Miracle-dz/UniFAR-FTUs huggingface dataset:
Allelic homogeneity due to a founder mutation in Japanese patients with lattice corneal dystrophy type IIIA.

Lattice corneal dystrophies (LCDs) are caused by mutations of the transforming growth factor beta-induced gene (TGFBI, formerly betaig-h3). LCD type IIIA (LCDIIIA) has been reported mostly from Japan. In this study, we demonstrate allelic homogeneity for Japanese patients with LCDIIIA, using intragenic polymorphic markers. When exon 11 of TGFBI was analyzed, all 18 patients examined were found to be heterozygous for both a P501T mutation and an IVS10-3C --> T variation. On the other hand, none of 54 normal Japanese control subjects had the P501T, and 5 of the controls were heterozygous for IVS10-3C --> T. Haplotype analysis of the patients revealed that both P501T and IVS10-3C --> T were located on the same chromosome, and a significant linkage disequilibrium (P < 0.001, Fisher's exact probability test) was observed between LCDIIIA (P501T) and IVS10-3C --> T. When exon 8 of the gene was analyzed, all these patients possessed the "G allele" of a 1028G/A polymorphism. A significant linkage disequilibrium (P < 0.003; chi-square test) was also observed between P501T and the G allele in the patients. These results suggest that allelic homogeneity seen in Japanese patients with LCDIIIA may result from a single founder mutation.
Mathematical modelling of mucus transport in diseased airways with effects of constriction of airway diameter and Mucus viscosity

In this paper, a coaxial flow of air and mucus in a circular tube under time dependent pressure gradient function is modelled and have been considered to study mucus transport in the diseased airway (Bronchial constriction). It is assumed that moist air (assumed to be an incompressible Newtonian fluid) and mucus flow under the quasi-steady state laminar condition caused by prolonged cough. The mucus layer is considered to be divided into two sub-layers, the one in contact with the air flow and the other sub-layer adjacent to the cilia bed, the effect of constriction of the airway diameter on mucus transport and mucus viscosity. The analysis and approximate result shows that mucus transport in constricted airway decreases as diameter changes. It is also shown that air flow rate affected by mucus transport and mucus viscosity in the constricted airway.
Home alone, and in danger.

For anyone who has ever worked in an emergency room, the presentation is all too familiar. The ambulance brings in a patient who is stuporous and dehydrated, often with decubitus ulcers and covered with feces and urine. No one knows of any family members, and the only accompanying medical information is “found at home. ” At times physicians seem to dislike caring for such patients. Their feelings range from embarrassment to hostility. Sometimes the patient is referred to demeaningly as “gomer,” “failure to thrive,” “social problem,” or worse. These reactions are not only unprofessional but also sad and ironic. As a .
Image Sensor Noise Parameter Estimation by Variance Stabilization and Normality Assessment

High-quality image denoising requires taking into account the dependence of the noise distribution on the original image. The parameters of this dependence are often unknown and we propose a new method to estimate them here. Using an optimization procedure, we find a variance-stabilizing transformation, which transforms the input image into an image with signal-independent noise. Principal component analysis of blocks of the transformed image allows estimation of the variance of the signal-independent noise so that the parameters of the original noise model can be computed. The image blocks for processing are selected in such a way that they have low stochastic texture strength but preserve the noise distribution. The algorithm does not require the original image to have homogeneous areas and can accurately process images with regular textures. It has high computational efficiency and smaller maximum estimation error compared with the state of the art. Our experiments have also shown that denoising with the noise parameters estimated by this method leads to the same results as denoising with the true noise parameters.
Effects of drought and salinity on maize phenology, morphology and productivity in a semi-arid environment

in rainfall patterns and temperature dynamics can seriously affect field crops and compromise productivity, due to increased drought and salinisation of agricultural land (Sarr et al., 2011). According to scenarios for climate change (IPCC, 2007), all these perturbations are predicted to become more accentuated in semi-arid areas, where competition for water resources for other human activities is also expected. Drought and salt stress are common threats for plant growth, development and survival in several Effects of drought and salinity on maize phenology, morphology and productivity in a semi-arid environment Romdhane Leila1,2, Dal Cortivo Cristian3, Vamerali Teofilo3*, Radhouane Leila2
Exploiting information theory for adaptive mobility and resource management in future cellular networks

