Miracle-dz/UniFAR-FTUs huggingface dataset:
Lung clearance index predicts pulmonary exacerbations in young patients with cystic fibrosis

Rationale The lung clearance index (LCI) is a promising endpoint for use in cystic fibrosis (CF) clinical trials, but correlations with validated clinical endpoints have not yet been established. Objective This study aimed to demonstrate that, in young patients with CF, baseline LCI predicts subsequent pulmonary exacerbation (PE) and correlates with the respiratory domain of the CF Questionnaire-Revised (CFQ-Rresp). Methods Baseline LCI, forced expiratory volume in 1 s (FEV1), CFQ-Rresp and PEs over the subsequent year were prospectively recorded in 63 patients aged 5–19 years. The ability of baseline LCI to predict PE was assessed using negative binomial regression models and Kaplan–Meier plots. Results Twenty-six patients (41%) experienced 48 PEs. Baseline LCI and FEV1 were predictors of PE. Compared with the quartile with the lowest LCI, the annual PE rate in increasing LCI quartiles was 2.9 (95% CI 0.5 to 16.5, p=0.238), 5.4 (95% CI 1.0 to 29.0, p=0.045) and 13.6 (95% CI 2.8 to 67.1, p=0.001). Similarly, time to first PE decreased with worsening LCI quartiles (log-rank test for trend, p<0.001). Furthermore, LCI correlated with CFQ-Rresp (r=−0.43, p<0.001). In the subgroup of 53 patients with normal FEV1, LCI was a predictor of PE. In this subgroup, LCI also correlated with CFQ-Rresp (r=−0.282, p=0.043). Conclusions Baseline LCI predicts PE in young patients with CF and correlates with CFQ-Rresp, a validated patient-reported outcome, even in the subgroup with normal FEV1. These data further support the use of LCI as a surrogate outcome measure in CF clinical trials.
DNA damage in peripheral blood lymphocytes of individuals residing near a wastewater drain and using underground water resources

Mahal is a linear village settlement situated about 0.5 km from an open waste‐water drain, the Tung Dhab drain, which carries effluents from local industrial sites. Villagers generally have a low‐to‐middle socio‐economic status and use ground water or a combination of ground water and tap water for drinking and for their other daily activities. The land in and around Mahal is used for agriculture and is irrigated by water from the Tung Dhab. The drain water contains heavy metals, and there is a possibility that these and other contaminants may reach the ground water table of Mahal and thereby compromise the health of the residents. The comet assay was performed on peripheral blood lymphocytes from Mahal villagers and revealed statistically significant increases in DNA damage as compared to a control group that does not use ground water. DNA damage was also significantly related to the age of the villagers and to the length of residence in the village. In the absence of other environmental exposures, it is concluded that the elevated DNA damage in the villagers is a consequence of continuous utilization of contaminated ground water. Environ. Mol. Mutagen. 43:235–242, 2004. © 2004 Wiley‐Liss, Inc.
Kir3-Based Inward Rectifier Potassium Current: Potential Role in Atrial Tachycardia Remodeling Effects on Atrial Repolarization and Arrhythmias

