Miracle-dz/UniFAR-FTUs huggingface dataset:
Association between Helicobacter pylori, cagA, and vacA Status and Clinical Presentation in Iranian Children

Objective Seroprevalence of H. pylori infection in Iran exceeds 65% of pediatric population. In this study, we intended to find association between the virulence genes (cagA and vacA) and clinical presentations. Methods H. pylori isolates were achieved from the gastric mucosa of children. In each case, the gastric biopsy specimens were cultured and the organisms identified. Detection of different genotypes was carried out by PCR method. Findings A total of 106 biopsy specimens were cultured and 33 H. pylori isolates obtained. Among these 33 H. pylori strains 24 (73%) were cagA-positive. Genotypes of vacA s1m2, s1m1, s2m2, and s2m1 were 45.5%, 30.3%, 21.2%, and 3%, respectively. Most female patients were infected with genotype s1m2. The vacA-m1 strains were significantly more common in patients with nodular gastritis. There were no statistical differences between the vacA and cagA genotypes and clinical outcomes. Conclusion The frequency of cagA genotype was high. In this study, nodular gastritis was a common finding and was rather significantly associated with m1 allele of vacA.
Towards large scale automated interpretation of cytogenetic biodosimetry data

Cytogenetic biodosimetry is the definitive test for assessing exposure to ionizing radiation. It involves manual assessment of the frequency of dicentric chromosomes (DCs) on a microscope slide, which potentially contains hundreds of metaphase cells. We developed an algorithm that can automatically and accurately locate centromeres in DAPI-stained metaphase chromosomes and that will detect DCs. In this algorithm, a set of 200-250 metaphase cell images are ranked and sorted. The 50 top-ranked images are used in the triage DC assay (DCA). To meet the requirement of DCA in a mass casualty event, we are accelerating our algorithm through parallelization. In this paper, we present our finding in accelerating our ranking and segmentation algorithms. Using data parallelization on a desktop system, the ranking module was up to 4-fold faster than the serial version and the Gradient Vector Flow module (GVF) used in our segmentation algorithm was up to 8-fold faster. Large scale data parallelization of the ranking module processed 18,694 samples in 11.40 hr. Task parallelization of Image ranking with parallelized labeling on a desktop computer reduced processing time by 20% of a serial process, and GVF module recoded with parallelized matrix inversion reduced time by 70%. Overall, we estimate that the automated DCA will require around 1 min per sample on a 64-core computing system. Our long-term goal is to implement these algorithms on a high performance computer cluster to assess radiation exposures for thousands of individuals in a few hours.
Non-price Drivers of Household Water Consumption

The unique role of marketing in bringing about voluntary behavior change is becoming more important in addressing a wide variety of societal challenges. Particular challenges where the role of marketing is becoming more prominent include a vast array of environmental issues (Kotler 2011). The research presented here outlines a social marketing intervention, Project Hydro, which was initiated to reduce household water consumption in a drought affected part of Australia. Project Hydro has led to a 30 percent reduction in household water consumption over five years. In contrast to costly supply side solutions, this research identifies key drivers of household water consumption, using a large scale survey extending the Theory of Planned Behaviour (TPB) to the context of household water consumption. Implications for policy makers and social marketers are discussed.
An inventory-based analysis of Canada's managed forest carbon dynamics, 1990 to 2008

