimental Design: Patients with advanced solid malignancies were treated with escalating doses of CUDC-427 orally on a daily 14-day on/7-day off schedule in 21-day cycles using a modified continuous reassessment method design. Blood samples were assayed to determine the pharmacokinetic properties, pharmacodynamic alterations of cellular IAP levels in peripheral blood mononuclear cells (PBMC), and monocyte chemoattractant protein-1 (MCP-1) levels. Results: Forty-two patients received 119 cycles of CUDC-427. Overall, the most common treatment-related toxicities were fatigue, nausea, vomiting, and rash. One DLT (grade 3 fatigue) occurred in a patient at 450 mg dose level during cycle 1, and 5 patients experienced AEs related to CUDC-427 that led to discontinuation and included grade 3 pruritus, and fatigue, and grade 2 drug hypersensitivity, pneumonitis, rash, and QT prolongation. The maximum planned dose of 600 mg orally daily for 2 weeks was reached, which allometrically scaled to exceed the IC90 in preclinical xenograft studies. Significant decreases in cIAP-1 levels in PBMCs were observed in all patients 6 hours after initial dosing. Responses included durable complete responses in one patient with ovarian cancer and one patient with MALT lymphoma. Conclusions: CUDC-427 can be administered safely at doses up to 600 mg daily for 14 days every 3 weeks. The absence of severe toxicities, inhibition of cIAP-1 in PBMC, and antitumor activity warrant further studies. Clin Cancer Res; 22(18); 4567–73. ©2016 AACR.
Development of Clay Tile Coatings for Steep-Sloped Cool Roofs

Most of the pitched roofs of existing buildings in Europe are covered by non-white roofing products, e.g., clay tiles. Typical, cost effective, cool roof solutions are not applicable to these buildings due to important constraints deriving from: (i) the owners of homes with roofs visible from the ground level; (ii) the regulation about the preservation of the historic architecture and the minimization of the visual environment impact, in particular in historic centers. In this perspective, the present paper deals with the development of high reflective coatings with the purpose to elaborate “cool” tiles with the same visual appearance of traditional tiles for application to historic buildings. Integrated experimental analyses of reflectance, emittance, and superficial temperature were carried out. Deep analysis of the reflectance spectra is undertaken to evaluate the effect of different mineral pigments, binders, and an engobe basecoat. Two tile typologies are investigated: substrate-basecoat-topcoat three-layer tile and substrate-topcoat two-layer tile. The main results show that the developed coatings are able to increase the overall solar reflectance by more than 20% with acceptable visual appearance, suitable for application in historic buildings. Additionally, the effect of a substrate engobe layer allows some further contribution to the increase of the overall reflectance characteristics.
Optimization of Individual Adaptation and Disability-Related Factors: Considerations for the Case Manager

Purpose: The purpose of this article is to review the literature on individual adaptation to physical-related disabilities. A majority of the literature reviewed focuses on lifestyle issues of the physically disabled or individuals with chronic illnesses. These include coping, adaptation, personal control, and the ability to achieve an optimal level of functioning. Optimal health and well-being are correlated with adaptation and individual characteristics which influence coping mechanisms. Socioeconomic, psychological, emotional, and spiritual needs are all associated with adaptation. Adaptation is a continuous, individualized, long-term, and often-complex process that has an unpredictable outcome. Each individual has different perceptions of how to optimize his or her health and well-being. Case managers of all disciplines must be prepared to be effective, clinical resources who can evaluate individual adaptation and disability-related factors. Coping mechanisms vary and individual outcomes are optimized by setting goals in the most effective manner possible. Primary practice setting: Multidisciplinary collaboration among individuals in medical, nursing, and social work environments such as acute care facilities, long-term care, subacute rehabilitation, and managed care organizations. Findings/conclusion: As case managers, it is inevitable that we will encounter adaptation and disability. Understanding our patient's individual descriptions of optimal health and well-being can help facilitate positive outcomes. Implications for case management practice: Multidisciplinary case managers are on the forefront of assisting individuals with adaptation and disability-related factors. Implementation strategies must include knowledge of, and utilization of, resources, and intercollaborative and intracollaborative networking. Further exploration is needed to assist in eliminating or minimizing nonadherence to coping with disability.
A freshly baked perspective on how we measure risk propensity in children

Children are notoriously fearless; running across slippery grass, eating bugs, and climbing up to the top of trees while their anxious parent yells at them to get down. Research on the development of risk propensity suggests that as we get older, risk aversion increases. However, there is little research on risk aversion within the preschool age range. The current study introduces the Child Risk Utility Measure (CRUM), a developmentally sensitive, dynamic task that measures risk propensity. We develop a novel cognitive modeling perspective to interpret our behavioral data and segregate the effects of risk propensity, probability learning, contaminant processes, and age effects within a unified framework. Unlike previous studies of risk propensity, we found reasonable evidence suggesting that preschool-aged children do not become more cautious as they get older. Any effect of age was attributed to confounds due to contaminant behavior. We suggest this as an alternative explanation for age effects in risk propensity during early childhood.
Self-assembled gold nanoparticles for in-vitro inhibition of bovine viral diarrhea virus as surrogate model for HCV

In these study, the antiviral activity and the in-vitro cytotoxic effect of functionalized gold nanoparticles (GNPS) were explored, which were previously assigned to possess in-vitro antiviral properties towards Human Immuno-diffiecny virus, Vesicular Stomatitis virus. To investigate the antiviral potential of prepared GNPS against cytopathic strain (NADL) bovine viral diarrhea virus (BVDV): citrated GNPS were synthesized and then PEG di-thiol functionalized. The NPS (before and after PEGlation) were characterized and their morphology studied via Transmission Electron Microscope (TEM), Absorption Spectra, Zeta Potential as well as the IR studies. The absorption spectra showed a red shifting in the λmax of citrated GNPS from 520 nm to 529 nm after PEGlation. The TEM images showed the particle size was around 12 nm and 15 nm for citrated and PEGlated GNPS, respectively with a distinguishable self-assembly for NPS over polymer. MTT cell viability assay did not show any cytotoxic effect for GNPs on MDBK cells with concentrations of 2 and 4 ppm. Afterward, GNPs’ antiviral activity has been determined. Our results showed that functionalized GNPs has limited in-vitro toxic effect in certain concentrations and also has a strong affinity to BVD virus as well as efficient attachment inhibitory effect.
An Efficient Fragile Watermarking Scheme for Pixel-Wise Tamper Detection

In this paper we propose a novel pixel-wise fragile watermarking scheme which is able to detect tampered pixels with very high probability. Based on a new technique called Image-Dependent Seed (IDS), the proposed method is not only efficient but also secure against many known attacks. Furthermore, the proposed scheme can be simply implemented with only bit-wise AND and Exclusive-OR operations.