Miracle-dz/UniFAR-FTUs huggingface dataset:
Pediatric viral human immunodeficiency virus type 1 RNA levels, timing of infection, and disease progression in African HIV-1-infected children.

OBJECTIVE To describe plasma human immunodeficiency virus type 1 (HIV-1) RNA levels in African HIV-1-infected children in relation to the timing of infection and disease progression. METHODS A retrospective cohort study was conducted of 80 children who were born to HIV-1-positive mothers and clinically followed from birth to 18 months of age in the ANRS 049 Ditrame project, Abidjan, Côte d'Ivoire (West Africa). The diagnosis and timing of pediatric HIV-1 infection were determined prospectively according to HIV-1 DNA polymerase chain reaction results. A total of 364 HIV-1 RNA viral load (VL) measurements were assessed retrospectively. Kaplan-Meier analyses and proportional hazards models were used to evaluate the prognostic value of pediatric VL and covariates for HIV disease progression or death. RESULTS Mean initial positive VL was significantly lower among children who were infected in utero (4.94 log10/mL, n = 12) than in children who were infected later (5.6-6.1 log10/mL, n = 68). In the first 6 months after diagnosis, HIV-1 RNA levels peaked (> or =6 log10/mL), regardless of timing of infection. Then, a slow decline (overall slope, -0.076 log10 copies/mL/mo) was observed until 18 months of age. A 1 log10 higher value of the pediatric peak VL (risk ratio [RR]: 1.85; 95% confidence interval [CI]: 1.0-3.44) and of the maternal VL at delivery (RR: 1.90; CI: 1.16-3.12) were independently associated with an increased risk of rapid progression to acquired immune deficiency syndrome (AIDS) or death at 18 months of life (23 AIDS diagnoses and 31 deaths). Disease progression or death was more rapid for girls than for boys (RR: 2.26; CI: 1.39-4.96). CONCLUSIONS In Africa, pediatric HIV-1 RNA levels are very close to those described in industrialized countries and seem to be predictive of AIDS stage or death, as in industrialized countries. With antiretroviral therapy becoming more widely available, the early identification and monitoring of pediatric HIV disease remains of paramount importance in Africa.
Automatic quantification of myocardial perfusion stress-rest change: a new measure of ischemia.

UNLABELLED In myocardial perfusion SPECT (MPS), ischemia is typically quantified as the difference between stress and rest defect sizes obtained by separate comparisons with stress and rest normal limits. Such an approach is not optimal because images are not compared directly with each other and a complex set of stress and rest normal limits is required. METHODS We developed a fully automatic technique to quantify stress-rest change. We applied it to 204 patients whose SPECT images were acquired using a same-day dual-isotope (99m)Tc/(201)Tl protocol and on whom coronary angiography had been performed. A 10-parameter registration of rest and stress images was performed by an iterative search of best translational, rotational, scaling, and optimal stress-rest count normalization parameters. Identical stress-rest 3-dimensional left ventricle (LV) contours were automatically derived from stress images. Integrated deficit counts (normalized rest-stress) within the LV volume were derived from registered image pairs. A global measure of ischemia (ISCH) was calculated as the ratio of the total deficit stress LV counts to the total rest LV counts. RESULTS Registration and derivation of quantitative measures were fully automatic. The average processing time was <40 s on a 2-GHz processor. When compared for prediction of stenosis, the area under the receiver operating characteristic curve (0.88 +/- 0.03) was significantly better for ISCH than that obtained by existing quantitative approaches, which use reference databases (0.80-0.82 +/- 0.03). The normalized stress-rest change could be visualized and localized directly on raw patient images using overlay display. CONCLUSION Automatic stress-rest MPS image registration allows a direct estimation of ischemia from SPECT that does not require comparisons with normal limits.
Predicting the stability of user interaction ties in Twitter

