Miracle-dz/UniFAR-FTUs huggingface dataset:
Two-dimensional combinatorial screening and the RNA Privileged Space Predictor program efficiently identify aminoglycoside–RNA hairpin loop interactions

Herein, we report the identification of RNA hairpin loops that bind derivatives of kanamycin A, tobramycin, neamine, and neomycin B via two-dimensional combinatorial screening, a method that screens chemical and RNA spaces simultaneously. An arrayed aminoglycoside library was probed for binding to a 6-nucleotide RNA hairpin loop library (4096 members). Members of the loop library that bound each aminoglycoside were excised from the array, amplified and sequenced. Sequences were analyzed with our newly developed RNA Privileged Space Predictor (RNA-PSP) program, which analyzes selected sequences to identify statistically significant trends. RNA-PSP identified the following unique trends: 5′UNNNC3′ loops for the kanamycin A derivative (where N is any nucleotide); 5′UNNC3′ loops for the tobramycin derivative; 5′UNC3′ loops for the neamine derivative; and 5′UNNG3′ loops for the neomycin B derivative. The affinities and selectivities of a subset of the ligand–hairpin loop interactions were determined. The selected interactions have Kd values ranging from 10 nM to 605 nM. Selectivities ranged from 0.4 to >200-fold. Interestingly, the results from RNA-PSP are able to qualitatively predict specificity based on overlap between the RNA sequences selected for the ligands. These studies expand the information available on small molecule–RNA motif interactions, which could be useful to design ligands targeting RNA.
Finite Element Analysis of the Effect of Flexible Pad on the Deformation of Metal Foils in Flexible Pad Laser Shock Microforming

Flexible Pad Laser Shock Forming (FPLSF) is a new microforming process using laser-induced shock pressure and a flexible pad. This process involves high strain-rate (~105 s-1) plastic deformation of metallic foils along with the hyperelastic deformation of the flexible elastomer pad over which the foil is positioned. This paper studies the influence of flexible pad on the shockwave propagation behavior and the plastic deformation of metal foil in FPLSF using finite element analysis. The effect of flexible pad materials such as silicone rubber, polyurethane rubber and natural rubber on the deformation of copper foils has been analysed in detail. An increase in crater depth is observed with the reduction in flexible pad hardness. However, it is found that there exists an optimum hardness of the flexible pad to achieve perfect hemispherical craters on metal foils, as bending of foils at non-deformed region is observed with softer pads whereas flattening of crater surface occurs with harder pads. The effect of flexible pad thickness on the foil deformation was analyzed at six different thickness levels: 300 μm, 600 μm, 900 μm, 1200 μm, 1500 μm, and 2000 μm. Similarly, there exists an optimum flexible pad thickness to maximize the crater depth and achieve the hemispherical shapes. Analysis of flexible pad thickness indicates that the pad thickness influences the elastic recovery of the flexible-pad and hence the plastic deformation of the metallic foils.
Peptides and receptors controlling root development

The growth of a plant's root system depends on the continued activity of the root meristem, and the generation of new meristems when lateral roots are initiated. Plants have developed intricate signalling systems that employ secreted peptides and plasma membrane-localized receptor kinases for short- and long-range communication. Studies on growth of the vascular system, the generation of lateral roots, the control of cell differentiation in the root meristem and the interaction with invading pathogens or symbionts has unravelled a network of peptides and receptor systems with occasionally shared functions. A common theme is the employment of conserved modules, consisting of a short signalling peptide, a receptor-like kinase and a target transcription factor, that control the fate and proliferation of stem cells during root development. This review intends to give an overview of the recent advances in receptor and peptide ligand-mediated signalling involved in root development.
How the Interval between Prime and Boost Injection Affects the Immune Response in a Computational Model of the Immune System

The immune system is able to respond more vigorously to the second contact with a given antigen than to the first contact. Vaccination protocols generally include at least two doses, in order to obtain high antibody titers. We want to analyze the relation between the time elapsed from the first dose (priming) and the second dose (boost) on the antibody titers. In this paper, we couple in vivo experiments with computer simulations to assess the effect of delaying the second injection. We observe that an interval of several weeks between the prime and the boost is necessary to obtain optimal antibody responses.
Synthesis of Silicon Nanowire Arrays by Metal-Assisted Chemical Etching in Aqueous NH4HF2 Solution

