Miracle-dz/UniFAR-FTUs huggingface dataset:
Standardization of the Tanner-Whitehouse bone age method in the context of automated image analysis

Background/aims: The Tanner-Whitehouse (TW) method for bone age determination has been the basis for many population studies and it is used in many clinics. However, TW bone age raters can differ systematically from each other. The aim of the study was to present a new standard version of TW bone age rating implemented by the automated BoneXpert method and calibrated on the manual TW stage ratings of the First Zurich Longitudinal Study. Subjects: Hand radiographs of 231 children born in 1954–1956 were recorded annually from an average age of 5–20 years. For validation, 76 X-rays of Tanner's original Gold Series from eight boys were used. Results: The root mean square deviation between manual and automated TW ratings in the Zurich data was 0.67 years for boys in the TW bone age range 5–15 years and 0.63 years for girls, 5–14 years. The new standard TW rating differs systematically from two previous TW versions of the automated method, based on different raters. Conclusion: The new automated TW ratings show good accuracy relative to the manual ratings of the Zurich data and the Gold Series. There are significant differences between manual TW raters, an effect which is eliminated with the automated method.
Ultrahigh molecular recognition specificity of competing DNA oligonucleotide strands in thermal equilibrium: a cooperative transition to order

The specificity of molecular recognition is important for molecular self-organization. A prominent example is the biological cell where a myriad of different molecular receptor pairs recognize their binding partners with astonishing accuracy within a highly crowded molecular environment. In thermal equilibrium it is usually admitted that the affinity of recognizer pairs only depends on the nature of the two binding molecules. Accordingly, Boltzmann factors of binding energy differences relate the molecular affinities among different target molecules that compete for the same probe. Here, we consider the molecular recognition of short DNA oligonucleotide single strands. We show that a better matching oligonucleotide can prevail against a disproportionally more concentrated competitor with reduced affinity due to a mismatch. We investigate the situation using fluorescence-based techniques, among them Förster resonance energy transfer and total internal reflection fluorescence excitation. We find that the affinity of certain strands appears considerably reduced only as long as a better matching competitor is present. Compared to the simple Boltzmann picture above we observe increased specificity, up to several orders of magnitude. We interpret our observations based on an energy-barrier of entropic origin that occurs if two competing oligonucleotide strands occupy the same probe simultaneously. Due to their differences in binding microstate distributions, the barrier affects the binding affinities of the competitors differently. Based on a mean field description, we derive a resulting expression for the free energy landscape, a formal analogue to a Landau description of phase transitions reproducing the observations in quantitative agreement as a result of a cooperative transition. The advantage of improved molecular recognition comes at no energetic cost other than the design of the molecular ensemble and the presence of the competitor. As a possible application, binding assays for the detection of single nucleotide polymorphisms in DNA strands could be improved by adding competing strands. It will be interesting to see if mechanisms along similar lines as exposed here contribute to the molecular synergy that occurs in biological systems.
Supplementary Materials For: Consistency of Random Forests

Technical Lemma 1. Assume that (H1) is satisfied and that L ≡ 0 for all cuts in some given cell A. Then the regression function m is constant on A. Proof of Technical Lemma 1. We start by proving the result in dimension p = 1. Letting A = [a, b] (0 ≤ a < b ≤ 1), and recalling that = − 1 (b − a) 2 b a m(t)dt 2 + 1 (b − a)(z − a) z a m(t)dt 2 + 1 (b − a)(b − z) b z m(t)dt 2. Let C = b a m(t)dt and M (z) = z a m(t)dt. Simple calculations show that L (1, z) = 1 (z − a)(b − z) M (z) − C z − a b − a 2 .
Synchrony in Heterogeneous Networks of Spiking Neurons

The emergence of synchrony in the activity of large, heterogeneous networks of spiking neurons is investigated. We define the robustness of synchrony by the critical disorder at which the asynchronous state becomes linearly unstable. We show that at low firing rates, synchrony is more robust in excitatory networks than in inhibitory networks, but excitatory networks cannot display any synchrony when the average firing rate becomes too high. We introduce a new regime where all inputs, external and internal, are strong and have opposite effects that cancel each other when averaged. In this regime, the robustness of synchrony is strongly enhanced, and robust synchrony can be achieved at a high firing rate in inhibitory networks. On the other hand, in excitatory networks, synchrony remains limited in frequency due to the intrinsic instability of strong recurrent excitation.
Efficient Mixed-Norm Regularization: Algorithms and Safe Screening Methods