In this paper, we analyze the stability of user interaction within Twitter focusing on link decay prediction: for a tweet created by one user mentioning another user we study the task of predicting the decay of the corresponding interaction link over time. For this task, we employ the history of timestamped mention interactions between both users as time series features. We also tackle the problem of efficiently balancing a large dataset with a skewed class distribution, which arises naturally in our context. The proposed impurity-based supervised sampling (ISS) approach balances the data in one pass by removing trivial training data of the overrepresented class. Our approach is evaluated using the well known Twitter dump of 2009 [25]. We show, that ISS outperforms down-sampling with regard to the resulting predictor performance.
Oral contraception but not menstrual cycle phase is associated with increased free cortisol levels and low hypothalamo-pituitary-adrenal axis reactivity

Background: In females, estrogen is a potential modulator of cortisol response to stressors. The aim of this study was to determine the influence of menstrual cycle phase, oral contraception (OC) use and exercise training on hypothalamo-pituitary-adrenal (HPA) axis activity and reactivity after physical stress. Aim: We investigated the effects of the menstrual cycle and OC use on exhaustive exercise-induced changes in free salivary cortisol concentrations and free urinary cortisol/cortisone excretion in healthy young women. Materials and subjects: Twenty-eight women were allocated to an untrained group (no.=16) or a trained group (no.=12), depending on their physical training background. The untrained group was composed of nine OC users (UNT-OC+) and seven eumenorrheic women (UNT-OC−) tested in the follicular and luteal phases, while the trained group was entirely composed of OC+ subjects (T-OC+). Methods: Three laboratory sessions were conducted in a randomised order: a prolonged exercise test, a short-term exercise test, and a control session. For each session, urine and saliva specimens were collected at rest (09: 00 h) and then, 30, 60 and 90 min later. Results: Estradiol fluctuation during the menstrual cycle phase did not alter free cortisol baseline values and responses to exercise. OC use was associated with increased free resting salivary concentrations and urinary cortisol excretion with blunted salivary cortisol response to prolonged exercise stimulation. No training effect was noted. Conclusions: OC but not menstrual cycle phase is associated with increased free cortisol levels and low HPA axis reactivity.
Imaging of water and fat fractions in high‐field MRI with multiple slice chemical shift‐selective inversion recovery

Fat and water fractions were quantified at high field using a chemical shift‐selective inversion recovery (CSS‐IR) sequence to address the major difficulties encountered at high field by phase‐sensitive techniques used for fat/water discrimination. Water‐ and fat‐suppressed images were perfectly registered, which is a prerequisite for quantification. Immunity of the inversion pulse to B1 field modulations and off‐resonance effects was tested for two adiabatic inversion pulses, with hyperbolic secant and asymmetric hyper‐pulse waveforms. Taking into account adiabaticity, immunity to off‐resonance, radiofrequency power requirements, and specific absorption rate, the former was chosen. A close correlation was found between fat content measured by CSS‐IR at 4.7 T (R2= 0.97, P < 0.001) and 9.4 T (R2= 0.99, P < 0.05) and that measured by Soxhlet extraction. Different sources of bias (lowsignal‐to‐noise ratio, magnetization transfer effect) are discussed. J. Magn. Reson. Imaging 2000;12:488–496. © 2000 Wiley‐Liss, Inc.
The common self-polar triangle of separate circles: Properties and applications to camera calibration

This paper investigates the properties of the common self-polar triangle of separate coplanar circles and applies them to camera calibration. We find that any two separate circles have a unique common self-polar triangle. In particular, we show that one vertex of the common self-polar triangle lies on the line at infinity. Given three separate circles, the line at infinity can be recovered using the vertices of the common self-polar triangles. Accordingly, the vanishing line of the support plane can be obtained in their images. This allows recovering the imaged circular points, which provides good constraints on the image of the absolute conic. Compared to previous calibration methods using separate circles, our approach can avoid solving quartic equation, which often causes numerical instability. In the application, we test one calibration algorithm and accurate results are achieved.
What Makes Green Cities Unique? Examining the Economic and Political Characteristics of the Grey-to-Green Continuum