We utilize tools from information theory to develop adaptive algorithms for two key problems in cellular networks: location tracking and resource management. The use of information theory is motivated by the fundamental observation that overheads in many aspects of mobile computing can be traced to the randomness or uncertainty in an individual user's movement behavior. We present a model-independent information-theoretic approach for estimating and managing this uncertainty, and relate it to the entropy or information content of the user's movement process. Information-theoretic mobility management algorithms are very simple, yet reduce overhead by /spl sim/80 percent in simulated scenarios by optimally adapting to each individual's movement. These algorithms also allow for flexible tradeoff between location update and paging costs. Simulation results demonstrate how an information-theory-motivated resource provisioning strategy can meet QoS bounds with very small wastage of resources, thus dramatically reducing the overall blocking rate.
Verifiable network function outsourcing: requirements, challenges, and roadmap

Network function outsourcing (NFO) enables enterprises and small businesses to achieve the performance and security benefits offered by middleboxes (e.g., firewall, IDS) without incurring high equipment or operating costs that such functions entail. In order for this vision to fully take root, however, we argue that NFO customers must be able to verify that the service is operating as intended w.r. t. : (1) functionality (e.g., did the packets traverse the desired sequence of middlebox modules? ); (2) performance (e.g., is the latency comparable to an "in-house" service? ); and (3) accounting (e.g., are the CPU/memory consumption being accounted for correctly? ). In this position paper, we formalize these requirements and present a high-level roadmap to address the challenges involved.
Invasive aspergillosis in patients with underlying liver cirrhosis: a prospective cohort study

The aim of this study was to determine the prevalence of invasive aspergillosis (IA) in patients with liver cirrhosis and the performance of serum galactomannan (GM) screening. Patients with decompensated liver cirrhosis and patients with compensated liver cirrhosis presenting with fever and/or respiratory symptoms were prospectively enrolled. All patients were screened by serum GM twice weekly irrespective of clinical signs and symptoms. Positive serum GM triggered work-up consisting of chest computed tomography and in case of pathological findings bronchoscopy. 150 patients were included in the study. Two (1.3%) had probable, one (0.7%) had possible, and 147 (98%) had no evidence of IA. Both patients with probable IA had compensated liver cirrhosis. Sensitivity for serum GM screening for probable versus no IA was 0.5 (95% CI, 0.09-0.91), specificity 0.97 (95% CI: 0.92-0.99), negative predictive value 0.99 (95% CI, 0.96-0.99) and positive predictive value (PPV) 0.17 (95% CI, 0.01-0.64). PPV was 0.5 (95% CI, 0.03-0.98) in patients with clinical suspicion of IA. In conclusion, prevalence of IA in patients with liver cirrhosis seems to be low. Targeted GM testing in case of clinical suspicion of IA may be associated with markedly higher PPVs when compared to universal GM screening in patients with liver cirrhosis.
A Portable Optimization Engine for Accelerating Irregular Data-Traversal Applications on SIMD Architectures