Background— We previously characterized a novel K+ current (IKH) with properties of constitutively active acetylcholine-related current in dog atrium. IKH is sensitive to tertiapin-Q (IC50 ≈10 nmol/L), a highly selective Kir3 current blocker. This study assessed the role of IKH in atrial tachycardia (AT)–remodeled canine left atrium (LA) with the use of tertiapin-Q as a probe. Methods and Results— Dogs were subjected to 7 to 13 days of AT (400 bpm). Coronary-perfused LA preparations were studied intact or subjected to cardiomyocyte isolation. IKH was recorded with patch-clamp methods. AT pacing increased time-dependent hyperpolarization-activated current (IKH) at −110 mV from −1.8±0.3 (control) to −3.4±0.5 pA/pF (AT) and the 100-nmol/L tertiapin-sensitive component from −1.5±0.4 (control) to −3.3±0.6 pA/pF (AT). Prolonged atrial tachyarrhythmias could be induced with single extrastimuli in AT-remodeled, but not control, preparations, reflecting the atrial fibrillation–promoting effects of AT remodeling. In AT-remodeled preparations, tachyarrhythmia duration averaged 11.0±5.2 seconds, with a cycle length of 108±6 ms. Tertiapin-Q decreased tachyarrhythmia duration (to 0.6±0.1 second; P<0.001) and increased tachyarrhythmia cycle length (to 175±10 ms; P<0.001). Atrial action potential duration (APD) was increased 65±6% by tertiapin in AT-remodeled hearts versus 19±2% (P<0.001) in control. In 2 AT-remodeled preparations, tachyarrhythmia lasted uninterrupted for >20 minutes; tertiapin-Q slowed and then terminated arrhythmia in both. Tertiapin had no effect on left ventricular cardiomyocyte currents or APD. Conclusions— AT remodeling increases IKH, and a highly selective Kir3 current antagonist, tertiapin-Q, increases APD and suppresses atrial tachyarrhythmias in AT-remodeled preparations without affecting ventricular electrophysiology. Constitutive acetylcholine-related K+ current contributes to AT-remodeling effects in dogs and is a potentially interesting antiarrhythmic target.
Characterization of Anammox Hydrazine Dehydrogenase, a Key N2-producing Enzyme in the Global Nitrogen Cycle*

Anaerobic ammonium-oxidizing (anammox) bacteria derive their energy for growth from the oxidation of ammonium with nitrite as the electron acceptor. N2, the end product of this metabolism, is produced from the oxidation of the intermediate, hydrazine (N2H4). Previously, we identified N2-producing hydrazine dehydrogenase (KsHDH) from the anammox organism Kuenenia stuttgartiensis as the gene product of kustc0694 and determined some of its catalytic properties. In the genome of K. stuttgartiensis, kustc0694 is one of 10 paralogs related to octaheme hydroxylamine (NH2OH) oxidoreductase (HAO). Here, we characterized KsHDH as a covalently cross-linked homotrimeric octaheme protein as found for HAO and HAO-related hydroxylamine-oxidizing enzyme kustc1061 from K. stuttgartiensis. Interestingly, the HDH trimers formed octamers in solution, each octamer harboring an amazing 192 c-type heme moieties. Whereas HAO and kustc1061 are capable of hydrazine oxidation as well, KsHDH was highly specific for this activity. To understand this specificity, we performed detailed amino acid sequence analyses and investigated the catalytic and spectroscopic (electronic absorbance, EPR) properties of KsHDH in comparison with the well defined HAO and kustc1061. We conclude that HDH specificity is most likely derived from structural changes around the catalytic heme 4 (P460) and of the electron-wiring circuit comprising seven His/His-ligated c-type hemes in each subunit. These nuances make HDH a globally prominent N2-producing enzyme, next to nitrous oxide (N2O) reductase from denitrifying microorganisms.
Multiple and cumulative impacts on the GBR: assessment of current status and development of improved approaches for management: Final Report Project 1.6

The Great Barrier Reef (GBR) is facing a suite of pressures and its status was recently assessed as poor and declining (GBRMPA Outlook Report 2014). Impacts on the GBR’s values do not occur in isolation but overlap in time and space, reducing its health and resilience. Understanding cumulative pressures and their impacts has become a priority for environmental policy, management and conservation globally. In Australia, it is imperative to improve our understanding of cumulative impacts from global and local stressors, and the ability to attribute those impacts to specific drivers and activities, as reflected in the Reef 2050 Long-Term Sustainability Plan. Despite such prioritisation, reef managers currently rely largely on qualitative tools to assess risks from cumulative impacts associated with development proposals.
Three perspectives on physical therapist managerial work.