In the United States, urbanization processes have resulted in a large variety—or “continuum”—of urban landscapes. One entry point for understanding the variety of landscape characteristics associated with different forms of urbanization is through a characterization of vegetative (green) land covers. Green land covers—i.e., lawns, parks, forests—have been shown to have a variety of both positive and negative impacts on human and environmental outcomes—ranging from increasing property values, to mitigating urban heat islands, to increasing water use for outdoor watering purposes. While considerable research has examined the variation of vegetation distribution within cities and related social and economic drivers, we know very little about whether or how the economic characteristics and policy priorities of green cities differ from those of “grey” cities—those with little green land cover. To address this gap, this paper seeks to answer the question how do the economic characteristics and policy priorities of green and grey cities differ in the United States? To answer this question, MODIS data from 2001 to 2006 are used to characterize 373 US cities in terms of their vegetative greenness. Information from the International City/County Management Association's (ICMA) 2010 Local Government Sustainability Survey and 2009 Economic Development Survey are used to identify key governance strategies and policies that may differentiate green from grey cities. Two approaches for data analysis—ANOVA and decision tree analysis—are used to identify the most important characteristics for separating each category of city. The results indicate that grey cities tend to place a high priority on economic initiatives, while green cities place an emphasis on social justice, land conservation, and quality of life initiatives.
Experimental Assessment of a New Type of Carbon-Coated ARTECOR® Vascular Prosthesis in Sheep

The aim of the study was to test and verify the characteristics of a new type of carbon-coated ARTECOR® vascular prosthesis developed at the Knitting Research Institute, a.s. Brno. Eight healthy Merino sheep, aged between 2 and 3 years, were implanted four types (A, B, C with diamond-like carbon (DLC) coating and D as a control without DLC) of vascular prostheses. The site of implantation was the common carotid artery; the length of the implant was 7 cm. All sheep received antibiotics prophylactically in accordance with the theory of the so-called “protected coagulum”. Doppler ultrasound examination was performed before finishing the operation to verify the patency of each prosthesis. During the study period the animals were closely observed. Prostheses were extirpated on day +/- 100 in 6 sheep and on day 182 in 2 sheep. Type B prosthesis showed better results according to its postoperative patency. The implant lumen was constantly 7 mm, whereas the use of other types resulted in lumen narrowing. Type B prosthesis has a deposition of DLC coating of a thickness of 20 nm with a high content of sp3 bonds (more diamond-like ones). The experimental type B of prosthesis ARTECOR® appears to be the most successful of the tested prostheses (at the end of the study all B-type prostheses remained patent). This prosthesis appears to better satisfy the rheologic characteristics for healing. Experimental work, vascular prosthesis, carbon coating, pre-clinical study The development of vascular prosthesis tries to ensure the longest period of lumen patency possible. It is well known that the lumen of the prosthesis must be as smooth as possible in order to improve the patency, while the outer layer or surface of the prosthesis should be rough for better healing. In this case carbon-coating is thought to improve this parameter and to reduce body reactions by being inert (Sawyer 1987). Each vascular prosthesis must comply with the following requirements:
Mathematically assisted adaptive body bias (ABB) for temperature compensation in gigascale LSI systems

Process variations and temperature variations can cause both the frequency and the leakage of the chip to vary significantly from their expected values, thereby decreasing the yield. Adaptive body bias (ABB) can be used to pull back the chip to the nominal operational region. We propose the use of this technique to counter temperature variations along with process variations. We present a CAD perspective for achieving process and temperature compensation using bidirectional ABB. Mathematical models are used to determine the exact amount of body bias required optimizing the delay and leakage, and an algorithmic flow that can be adopted for gigascale LSI systems is provided
Protective Effect of Brazilian Propolis against Liver Damage with Cholestasis in Rats Treated with α-Naphthylisothiocyanate