One-step metal-assisted electroless chemical etching of p-type silicon substrate in NH4HF2/AgNO3 solution was investigated. The effect of different etching parameters including etching time, temperature, AgNO3 concentration and NH4HF2 concentration were investigated. The etched layers formed were investigated by scanning electron microscopy (SEM) and Photoluminescence. It was found that the etched layer was formed by well-aligned silicon nanowires. It is noted that their density and length strongly depend on etching parameters. Room temperature photoluminescence (PL) from etched layer was observed. It was observed that PL peak intensity increases significantly with AgNO3 concentration.
Fewer Circulating Endothelial Progenitor Cells in Newly Diagnosed Neovascular AMD Patients

Objective: Patients with age-related macular degeneration (AMD) exhibit pathologic neovascularization under the retina, with choroidal neovascularization (CNV) suggestive of defective angiogenesis. The endothelial progenitor cells (EPCs) present in the peripheral blood contribute to angiogenesis and vasculogenesis, and their regulation is altered in several vascular disorders. We investigated whether the numbers and functional properties of EPCs may be disordered in newly diagnosed neovascular AMD. Methods Fifteen suitable AMD patients and 10 controls matched for age, risk factors for atherosclerosis and use of medi- cation that could influence the circulating pool of EPCs were studied. Circulating EPCs were assayed by the col- ony-forming unit (CFU) method. The EPCs' adhesive capacity was studied by evaluating their ability to attach to fi- bronectin and cultured endothelial cells. Serum levels of vascular endothelial growth factor (VEGF) were studied and cor- related with EPC numbers. Results: The patients had significantly fewer circulating EPCs(16.5±2.8) compared to their controls (31±4.6; p=0.0085). The functional properties of both groups' EPCs were similar. Conclusions: The peripheral circulating pool of endothelial stem cells is altered in patients with newly diagnosed neovas- cular AMD, suggesting that pathologic angiogenesis may result from or influence the regulation of endothelial precursor circulation.
A Novel Biometrics Triggered Watermarking Of Images Based On Wavelet Based Contourlet Transform

The rapid development of network and digital technology has led to several issues to the digital content. The technical solution to provide law enforcement and copyright protection is achieved by digital watermarking Digital watermarking is the process of embedding information into a digital image in a way that is difficult to remove. The proposed method contains following phases (i) Pre-processing of biometric image (ii) key generation from the biometrics of the owner/user and randomization of the host image using Speeded-Up Robust Features (SURF) (iii) Wavelet-Based Contourlet Transform (WBCT) is applied on the host image. The WBCT can give the anisotropy optimal representation of the edges and contours in the image by virtue of the characteristics of multiscale framework and multi-directionality (iv) Singular Value Decomposition (SVD) is enforced over the watermark image (v) Embedding of the host image with the watermark image. The comparative analysis confirms the efficiency and robustness of the proposed system
Multidisciplinary team care in rehabilitation: an overview of reviews.

OBJECTIVES To systematically investigate current scientific evidence about the effectiveness of multidisciplinary team rehabilitation for different health problems. DATA SOURCES A comprehensive literature search was conducted in Cochrane, Medline, DARE, Embase, and Cinahl databases, and research from existing systematic reviews was critically appraised and summarized. STUDY SELECTION Using the search terms "rehabilitation", "multidisciplinary teams" or "team care", references were identified for existing studies published after 2000 that examined multidisciplinary rehabilitation team care for adults, without restrictions in terms of study population or outcomes. The most recent reviews examining a study population were selected. DATA EXTRACTION Two reviewers independently extracted information about study populations, sample sizes, study designs, rehabilitation settings, the team, interventions, and findings. DATA SYNTHESIS A total of 14 reviews were included to summarize the findings of 12 different study populations. Evidence was found to support improved functioning following multidisciplinary rehabilitation team care for 10 of 12 different study population: elderly people, elderly people with hip fracture, homeless people with mental illness, adults with multiple sclerosis, stroke, acquired brain injury, chronic arthropathy, chronic pain, low back pain, and fibromyalgia. Whereas evidence was not found for adults with amyetrophic lateral schlerosis, and neck and shoulder pain. CONCLUSION Although these studies included heterogeneous patient groups the overall conclusion was that multidisciplinary rehabilitation team care effectively improves rehabilitation intervention. However, further research in this area is needed.
Explorative navigation of mobile sensor networks using sparse Gaussian processes