Fine-grained data parallelism is increasingly common in the form of longer vectors integrated with mainstream processors (SSE, AVX) and various GPU architectures. This article develops support for exploiting such data parallelism for a class of nonnumeric, nongraphic applications, which perform computations while traversing many independent, irregular data structures. We address this problem by developing several novel techniques. First, for code generation, we develop an intermediate language for specifying such traversals, followed by a runtime scheduler that maps traversals to various SIMD units. Second, we observe that good data locality is crucial to sustained performance from SIMD architectures, whereas many applications that operate on irregular data structures (e.g., trees and graphs) have poor data locality. To address this challenge, we develop a set of data layout optimizations that improve spatial locality for applications that traverse many irregular data structures. Unlike prior data layout optimizations, our approach incorporates a notion of both interthread and intrathread spatial reuse into data layout. Finally, we enable performance portability (i.e., the ability to automatically optimize applications for different architectures) by accurately modeling the impact of inter- and intrathread locality on program performance. As a consequence, our model can predict which data layout optimization to use on a wide variety of SIMD architectures. To demonstrate the efficacy of our approach and optimizations, we first show how they enable up to a 12X speedup on one SIMD architecture for a set of real-world applications. To demonstrate that our approach enables performance portability, we show how our model predicts the optimal layout for applications across a diverse set of three real-world SIMD architectures, which offers as much as 45% speedup over a suboptimal solution.
The Cytoskeleton and the Peroxisomal-Targeted SNOWY COTYLEDON3 Protein Are Required for Chloroplast Development in Arabidopsis[W]

This report characterizes snowy cotyledon3, a mutant with disrupted chloroplast development that reveals a requirement for the cytoskeleton and peroxisomes in chloroplast biogenesis. Here, we describe the snowy cotyledon3 (sco3-1) mutation, which impairs chloroplast and etioplast development in Arabidopsis thaliana seedlings. SCO3 is a member of a largely uncharacterized protein family unique to the plant kingdom. The sco3-1 mutation alters chloroplast morphology and development, reduces chlorophyll accumulation, impairs thylakoid formation and photosynthesis in seedlings, and results in photoinhibition under extreme CO2 concentrations in mature leaves. There are no readily apparent changes to chloroplast biology, such as transcription or assembly that explain the disruption to chloroplast biogenesis. Indeed, SCO3 is actually targeted to another organelle, specifically to the periphery of peroxisomes. However, impaired chloroplast development cannot be attributed to perturbed peroxisomal metabolic processes involving germination, fatty acid β-oxidation or photorespiration, though there are so far undescribed changes in low and high CO2 sensitivity in seedlings and young true leaves. Many of the chloroplasts are bilobed, and some have persistent membranous extensions that encircle other cellular components. Significantly, there are changes to the cytoskeleton in sco3-1, and microtubule inhibitors have similar effects on chloroplast biogenesis as sco3-1 does. The localization of SCO3 to the periphery of the peroxisomes was shown to be dependent on a functional microtubule cytoskeleton. Therefore, the microtubule and peroxisome-associated SCO3 protein is required for chloroplast development, and sco3-1, along with microtubule inhibitors, demonstrates an unexpected role for the cytoskeleton and peroxisomes in chloroplast biogenesis.
Fading Channel Characterization over Frequency Hopping Spread Spectrum

The number of radio systems operating in the 2.4 GHz band is rising as a result of increased usage of wireless technologies. Since such devices interfere with one another, satisfactory co-existence becomes important. Several techniques serve to reduce the interference. Included among these are frequency hopping (FH) and power control. From the simulation results it can be seen that frequency hopping provides a significant improvement in the channel coherence time. At Doppler frequencies exceeding a certain level hopping provides a small improvement. While at lower Doppler frequencies, the effect of FH dominate the multipath fading. As a result, the hopped systems provide a coherence time which is largely independent of Doppler frequency.
Low-complexity computation of visual information fidelity in the discrete wavelet domain

The visual information fidelity (VIF) index is an objective quality metric that gives very accurate image similarity scores, but at the cost of very high computational complexity. In this paper, a method is presented for calculating VIF in the discrete wavelet domain using the Haar wavelet. The proposed method exploits scalar Gaussian Scale Mixture (GSM) instead of vector GSM for calculating the prediction scores. The complexity of the proposed method is assessed for five different popular image sizes and compared to other methods based on a C/C++ implementation of the algorithms. Experimental results show that the proposed method can compute the visual quality score with less than 30% of the computational complexity of the well-known SSIM index, with greater accuracy than that achieved by the original VIF index method (at about 5% of its computational complexity).
Inducible gene deletion reveals different roles for B‐Raf and Raf‐1 in B‐cell antigen receptor signalling