Sparse learning has recently received increasing attention in many areas including machine learning, statistics, and applied mathematics. The mixed-norm regularization based on the l1/lq norm with q > 1 is attractive in many applications of regression and classification in that it facilitates group sparsity in the model. The resulting optimization problem is, however, challenging to solve due to the inherent structure of the l1/lq-regularization. Existing work deals with special cases including q = 2,∞, and they can not be easily extended to the general case. In this paper, we propose an efficient algorithm based on the accelerated gradient method for solving the l1/lq-regularized problem, which is applicable for all values of q larger than 1, thus significantly extending existing work. One key building block of the proposed algorithm is the l1/lq-regularized Euclidean projection (EP1q). Our theoretical analysis reveals the key properties of EP1q and illustrates why EP1q for the general q is significantly more challenging to solve than the special cases. Based on our theoretical analysis, we develop an efficient algorithm for EP1q by solving two zero finding problems. To further improve the efficiency of solving large dimensional l1/lq regularized problems, we propose an efficient and effective “screening” method which is able to quickly identify the inactive groups, i.e., groups that have 0 components in the solution. This may lead to substantial reduction in the number of groups to be entered to the optimization. An appealing feature of our screening method is that the data set needs to be scanned only once to run the screening. Compared to that of solving the l1/lq-regularized problems, the computational cost of our screening test is negligible. The key of the proposed screening method is an accurate sensitivity analysis of the dual optimal solution when the regularization parameter varies. Experimental results demonstrate the efficiency of the proposed algorithm.
Use of multi-annual MODIS Land Surface Temperature data for the characterization of the heat requirements for grapevine varieties

Heat requirements for grapevine varieties have been widely used to characterize potential growing regions for viticulture. One of the most important indices is the Winkler Index (WI) defined as the total summation of daily average air temperature above 10 °C from 1st of April to 31th of October in the Northern hemisphere [1]. Mapping of the WI is commonly based on temperature data from meteorological stations. However, in complex terrain such as the European Alps, these are usually irregularly and sparsely distributed or unavailable. This renders traditional geospatial interpolation approaches difficult to become reliable. As an alternative, thermal remote sensing data, which are intrinsically spatialised, can be used. The aim of this work was to provide time series of Winkler Index maps from 2003 to 2010, by means of the MODIS Land Surface Temperature (LST) data and to validate the maps using ground truth data, collected by two weather station networks.
Identification of Cinnabarinic Acid as a Novel Endogenous Aryl Hydrocarbon Receptor Ligand That Drives IL-22 Production

The aryl hydrocarbon receptor (AHR) binds to environmental toxicants including synthetic halogenated aromatic hydrocarbons and is involved in a diverse array of biological processes. Recently, the AHR was shown to control host immunity by affecting the balance between inflammatory T cells that produce IL-17 (Th17) and IL-22 versus regulatory T cells (Treg) involved in tolerance. While environmental AHR ligands can mediate this effect, endogenous ligands are likely to be more relevant in host immune responses. We investigated downstream metabolites of tryptophan as potential AHR ligands because (1) tryptophan metabolites have been implicated in regulating the balance between Th17 and Treg cells and (2) many of the AHR ligands identified thus far are derivatives of tryptophan. We characterized the ability of tryptophan metabolites to bind and activate the AHR and to increase IL-22 production in human T cells. We report that the tryptophan metabolite, cinnabarinic acid (CA), is an AHR ligand that stimulates the differentiation of human and mouse T cells producing IL-22. We compare the IL-22-stimulating activity of CA to that of other tryptophan metabolites and define stimulation conditions that lead to CA production from immune cells. Our findings link tryptophan metabolism to AHR activation and define a novel endogenous AHR agonist with potentially broad biological functions.
Sorafenib induces growth suppression in mouse models of gastrointestinal stromal tumor

Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor of the gastrointestinal tract. Current therapeutic options include surgery and targeted molecular approaches such as imatinib and sunitinib. Our aim was to establish patient-derived GIST xenografts for the use of screening new drugs and improving current treatment regimens used in GIST. In this present study, we investigate the antitumor activity of sorafenib against patient-derived GIST xenografts. Murine xenograft models were given two oral doses of sorafenib daily for 30 days and growth of established tumor xenografts was monitored at least twice weekly by vernier caliper measurements. Western blotting was then used to determine changes in proteins in these xenografts before and after sorafenib therapy. Apoptotic and cell proliferation were analyzed by immunohistochemisty. Our data found that oral administration of sorafenib to mice, bearing patient-derived GIST xenografts, resulted in dose-dependent inhibition of tumor growth. Sorafenib-induced growth inhibition was associated with decreased cell proliferation, increased apoptosis, and reduction in tumor angiogenesis. Western blot analysis revealed that sorafenib inhibited C-Raf, phospho-extracellular signal-regulated kinase 1/2, and phospho-MEK1 (Thr286) slightly as well as phospho-c-Kit (Tyr568/Tyr570), phospho- platelet-derived growth factor receptor β (Tyr1021), and phospho-Flk1 (Tyr951), suggesting that sorafenib inhibited GIST growth by blocking the Raf/MEK/extracellular signal-regulated kinase pathway and angiogenesis. Sorafenib also induced cell cycle arrest, evident through increased levels of p15 and p27 and decreased levels of p21, cyclin A, cyclin B1, and cdc-2. Our study provides a strong rationale for the clinical investigation of sorafenib in patients with GIST as well as an established platform for further drug evaluation studies using GIST xenograft models. [Mol Cancer Ther 2009;8(1):152–9]
Parity-Scan Design to Reduce the Cost of Test Application