This paper presents an explorative navigation method using sparse Gaussian processes for mobile sensor networks. We first show that a near-optimal approximation is possible with a subset of measurements if we select the subset carefully, i.e., if the correlation between the selected measurements and the remaining measurements is small and the correlation between the prediction locations and the remaining measurements is small. An estimation method based on a subset of measurements is desirable for mobile sensor networks since we can always bound computational and memory requirements and unprocessed raw measurements can be easily shared with other agents for further processing (e.g., consensus-based distributed algorithms or distributed learning). We then present an explorative navigation method using sparse Gaussian processes with a subset of measurements. Using the explorative navigation method, mobile sensor networks can actively seek for new measurements to reduce the prediction error and maintain high-quality estimation about the field of interest indefinitely with limited memory.
Deposited in DRO : 13 October 2015 Version of attached le : Accepted Version Peer-review status of attached le : Peer-reviewed Citation for published item :

In this paper we develop the a posteriori error estimation of hp–version discontinuous Galerkin composite finite element methods for the discretization of second–order elliptic partial differential equations. This class of methods allows for the approximation of problems posed on computational domains which may contain a huge number of local geometrical features, or microstructures. While standard numerical methods can be devised for such problems, the computational effort may be extremely high, as the minimal number of elements needed to represent the underlying domain can be very large. In contrast, the minimal dimension of the underlying composite finite element space is independent of the number of geometric features. Computable bounds on the error measured in terms of a natural (mesh-dependent) energy norm are derived. Numerical experiments highlighting the practical application of the proposed estimators within an automatic hp–adaptive refinement procedure will be presented.
An efficient throughput improvement through bandwidth awareness in cognitive radio networks

This paper proposes a bandwidth-aware localized-routing algorithm that is capable of sensing the available spectrum bands within a two-hop neighboring for choosing the highly opportunistic routes. A mixed-integer linear programming (MILP) is utilized to formulate the optimization problem. Then, the proposed algorithm is used to determine the maximum bandwidth possible of link pairs via a bandwidth approximation process of relaxed variables. Thereby, the proposed algorithm can allow selected routes corresponding to maximum bandwidth possible between cognitive radio (CR) users through link pairs in cognitive radio networks. By comparing the solution values to previous works, simulation results demonstrate that the proposed algorithm can offer a closed-optimal solution for routing performance in cognitive radio networks. The contribution of this paper is achieved through approximately 50% throughput utilized in the network.
A Mild Impairment of Mitochondrial Electron Transport Has Sex-Specific Effects on Lifespan and Aging in Mice

Impairments of various aspects of mitochondrial function have been associated with increased lifespan in various model organisms ranging from Caenorhabditis elegans to mice. For example, disruption of the function of the ‘Rieske’ iron-sulfur protein (RISP) of complex III of the mitochondrial electron transport chain can result in increased lifespan in the nematode worm C. elegans. However, the mechanisms by which impaired mitochondrial function affects aging remain under investigation, including whether or not they require decreased electron transport. We have generated knock-in mice with a loss-of-function Risp mutation that is homozygous lethal. However, heterozygotes (Risp+/P224S) were viable and had decreased levels of RISP protein and complex III enzymatic activity. This decrease was sufficient to impair mitochondrial respiration and to decrease overall metabolic rate in males, but not females. These defects did not appear to exert an overtly deleterious effect on the health of the mutants, since young Risp+/P224S mice are outwardly normal, with unaffected performance and fertility. Furthermore, biomarkers of oxidative stress were unaffected in both young and aged animals. Despite this, the average lifespan of male Risp+/P224S mice was shortened and aged Risp+/P224S males showed signs of more rapidly deteriorating health. In spite of these differences, analysis of Gompertz mortality parameters showed that Risp heterozygosity decreased the rate of increase of mortality with age and increased the intrinsic vulnerability to death in both sexes. However, the intrinsic vulnerability was increased more dramatically in males, which resulted in their shortened lifespan. For females, the slower acceleration of age-dependent mortality results in significantly increased survival of Risp+/P224S mice in the second half of lifespan. These results demonstrate that even relatively small perturbations of the mitochondrial electron transport chain can have significant physiological effects in mammals, and that the severity of those effects can be sex-dependent.
Fast Entropy Clustering of sparse high dimensional binary data

We introduce Sparse Entropy Clustering (SEC) which uses minimum entropy criterion to split high dimensional binary vectors into groups. The idea is based on the analogy between clustering and data compression: every group is reflected by a single encoder which provides its optimal compression. Following the Minimum Description Length Principle the clustering criterion function includes the cost of encoding the elements within clusters as well as the cost of clusters identification. Proposed model is adopted to the sparse structure of data - instead of encoding all coordinates, only non-zero ones are remembered which significantly reduces the computational cost of data processing. Our theoretical and experimental analysis proves that SEC works well with imbalance data, minimizes the average entropy within clusters and is able to select the correct number of clusters.
The Design of Clocked-Comparator-Based Time-Interval Measurement Circuit for Pulse ToF Measurement