We examined the protective effect of Brazilian propolis against liver damage with cholestasis in rats treated with α-naphthylisothiocyanate (ANIT) in comparison with that of vitamin E (VE). Rats orally received Brazilian propolis ethanol extract (BPEE) (25, 50, or 100 mg/kg), VE (250 mg/kg) or vehicle at 12 h after intraperitoneal injection of ANIT (75 mg/kg) and were killed 24 h after the injection. Vehicle-treated rats showed liver cell damage and cholestasis, judging from the levels of serum marker enzymes and components. The vehicle group had increased serum total cholesterol, triglyceride, phospholipid, and lipid peroxide levels, increased hepatic lipid peroxide, reduced glutathione, and ascorbic acid levels and myeloperoxidase activity, and decreased hepatic superoxide dismutase activity. BPEE (50 mg/kg) administered to ANIT-treated rats prevented liver cell damage and cholestasis and attenuated these serum and hepatic biochemical changes except hepatic ascorbic acid, although administered BPEE (25 or 100 mg/kg) was less effective. VE administered to ANIT-treated rats prevented liver cell damage, but not cholestasis, and attenuated increased serum lipid peroxide level, increased hepatic lipid peroxide level and myeloperoxidase activity, and decreased hepatic superoxide dismutase activity. These results indicate that BPEE protects against ANIT-induced liver damage with cholestasis in rats more effectively than VE.
A Brief State of the Art for Ontology Authoring

One of the main challenges for building the Semantic web is Ontology Authoring. Controlled Natural Languages CNLs offer a user friendly means for non-experts to author ontologies. This paper provides a snapshot of the state-of-the-art for the core CNLs for ontology authoring and reviews their respective evaluations.
Analysis of multispectral images of paintings

One hundred paintings conserved in several museums have been scanned by the C2RMF using the multi-spectral CRISATEL camera [3]. These high resolution images allow us to not only generate an accurate colour image under any chosen illuminant, but also allow us to reconstruct the reflectance spectra at each pixel. Such images can be used for a visual qualitative as well as measurement-based quantitative scientific analysis of the work of art. Several image processing tools have been developped to allow us to perform these analyses. The IIPImage system [2] enables us to visualize high resolution multi-spectral 16 bit images, view image details in colour or for each spectral channel and to super-impose and compare different wavelengths. A complementary viewing system uses an innovative 3D graphics hardware-accelerated viewer to allow us to reconstruct the resulting colour dynamically while interactively changing the light spectrum. The system also allows us to perform segmentation, view the colour distribution for a particular colour-space and perfonn dynamic spectral reconstruction.
Graceful Degradation of Collision Handling in Physically Based Animation

Interactive simulation is made possible in many applications by simplifying or culling the finer details that would make real‐time performance impossible. This paper examines detail simplification in the specific problem of collision handling for rigid body animation. We present an automated method for calculating consistent collision response at different levels of detail. The mechanism works closely with a system which uses a pre‐computed hierarchical volume model for collision detection.
Corrigendum: Information Search in Decisions From Experience: Do Our Patterns of Sampling Foreshadow Our Decisions?

Original article: Hills, T. T. , & Hertwig, R. (2010). Information search in decisions from experience: Do our patterns of sampling foreshadow our decisions? Psychological Science, 21, 1787–1792. doi:10.1177/0956797610387443
Soluble APP functions as a vascular niche signal that controls adult neural stem cell number

The molecular mechanism by which NSC number is controlled in the neurogenic regions of the adult brain is not fully understood but it has been shown that vascular niche signals regulate neural stem cell (NSC) quiescence and growth. Here, we have uncovered a role for soluble amyloid precursor protein (sAPP) as a vascular niche signal in the subventricular zone (SVZ) of the lateral ventricle of the adult mouse brain. sAPP suppresses NSC growth in culture. Further in vivo studies on the role of APP in regulating NSC number in the SVZ clearly demonstrate that endothelial deletion of App causes a significant increase in the number of BrdU label-retaining NSCs in the SVZ, whereas NSC/astrocyte deletion of App has no detectable effect on the NSC number. Taken together, these results suggest that endothelial APP functions as a vascular niche signal that negatively regulates NSC growth to control the NSC number in the SVZ. Summary: Endothelium-derived soluble amyloid precursor protein negatively regulates the growth of neural stem cells to control neural stem cell number in the subventricular zone of the adult mouse brain.
Segmentation of S1–S2 sounds in phonocardiogram records using wavelet energies