Canada's forests play an important role in the global carbon (C) cycle because of their large and dynamic C stocks. Detailed monitoring of C exchange between forests and the atmosphere and improved understanding of the processes that affect the net ecosystem exchange of C are needed to improve our understanding of the terrestrial C budget. We estimated the C budget of Canada's 2.3 × 106 km2 managed forests from 1990 to 2008 using an empirical modelling approach driven by detailed forestry datasets. We estimated that average net primary production (NPP) during this period was 809 ± 5 Tg C yr−1 (352 g C m−2 yr−1) and net ecosystem production (NEP) was 71 ± 9 Tg C yr−1 (31 g C m−2 yr−1). Harvesting transferred 45 ± 4 Tg C yr−1 out of the ecosystem and 45 ± 4 Tg C yr−1 within the ecosystem (from living biomass to dead organic matter pools). Fires released 23 ± 16 Tg C yr−1 directly to the atmosphere, and fires, insects and other natural disturbances transferred 52 ± 41 Tg C yr−1 from biomass to dead organic matter pools, from where C will gradually be released through decomposition. Net biome production (NBP) was only 2 ± 20 Tg C yr−1 (1 g C m−2 yr−1); the low C sequestration ratio (NBP/NPP=0.3%) is attributed to the high average age of Canada's managed forests and the impact of natural disturbances. Although net losses of ecosystem C occurred during several years due to large fires and widespread bark beetle outbreak, Canada's managed forests were a sink for atmospheric CO2 in all years, with an uptake of 50 ± 18 Tg C yr−1 [net ecosystem exchange (NEE) of CO2=−22 g C m−2 yr−1].
Refined human-robot interaction through retro-projected robotic heads

We present an overview of the LightHead robot and its retro-projected face, followed by opportunities for this technology to push the state-of-the-art in HRI. Through comparison with existing robot head technologies, we show how retro-projected faces can provide a means to display human social-emotional behaviours including subtle social cues not achievable with other robotic heads.
Hippocampal Hyperexcitability Underlies Enhanced Fear Memories in TgNTRK3, a Panic Disorder Mouse Model

Panic attacks are a hallmark in panic disorder (PAND). During the panic attack, a strong association with the surrounding context is established suggesting that the hippocampus may be critically involved in the pathophysiology of PAND, given its role in contextual processing. We previously showed that variation in the expression of the neurotrophin tyrosine kinase receptor type 3 (NTRK3) in both PAND patients and a transgenic mouse model (TgNTRK3) may have a role in PAND pathophysiology. Our study examines hippocampal function and activation of the brain fear network in TgNTRK3 mice. TgNTRK3 mice showed increased fear memories accompanied by impaired extinction, congruent with an altered activation pattern of the amygdala—hippocampus—medial prefrontal cortex fear circuit. Moreover, TgNTRK3 mice also showed an unbalanced excitation-to-inhibition ratio in the hippocampal cornu ammonis 3 (CA3)–CA1 subcircuit toward hyperexcitability. The resulting hippocampal hyperexcitability underlies the enhanced fear memories, as supported by the efficacy of tiagabine, a GABA reuptake inhibitor, to rescue fear response. The fearful phenotype appears to be the result of hippocampal hyperexcitability and aberrant fear circuit activation. We conclude that NTRK3 plays a role in PAND by regulating hippocampus-dependent fear memories.
Extended and Unscented Kitchen Sinks

We propose a scalable multiple-output generalization of unscented and extended Gaussian processes. These algorithms have been designed to handle general likelihood models by linearizing them using a Taylor series or the Unscented Transform in a variational inference framework. We build upon random feature approximations of Gaussian process covariance functions and show that, on small-scale single-task problems, our methods can attain similar performance as the original algorithms while having less computational cost. We also evaluate our methods at a larger scale on MNIST and on a seismic inversion which is inherently a multi-task problem.
Planar Straight-Line Embedding of Double-Tree Scan Architecture on a Rectangular Grid

Double-tree-scan (DTS) is a new scan-path architecture that is deemed to be suitable for low-power testing of VLSI circuits. A full DTS resembles two complete k-level (k > 0) binary trees whose leaf nodes are merged pair-wise, and thus consists of exactly N$_{k}$ = 3 × 2$^{k}$ − 2 nodes. In this paper, the problem of planar straight-line embedding of a "double-tree graph" on a rectangular grid is investigated and an O(N$_{k}$) time algorithm for drawing it, is described. The embedding requires at most 2N$_{k}$ grid points, with an aspect ratio lying between 1 and f. Next, techniques of embedding a partial DTS is considered when the number of nodes n ≠ 3 × 2$^{k}$ − 2, for some k. Layouts of double-tree scan-paths for some benchmark circuits are also presented to demonstrate the results.
Surface Segmentation Using Global Conformal Structure