A clocked-comparator-based time-interval measurement approach is proposed for the measurement of the time-of-flight (ToF) of wave pulses in a threshold-crossing-detection-based pulse ToF range-finding application. As compared to the conventional TDC-based pulse ToF measurement approach, the proposed approach does not require the use of extra channels in the case where multiple echoes can be expected for every wave pulse launched. As compared to the conventional (flash) analog-to-digital converter-based pulse ToF measurement approach, the proposed approach allows for a simpler backend digital processing and does not require the comparators used in the measurement to be skew-less. Meanwhile, the approach leverages on the strength of a clocked comparator circuit, which can be designed with a very wide sampling bandwidth. A clocked-comparator-based time-interval measurement circuit with a ~7-GHz bandwidth was assembled using low cost commercial-of-the-shelf components. The measurements done using the measurement circuit agree to within 10 ps with the same measurements done using a 13-GHz, 40-GSa/s oscilloscope and are precise to within ±15 ps in terms of their $2\sigma $ range.
The Clinical Research Data Repository of the US National Institutes of Health

The US National Institutes of Health (NIH) includes 27 institutes and centers, many of which conduct clinical research. Previously, data collected in research trials has existed in multiple, disparate databases. This paper describes the design, implementation and experience to date with the Biomedical Translational Research Information System (BTRIS), being developed at NIH to consolidate clinical research data. BTRIS is intended to simplify data access and analysis of data from active clinical trials and to facilitate reuse of existing data to answer new questions. Unique aspects of the system includes a Research Entities Dictionary that unifies all controlled terminologies used by source systems and a hybrid data model that unifies parts of the source data models and include other data in entity-attribute value tables. BTRIS currently includes over 300 million rows of data, from three institutes, ranging from 1976 to present. Users are able to retrieve data on their own research subjects in identified form as well as deidentified data on all subjects.
Partially tagged image clustering

With the growth of tagged images, researchers are using this highly semantic tag information to assist some vision tasks such as image clustering. However, users may not tag some images at all or some of the images are partially annotated, and this will lead to performance degradation, which is rarely considered by previous works. To alleviate this problem, we propose a new model for image clustering assisted by partially observed tags. Our model enforces sparse representations obtained through sparse coding and latent tag representations learned via matrix factorization to be consistent with the partial image-tag observations. The partition of image database is finally performed using clustering algorithms (e.g., k-means) on the sparse representations. Extensive experiments demonstrate that the proposed model performs better than the state-of-the-art methods.
Effects of iron supplementation in nonanemic pregnant women, infants, and young children on the mental performance and psychomotor development of children: a systematic review of randomized controlled trials.

BACKGROUND Uncertainty exists regarding the effects of iron supplementation on neurodevelopmental outcomes in the absence of anemia. OBJECTIVE Our objective was to evaluate the effects of iron supplementation in nonanemic pregnant women and in nonanemic healthy children aged <3 y on the mental performance and psychomotor development of children. DESIGN In this systematic review, MEDLINE, EMBASE, and The Cochrane Library were searched through December 2009 for randomized controlled trials (RCTs). RESULTS None of 5 RCTs individually showed a beneficial effect of iron supplementation during early life on the Mental Developmental Index of the Bayley Scales of Infant Development at different ages throughout the first 18 mo. Meta-analysis of 3 RCTs (n = 561) showed that, compared with placebo, supplementation with iron had no significant effect on children's Mental Developmental Index at approximately 12 mo of age (weighted mean difference: 1.66; 95% CI: -0.14, 3.47). Three of 5 RCTs showed a beneficial effect of iron supplementation on the Psychomotor Development Index at some time points, whereas 2 did not. Meta-analysis of 3 RCTs (n = 561) showed significant improvement on the Psychomotor Development Index at approximately 12 mo of age in the iron-supplemented group compared with the control group (weighted mean difference: 4.21; 95% CI: 2.31, 6.12). Two RCTs showed no effect of iron supplementation on behavior. Neither of the 2 RCTs that addressed the influence of prenatal iron supplementation showed an effect of iron on either the intelligence quotient or behavioral status of the children. CONCLUSION Limited available evidence suggests that iron supplementation in infants may positively influence children's psychomotor development, whereas it does not seem to alter their mental development or behavior.