Points out that scan design approach is representative of those techniques that can reduce the cost of test generation for sequential circuits. However, the length of a test sequence for the scan design approach can grow quite large due to the scan operation shifting the values into the scan chain, which makes the cost of test application large. A design-for-testability approach called parity-scan design which can reduce the cost of test application as well as the cost of test generation for sequential circuits is discussed. The parity-scan design approach is a combination of scan technique and parity testing. Two types of parity-scan designs, preparity and postparity scan design, are presented. Experiments on ISCAS89 circuits show that as high as 91.2% (91.1%) test length reduction and 32.4% (27.0%) average reduction can be obtained for preparity (postparity) scan design under the single scan chain approach. More reduction can be achieved by applying a multiple scan chain technique. >
Detection of hepatitis E virus (HEV) through the different stages of pig manure composting plants

Hepatitis E virus (HEV) is an increasing cause of acute hepatitis in industrialized countries. The aim of this study was to evaluate the presence of HEV in pig manure composting plants located in Spain. For this purpose, a total of 594 samples were taken in 54 sampling sessions from the different stages of composting treatment in these plants as follows: slurry reception ponds, anaerobic ponds, aerobic ponds, fermentation zone and composting final products. HEV was detected by reverse transcription polymerase chain reaction (RT‐nested PCR) in four (80%) of five plants studied, mainly in the first stages of the process. HEV was not detected in any final product (compost) sample, destined to be commercialized as a soil fertilizer, suggesting that composting is a suitable method to eliminate HEV and thus, to reduce the transmission of HEV from pigs to humans.
Lyrics-to-Audio Alignment by Unsupervised Discovery of Repetitive Patterns in Vowel Acoustics

Most of the previous approaches to lyrics-to-audio alignment used a pre-developed automatic speech recognition (ASR) system that innately suffered from several difficulties to adapt the speech model to individual singers. A significant aspect missing in previous works is the self-learnability of repetitive vowel patterns in the singing voice, where the vowel part used is more consistent than the consonant part. Based on this, our system first learns a discriminative subspace of vowel sequences, based on weighted symmetric non-negative matrix factorization, by taking the self-similarity of a standard acoustic feature as an input. Then, we make use of canonical time warping, derived from a recent computer vision technique, to find an optimal spatiotemporal transformation between the text and the acoustic sequences. Experiments with Korean and English data sets showed that deploying this method after a pre-developed, unsupervised, singing source separation achieved more promising results than the other state-of-the-art unsupervised approaches and an existing ASR-based system.
What Role do Banks play in Monetary Policy Transmission in EU Accession Countries

After the accession of the candidate countries to the European Union in 2004, the European Central Bank will need to pursue monetary policy in an enlarged euro zone. I empirically investigate the role of banks in monetary policy transmission in the accession countries. Banks are of major importance for the financing of firms and thus the adjustment of their lending in response to monetary policy actions potentially constitutes an important channel through which monetary policy works. Banks are exposed to problems of asymmetric information therefore it is shown that a change in interest rates has distributional effects across banks facing different degrees of informational asymmetries. This paper tests the prediction that banks differ in the characteristics such as relative size, level of liquidity, capitalization and ownership structure contributing to various reactions in response to monetary tightening. JEL codes: E50, E52, G21, C23, P 34
Detrimental effects of BOLD signal in arterial spin labeling fMRI at high field strength

Arterial spin labeling (ASL) MRI is a useful technique for noninvasive measurement of cerebral blood flow (CBF) in humans. High field strength provides a unique advantage for ASL because of longer blood T1 relaxation times, making this technique a promising quantitative approach for functional brain mapping. However, higher magnetic field also introduces new challenges. Here it is shown that the CBF response determined using ASL functional MRI (fMRI) at 3.0 T contains significant contamination from blood‐oxygenation‐level‐dependent (BOLD) effects. Due to interleaved acquisitions of label and control images, difference in blood oxygenation status between these two scans can cause incomplete cancellation of the static signal upon image subtraction, resulting in a BOLD‐related artifact in the estimated CBF hemodynamics. If not accounted for, such an effect can complicate the interpretation of the ASL results, e.g., causing a delayed onset and offset of the response, or inducing an artifactual poststimulus undershoot. The BOLD contribution also decreases the sensitivity of ASL‐based fMRI. Correction methods are proposed to reduce the artifact, giving increased number of activated voxels (18 ± 5%, P = 0.006) and more accurate estimation of CBF temporal characteristics. Magn Reson Med, 2006. © 2006 Wiley‐Liss, Inc.
APPLICATION OF HEAT PUMP SYSTEM TO THE AIR TEMPERATURE CONTROL IN GROWTH CHAMBER