Surface segmentation is a fundamental problem in computer graphics. It has various applications such as metamorphosis, surface matching, surface compression, 3D shape retrieval, texture mapping, etc. All orientable surfaces are Riemann surfaces, and admit conformal structures. This paper introduces a novel surface segmentation algorithm based on its conformal structure. Each segment can be conformally mapped to a planar rectangle, and the transition maps are planar translations. The segmentation is intrinsic to the surface, independent of the embed- ding, and consistent for surfaces with similar geometries. By using segmentation based on conformal structure, the mapping between surfaces with arbitrary topologies can be constructed explicitly. The method is rigorous, efficient and automatic. The segmentation can be applied to surface morphing, construct conformal geometry image, convert mesh to Spline surface, solve Partial Differential Equations on arbitrary surfaces, etc.
Excitonic Eigenstates of Disordered Semiconductor Quantum Wires: Adaptive Wavelet Computation of Eigenvalues for the Electron-Hole Schrödinger Equation

A novel adaptive approach to compute the eigenenergies and eigenfunctions of the two-particle (electron-hole) Schrodinger equation including Coulomb attraction is presented. As an example, we analyze the energetically lowest exciton state of a thin one-dimensional semiconductor quantum wire in the presence of disorder which arises from the non-smooth interface between the wire and surrounding material. The eigenvalues of the corresponding Schrodinger equation, i.e., the one-dimensional exciton Wannier equation with disorder, correspond to the energies of excitons in the quantum wire. The wavefunctions, in turn, provide information on the optical properties of the wire. We reformulate the problem of two interacting particles that both can move in one dimension as a stationary eigenvalue problem with two spacial dimensions in an appropriate weak form whose bilinear form is arranged to be symmetric, continuous, and coercive. The disorder of the wire is modelled by adding a potential in the Hamiltonian which is generated by normally distributed random numbers. The numerical solution of this problem is based on adaptive wavelets. Our scheme allows for a convergence proof of the resulting scheme together with complexity estimates. Numerical examples demonstrate the behavior of the smallest eigenvalue, the ground state energies of the exciton, together with the eigenstates depending on the strength and spatial correlation of disorder.
ReSA: Architecture for resources sharing between clouds

Cloud computing has emerged as paradigm for hosting and delivering services over the Internet. It is evolved as a key computing platform for delivering on-demand resources that include infrastructures, software, applications, and business processes. Mostly, clouds are deployed in a way that they are often isolated from each other. These implementations cause lacking of resources collaboration between different clouds. For example, cloud consumer requests some resource and that is not available at that point in time. Client satisfaction is important for business as denying the client may be expensive in many ways. To fulfill the client request, the cloud may ask the requested resource from some other cloud. In this research paper we aim to propose a trust worthy architecture named ReSA (Resource Sharing Architecture) for sharing on-demand resources between different clouds that may be managed under same or different rules, policies and management.
86 dB DR Cross-Coupled Time-Interleaved xx ADC for Audio Signal Band with 322 ΣA Current Consumption

An audio band sigma-delta ADC based on a new time-interleaved xx scheme isdescribed. The circuit achieves a very low power operation with the large dynamic range required for audio applications. This modified two channel time-interleaved scheme improves the power efficiency thanks to halved operating frequency in the paths, and a reduced number of levels in ADC and DAC. This sigma-delta modulator fabricated in a 0.18 μm CMOS process uses 1.8 V supply and ±0.5 V input range. Experimental results show that with a 35 dBFS input sine wave there are no tones above a 110 dB noise floor.
Evidence of Natural Hybridization in Brazilian Wild Lineages of Saccharomyces cerevisiae