Engagement of the B‐cell antigen receptor (BCR) leads to activation of the Raf–MEK–ERK pathway and Raf kinases play an important role in the modulation of ERK activity. B lymphocytes express two Raf isoforms, Raf‐1 and B‐Raf. Using an inducible deletion system in DT40 cells, the contribution of Raf‐1 and B‐Raf to BCR signalling was dissected. Loss of Raf‐1 has no effect on BCR‐mediated ERK activation, whereas B‐Raf‐deficient DT40 cells display a reduced basal ERK activity as well as a shortened BCR‐mediated ERK activation. The Raf‐1/B‐Raf double deficient DT40 cells show an almost complete block both in ERK activation and in the induction of the immediate early gene products c‐Fos and Egr‐1. In contrast, BCR‐mediated activation of nuclear factor of activated T cells (NFAT) relies predominantly on B‐Raf. Furthermore, complementation of Raf‐1/B‐Raf double deficient cells with various Raf mutants demonstrates a requirement for Ras‐GTP binding in BCR‐mediated activation of both Raf isoforms and also reveals the important role of the S259 residue for the regulation of Raf‐1. Our study shows that BCR‐mediated ERK activation involves a cooperation of both B‐Raf and Raf‐1, which are activated specifically in a temporally distinct manner.
Did copayment changes reduce health service utilization among CHIP enrollees? Evidence from Alabama.

OBJECTIVE To explore whether health care utilization changed among enrollees in Alabama's CHIP program, ALL Kids, following copayment increases at the beginning of fiscal year 2004. DATA SOURCES Data on all ALL Kids enrollees over 1999-2009 are obtained from claims files and the state's administrative database. STUDY DESIGN We use pooled month-level data for all enrollees and conduct covariate-adjusted segmented regression models. Health services considered are inpatient care, emergency department (ED) visits, brand-name prescription drugs, generic prescription drugs, physician office visits and outpatient-services, ambulance services, allergy treatments, and non-preventive dental services. Physician well-visits, preventive dental services, and service use by Native-Americans--which saw no copayment increases--serve as counterfactuals. PRINCIPAL FINDINGS There are significant declines in utilization for inpatient care, physician visits, brand-name medications, and ED visits following the copayment increases. By and large, utilization did not decline, or declined only temporarily, for those services and for those enrollees that who not subject to increased copayments. CONCLUSIONS Copayment increases reduced utilization of many health services among ALL Kids enrollees. Concerns remain regarding the long-term health consequences to low-income children of copayment-induced reductions in health care utilization.
Designing and Evaluating a Russian Tagset

This paper reports the principles behind designing a tagset to cover Russian morphosyntactic phenomena, modifications of the core tagset, and its evaluation. The tagset is based on the MULTEXT-East framework, while the decisions in designing it were aimed at achieving a balance between parameters important for linguists and the possibility to detect and disambiguate them automatically. The final tagset contains about 500 tags and achieves about 95% accuracy on the disambiguated portion of the Russian National Corpus. We have also produced a test set that can be shared with other researchers.
Design and signal integrity analysis of high bandwidth memory (HBM) interposer in 2.5D terabyte/s bandwidth graphics module

Spurred by the industrial demands for terabyte/s bandwidth graphics module, high bandwidth memory (HBM) has been emerged to overcome the limitations of conventional DRAMs. Additionally, due to the fine pitch and high density interconnect routing between GPU and 4 HBMs in 2.5D terabyte/s bandwidth graphics module, HBM interposer has also been to the force. However, several signal integrity issues of the HBM interposer occur due to the manufacturing process constraints. In this paper, we design the HBM interposer using 6 layers redistribution layer (RDL) and TSVs in 2.5D terabyte/s bandwidth graphics module. And then, in the designed HBM interposer, electrical performance of the HBM interposer channels using M1, M3, and M5 layer is analyzed by simulation in the frequency-and time-domain. With the simulation results, it is observed that the designed HBM interposer shows good signal integrity.
Groundwater resources, climate and vulnerability