CHIKUSHI J., TOH K. and EGUCHI H. Application of heat pump system to the air temperature control in growth chamber. BIOTRONICS 18, 67-73, 1989. The heat pump system with a comparator and a blind controller was applied to the air temperature control in a growth chamber. Settling time in step re­ sponse, the accuracy in the fixed command control of air temperature and the power requirements of the control were examined. It was found in the charac­ teristics that the response times are relatively short, and the accuracies are about ± 1QC. The system was simpler and able to be driven with smaller power requirements, as compared with the other prevailed systems. Thus, the con­ struction cost and the running energy were extremely low. From these facts, it was suggested that the heat pump system is useful for the air temperature control in the growth chamber.
[Nutritional physiology studies in pigs on the evaluation of modified proteins. 1. Results of the estimation of N-turnover, apparent and true digestibility of proteins in addition to apparent and true absorption of amino acids in the entire digestive tract].

Sulfuric acid-casein (A), spray dried isolated Vicia faba protein (B), Vicia faba protein/casein (1 : 1) protein fibres-untreated (C), treated with dialdehyde starch (D) or aluminum chloride (E) and meal of Vicia faba (F) were studied as sole protein sources in semisynthetic feed mixtures on 13 female pigs (40 to 45 kg body weight). Total utilization of nitrogen (b-value, PNu) and intermediate utilization (BW) were highest in A, followed by C. Protein C was superior to D. Protein E showed a drastic drop in protein quality compared with D because of a high decrease in S-containing amino acids content, however, their efficiency (bc-1-value) was not limited. Despite of a higher apparent digestibility by approximately 17 units in protein B, proteins B and F showed a similar quality. The true absorption of cystine (estimated by the balance of digestive tract) was corresponding to the protein quality of the respective step of treatment of protein C and was used for the correction of the gross content is S-containing amino acids.
On The Use of Eddy Current Brakes as Tunable, Fast Turn-On Viscous Dampers For Haptic Rendering

We describe the use of eddy current brakes as fast turn-on, tunable, linear dampers for haptic rendering using a prototype haptic device outfitted with eddy current brakes. We show that at the speeds typically required for haptic interaction, eddy-current-induced drag is proportional to velocity. We also show that a modulation rate of approximately 250 Hz can easily be achieved with off the shelf components. A method for decoupling the damping at the end effector is discussed. We discuss the results from haptic experiments for rendering viscosity, virtual walls and virtual friction. Experimental results show that the addition of programmable physical damping improves impedance and stability for rendering with negligible computational cost.
Osteogenic Potential of Dental Mesenchymal Stem Cells in Preclinical Studies: A Systematic Review Using Modified ARRIVE and CONSORT Guidelines

Background and Objective. Dental stem cell-based tissue engineered constructs are emerging as a promising alternative to autologous bone transfer for treating bone defects. The purpose of this review is to systematically assess the preclinical in vivo and in vitro studies which have evaluated the efficacy of dental stem cells on bone regeneration. Methods. A literature search was conducted in Ovid Medline, Embase, PubMed, and Web of Science up to October 2014. Implantation of dental stem cells in animal models for evaluating bone regeneration and/or in vitro studies demonstrating osteogenic potential of dental stem cells were included. The preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines were used to ensure the quality of the search. Modified ARRIVE (Animal research: reporting in invivo experiments) and CONSORT (Consolidated reporting of trials) were used to critically analyze the selected studies. Results. From 1914 citations, 207 full-text articles were screened and 137 studies were included in this review. Because of the heterogeneity observed in the studies selected, meta-analysis was not possible. Conclusion. Both in vivo and in vitro studies indicate the potential use of dental stem cells in bone regeneration. However well-designed randomized animal trials are needed before moving into clinical trials.
LMS: Past, Present and Future

We sketch some aspects of LMS particularly focussing on some puzzles, problems and potentials. We explain the ’independence heuristic’ by means of averaging theory for which we give a simple expose’. We suggest an explanation for the ’urban myth’ that white noise only performance formulae can be used as surrogates for the correct performance formulae which involve autocorrelations.We then extend the discussion to more recent network versions such as diffusion LMS. We show that the sharing aspect of network LMS algorithms induces a two time scale structure (something not yet widely known) and exhibit its consequences. We comment on the recent upsurge of interest in ‘online learning’ in machine learning and its failure to reference the adaptive signal processing literature. Finally we speculate on future developments of LMS.