The natural biology of Saccharomyces cerevisiae, the best known unicellular model eukaryote, remains poorly documented and understood although recent progress has started to change this situation. Studies carried out recently in the Northern Hemisphere revealed the existence of wild populations associated with oak trees in North America, Asia, and in the Mediterranean region. However, in spite of these advances, the global distribution of natural populations of S. cerevisiae, especially in regions were oaks and other members of the Fagaceae are absent, is not well understood. Here we investigate the occurrence of S. cerevisiae in Brazil, a tropical region where oaks and other Fagaceae are absent. We report a candidate natural habitat of S. cerevisiae in South America and, using whole-genome data, we uncover new lineages that appear to have as closest relatives the wild populations found in North America and Japan. A population structure analysis revealed the penetration of the wine genotype into the wild Brazilian population, a first observation of the impact of domesticated microbe lineages on the genetic structure of wild populations. Unexpectedly, the Brazilian population shows conspicuous evidence of hybridization with an American population of Saccharomyces paradoxus. Introgressions from S. paradoxus were significantly enriched in genes encoding secondary active transmembrane transporters. We hypothesize that hybridization in tropical wild lineages may have facilitated the habitat transition accompanying the colonization of the tropical ecosystem.
The ISL Baseline Lecture Transcription System for the TED Corpus

This paper describes the Interactive Systems Laboratories’ automatic lecture transcription system for the Translanguage English Database (TED) corpus, which provides text-hypothesis for the International Workshop on Speech Summarization for Information Extraction and Machine Translation. Furthermore the paper gives a short analysis of speaking style characteristics, in particular addressing native vs. non-native speech. The data for automatic transcription is divided into a native and a nonnative test set. The best word error rate for the native data set is 28.5% while for the non-native set the best result shows 31.0%.
Control of decoherence: Dynamical decoupling versus quantum Zeno effect: A case study for trapped ions

The control of thermal decoherence via dynamical decoupling and via the quantum Zeno effect (Zeno control) is investigated for a model of trapped ion, where the dynamics of two low-lying hyperfine states undergoes decoherence due to the thermal interaction with an excited state. Dynamical decoupling is a procedure that consists in periodically driving the excited state, while the Zeno control consists in frequently measuring it. When the control frequency is high enough, decoherence is shown to be suppressed. Otherwise, both controls may accelerate decoherence. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Dynamics of the Liver Stiffness Value Using Transient Elastography during the Perioperative Period in Patients with Valvular Heart Disease

Background/Aims Liver congestion due to heart failure in patients with valvular heart disease (VHD) can result in an overestimate of the liver stiffness (LS) as assessed by transient elastography (TE). This prospective pilot study investigated the dynamics of LS during the perioperative valve operation period. Methods Thirty-two patients who underwent a valve operation (case) and 12 who underwent a varicose vein operation (control) were prospectively enrolled. LS and cardiologic parameters at three time points [baseline, post-operative day (POD)7, and POD90] were collected. Results LS at three time points were consistently higher in the case group than those in the control group, although all participants did not show evidence of underlying chronic liver disease (all P<0.05). In the case group, LS at POD7 increased slightly from the LS at baseline (median 7.9→8.4 kPa, P = 0.816), whereas LS at POD90 decreased significantly from the LS at POD7 (median 8.4→6.0 kPa; P = 0.026). LS was significantly correlated with N-terminal-pro brain natriuretic peptide (NT-proBNP) (ρ = 0.412), left ventricular ejection fraction (ρ = −0.494), and central venous pressure during the operation (ρ = 0.555) at baseline (all P<0.05). LS was significantly correlated with NT-proBNP (ρ = 0.526) and right ventricular pressure (ρ = 0.572) at POD7, whereas LS was significantly correlated with NT-proBNP (ρ = 0.590) at POD90 (all P<0.05). Conclusions LS can be overestimated in patients with VHD due to hepatic congestion. However, LS can be dynamically reversed during the perioperative period reflecting the restoration of cardiac function after a successful operation.
Biological significance in forward and backward blocking: resolution of a discrepancy between animal conditioning and human causal judgment.

Similarities between Pavlovian conditioning in nonhumans and causal judgment by humans suggest that similar processes operate in these situations. Notably absent among the similarities is backward blocking (i.e., retrospective devaluation of a signal due to increased valuation of another signal that was present during training), which has been observed in causal judgment by humans but not in Pavlovian responding by animals. The authors used rats to determine if this difference arises from the target cue being biologically significant in the Pavlovian case but not in causal judgment. They used a sensory preconditioning procedure in Experiments 1 and 2, in which the target cue retained low biological significance during the treatment, and obtained backward blocking. The authors found in Experiment 3 that forward blocking also requires the target cue to be of low biological significance. Thus, low biological significance is a necessary condition for a stimulus to be vulnerable to blocking.
Improved segmentation of focal cortical dysplasia lesions on MRI using expansion towards cortical boundaries