Locating S1 and S2 sounds in order to diagnose diseases by classifying through the determination of systole and diastole phases is of great significance. The method suggested in this study is available for the segmentation of S1-S2 sounds in heart sounds (HSs) acquired in real-time and it also renders the classifying possible, thereby ensuring a correct diagnosis. In this study, multi-band wavelet energy (WTE) method was proposed for the segmentation of S1-S2 sounds in 16 different HS types. After normalizing the heart sound, the signal is filtered by using wavelet transform, after than S1-S2 sounds are segmented by using multi-band wavelet energy method. For comparison, besides the method which is proposed, two different methods are investigated. One of them is segmentation of S1-S2 sounds using multi-band wavelet Shannon energy (WSE) method and the other is segmentation of S1-S2 sounds using homomorphic filtering (HMF) method. The highest performances are achieved by the proposed WTE method; 91% and 89% segmentation accuracies are obtained for SI and S2 sounds, respectively. The methods' robustness to noise was also analysed.
Optimal Detection of Flash Intensity Differences Using Rod Photocurrent Observations

The rod photocurrent contains two noise components that may limit the detectability of flash intensity increments. The limits imposed by the low- and high-frequency noise components were assessed by computing the performance of an optimal detector of increments in flash intensity. The limits imposed by these noise components depend on the interval of observation of the photocurrent signal. When the entire photocurrent signal, lasting 3 or more seconds, is observed, the low-frequency component of the photocurrent noise (attributed to the quantal noise of the incoming light, as well as random isomerizations of enzymes within the phototransduction cascade) is the most significant limitation on detectability. When only the first 380 ms or less is observed, the high-frequency component of the noise (due to the thermal isomerizations of the cGMP-gated channel) presents a significant limit on the detectability of flashes.
Identification of differentially expressed microRNAs by microarray: a possible role for microRNAs gene in medulloblastomas.

BACKGROUND MicroRNAs (miRNAs) are small noncoding regulatory RNAs whose aberrant expression may be observed in many malignancies. However, few data are yet available on human primary medulloblastomas. This work aimed to identify that whether miRNAs would be aberrantly expressed in tumor tissues compared with non-tumorous cerebellum tissues from same patients, and to explore a possible role during carcinogenesis. METHODS A high throughput microRNA microarray was performed in human primary medulloblastoma specimens to investigate differentially expressed miRNAs, and some miRNAs were validated using real-time quantitative RT-PCR method. In addition, the predicted target genes for the most significantly down- or up-regulated miRNAs were analyzed by using a newly modified ensemble algorithm. RESULTS Nine miRNA species were differentially expressed in medulloblastoma specimens versus normal non-tumorous cerebellum tissues. Of these, 4 were over expressed and 5 were under expressed. The changes ranged from 0.02-fold to 6.61-fold. These findings were confirmed using real-time quantitative RT-PCR for most significant deregulated miRNAs (miR-17, miR-100, miR-106b, and miR-218) which are novel and have not been previously published. Interestingly, most of the predicted target genes for these miRNAs were involved in medulloblastoma carcinogenesis. CONCLUSIONS MiRNAs are differentially expressed between human medulloblastoma and non-tumorous cerebellum tissue. MiRNAs may play a role in the tumorigenesis of medulloblastoma and maybe serve as potential targets for novel therapeutic strategies in future.
Meraculous: De Novo Genome Assembly with Short Paired-End Reads

We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia stipitis. More than 95% of the genome is recovered, with no errors; half the assembled sequence is in contigs longer than 101 kilobases and in scaffolds longer than 269 kilobases. Incorporating fosmid ends recovers entire chromosomes. Meraculous relies on an efficient and conservative traversal of the subgraph of the k-mer (deBruijn) graph of oligonucleotides with unique high quality extensions in the dataset, avoiding an explicit error correction step as used in other short-read assemblers. A novel memory-efficient hashing scheme is introduced. The resulting contigs are ordered and oriented using paired reads separated by ∼280 bp or ∼3.2 kbp, and many gaps between contigs can be closed using paired-end placements. Practical issues with the dataset are described, and prospects for assembling larger genomes are discussed.