Groundwater is an important component of the freshwater system and its role is becoming even more prominent as the more accessible surface water resources become increasingly exploited to support increasing populations and development. Yet despite its significance, there has been comparatively little research conducted on groundwater relative to surface water resources, particularly in the context of climate change impact assessment. This focus issue has therefore been assembled to expand upon the currently limited knowledge of groundwater systems and their links with climate. Many of the papers included here explore the interrelated issues of groundwater resources, climate-related changes and vulnerabilities at a regional scale in different continents and globally. See the PDF for the full text of the editorial. Focus on Groundwater Resources, Climate and Vulnerability Contents Groundwater: from mystery to management T N Narasimhan Simulated response of groundwater to predicted recharge in a semi-arid region using a scenario of modelled climate change M W Toews and D M Allen Long-term climatic change and sustainable ground water resources management Hugo A Loáiciga Climate change and groundwater: India's opportunities for mitigation and adaptation Tushaar Shah Vulnerability to the impact of climate change on renewable groundwater resources: a global-scale assessment Petra Döll Influence of soil heterogeneity on evapotranspiration under shallow water table conditions: transient, stochastic simulations Stefan J Kollet Nutrient cycling and N2O emissions in a changing climate: the subsurface water system role Georgia Destouni and Amélie Darracq Rainfall intensity and groundwater recharge: empirical evidence from the Upper Nile Basin M Owor, R G Taylor, C Tindimugaya and D Mwesigwa
EVEREST: a collection of evolutionary conserved protein domains

Protein domains are subunits of proteins that recur throughout the protein world. There are many definitions attempting to capture the essence of a protein domain, and several systems that identify protein domains and classify them into families. EVEREST, recently described in Portugaly et al. (2006) BMC Bioinformatics, 7, 277, is one such system that performs the task automatically, using protein sequence alone. Herein we describe EVEREST release 2.0, consisting of 20 029 families, each defined by one or more HMMs. The current EVEREST database was constructed by scanning UniProt 8.1 and all PDB sequences (total over 3 000 000 sequences) with each of the EVEREST families. EVEREST annotates 64% of all sequences, and covers 59% of all residues. EVEREST is available at . The website provides annotations given by SCOP, CATH, Pfam A and EVEREST. It allows for browsing through the families of each of those sources, graphically visualizing the domain organization of the proteins in the family. The website also provides access to analyzes of relationships between domain families, within and across domain definition systems. Users can upload sequences for analysis by the set of EVEREST families. Finally an advanced search form allows querying for families matching criteria regarding novelty, phylogenetic composition and more.
Computer‐based assessment of student performance in programing courses

In this study, the score equivalence of computer‐based assessment (CBA) and paper‐and‐pencil testing (PPT) in an undergraduate course of introductory computer programing at the National Technical University of Athens' School of Chemical Engineering, was examined. The research was carried out with 211 students participating, and was realized by a specially constructed CBA platform as well as the classical PPT. Both types of assessment included the same questions of multiple‐choice type, completing and correcting code in Fortran, as well as writing Fortran code from scratch. The results showed that, in general, students performed better and received higher scores under CBA compared to PPT. In particular, the very good students benefited from the advantages that the computer compiler offers in debugging code and completing code exercises and, thus, received relatively higher scores in these parts of the test. Moreover, switching answers and devoting more time‐on‐task was found to be beneficial for the students' performance. Overall, the findings of this study revealed that the actual programing abilities of the students are better evaluated using such CBA tests. © 2011 Wiley Periodicals, Inc. Comput Appl Eng Educ 21: 671–683, 2013