Focal cortical dysplasia (FCD), a malformation of cortical development, is an important cause of intractable epilepsy. On magnetic resonance images (MRI), FCD lesions are difficult to distinguish from healthy cortex and defining their spatial extent is challenging. We previously introduced a method to segment FCD lesions on MRI, relying on a 3D deformable model driven by MR features of FCD. In the present paper, we propose to improve our approach by adding a second evolution step which expands the result towards the cortical boundaries. A quantitative evaluation was performed in 18 FCD patients by comparison with manually traced lesion labels. The proposed approach achieved a strong agreement with the manual labels and substantially improved the results obtained with our previous method
Preoperative Bone Mineral Density and Bone Turnover in Women Before Primary Knee Arthroplasty

Purpose: The preoperative prevalence of osteoporosis and/or osteopenia and overall bone quality in prospective total knee arthroplasty (TKA) patients may affect the postoperative outcome after prosthetic insertion into the bone. The purpose of this study is to determine the baseline bone mineral density (BMD) and bone turnover in preoperative, female, primary TKA patients. Methods: We prospectively measured the lumbar spine and hip BMDs using dual-energy X-ray absorptiometry (DEXA) scans in a cohort of 119 knees (107 patients) one day before surgery. We also assessed bone turnover using urinary levels of N-telopeptide (NTX), a type I collagen crosslinker, normalized to creatinine. Results: The prevalence of osteoporosis by DEXA scan (T-score ≤ −2.5) among the TKAs was 12% in the spine and 10% in the hip. Eighty-three knees (70%) had osteopenia or osteoporosis of either the spine or hip. The mean T-score of the spine was −0.7 (SD 1.6), which is within normal limits, and of the hip was −1.2 (SD 1.0), which is defined as osteopenia. The mean Z-scores of 0.9 (SD 1.4) in the spine and 0.6 (SD 0.9) in the hip were positive. The median urinary NTX/creatinine ratio was elevated at 58.1 (interquartile range: 13.7 to 188.4). Conclusion: Based on Z-scores, the TKA patients had higher spine and hip BMDs than the age-matched general population. Elevated NTX levels may suggest a systemic or local abnormal bone turnover. Further study is needed to determine whether such turnover, as a type of patient-related medical systemic disorder, affects postoperative clinical outcomes.
Evaluate and optimize parallel Barnes-Hut algorithm for emerging many-core architectures

This paper focuses on the use of Network-on-Chip (NoC) accelerators for Barnes-Hut N-Body simulations. NoC-based architecture is proposed to solve the communication bottleneck of processors with hundreds or even thousands of cores. An N-body simulation approximates the evolution of a system of bodies, e.g. an astrophysical system where each body represents a star or a galaxy. Despite the fact that the behaviour of Barnes-Hut algorithm has been studied on conventional multicore systems, graphics processing units and other accelerators, we explore key performance issues in the context of NoC platform. We investigate serial and parallel implementations, where the parallel version is analyzed in terms of network traffic. The results revealed that hot-spot and bursty traffic can congest the network, while long distance communication deteriorated system performance further. We propose algorithmic and interconnection optimizations. These include improved data locality, proper mapping and partially diagonal network. Evaluation results show that, compared with the original implementation, the average execution time and energy delay product are reduced by 25.3% and 31.6% respectively. The proposed design achieved 55.4× speed-up over 64 threads.
Optimal Annuitization with Stochastic Mortality and Correlated Longevity Costs

The conventional wisdom since Yaari (1965) is that households without a bequest motive should fully annuitize their investments. Numerous market frictions do not break this sharp result. We modify the Yaari framework by allowing a household’s mortality risk itself to be stochastic due to health shocks. A lifetime annuity still helps to hedge longevity risk. But the annuity’s remaining present value is correlated with longevity costs, such as those for nursing home care, thereby reducing annuity demand, even without ad-hoc “liquidity constraints. ” We find that most households should not hold a positive level of annuities, and many should hold negative amounts.