BACKGROUND AND PURPOSE The nature of managerial work in the commercial sector has not been studied since the 1970s, and little is known about the work of managers in the health care sector. In this study, the perceived importance of managerial role and skill categories among 3 groups of physical therapists were studied to better understand the work priorities of physical therapist managers. SUBJECTS Two groups of subjects were physical therapist managers in hospitals or private practices. A third group consisted of faculty members in professional physical therapist education programs. METHODS Respondents (n=343) rated the importance of 75 managerial activities. Responses related to 16 predetermined work categories were placed in rank order by group. A multivariate analysis of variance (MANOVA) was used to identify differences among groups. RESULTS All groups identified communication, financial control, entrepreneur, resource allocator, and leader as the 5 most important categories and rated technical expert and figurehead as least important. The MANOVA showed differences between faculty members and private practice managers in 15 work categories, between hospital-based managers and private practice managers in 9 categories, and between faculty members and hospital-based managers in 8 categories. DISCUSSION AND CONCLUSION Work setting appears to have an impact on level of importance placed on managerial work categories. The strongest candidates for "universal" physical therapist managerial work categories were communication, financial control, and resource allocator.
The effects of a 16-week aerobic exercise programme on cognitive function in people living with HIV

ABSTRACT High levels of cardiovascular fitness and physical activity are associated with higher levels of cognitive function in people with HIV, thus, they may reduce the risk of developing HIV-associated neurocognitive disorder (HAND). This study aimed to investigate the effects of a 16-week aerobic exercise intervention on cognitive function in people with HIV. Eleven participants living with HIV were recruited into the study. Participants were randomised into either an exercise group (n = 5), that completed a 16-week aerobic exercise programme training, 3 times per week (2 supervised sessions and one unsupervised session) or a control group (n = 6) that received no intervention. Outcomes measured included cognitive function (Montreal cognitive assessment (MOCA) and the Trail making tests A and B), aerobic fitness (modified Bruce protocol), sleep quality (Pittsburgh sleep quality index; PSQI) and physical activity levels (seven-day accelerometry). At baseline, higher levels of moderate physical activity were positively correlated with higher MOCA scores and levels of aerobic fitness were negatively associated with Trail A scores (P = 0.04 and P = 0.001 respectively). However, exercise training did not induce any significant improvements in cognitive function or aerobic fitness. The overall mean adherence rate to the exercise programme was 60%. In conclusion, in the present study a 16-week aerobic exercise intervention did not affect the cognitive function of participants with HIV. It is likely that longer intervention periods and/or higher adherence rates to exercise might be needed for an aerobic exercise programme to be effective in improving cognitive function in a cohort with no baseline cognitive impairments.
MOSAR: A Multi-Objective Strategy for Hiding Sensitive Association Rules Using Genetic Algorithm

ABSTRACT It seems very realistic to find different aspects in a problem solution like rule hiding. Based on this point of view, Availability, Sensitivity, and Conflict are defined as the novel measurements to detect specific transactions in each transactional database in an effective way. At this point, it will be helpful for decision makers to consider such aspects on their solutions to hide sensitive association rules (ARs). Accordingly, the authors put forward a fitness function of genetic algorithm adjusted to the proposed measurements for hiding sensitive rules of the original database. Experimental study shows that the MOSAR algorithm outperforms traditional approach (Decrease Support of Right Hand Side algorithm) in view of reducing ARs in conflict with sensitive ARs, as a side effect in sensitive rule hiding process. Furthermore, this approach is applicable to do its best in banking systems, where database is to be shared through the networks, to protect strategic information after a serious attack.
Modular FEM framework "ModFem" for generic scientific parallel simulations

We present the design and its' implementation for a flexible and robust parallel modular finite element (FEM) framework, called ModFem. The design is based on reusable modules which use narrow and well-defined interfaces to cooperate. At the top of the architecture there are problem dependent modules. Problem dependent modules can be additionally grouped together by "super-modules". This structure allows for applying the sequential codes to parallel environments and also support solving multi-physics and multi-scale problems.
Automated spike sorting algorithm based on Laplacian eigenmaps and k-means clustering

This study presents a new automatic spike sorting method based on feature extraction by Laplacian eigenmaps combined with k-means clustering. The performance of the proposed method was compared against previously reported algorithms such as principal component analysis (PCA) and amplitude-based feature extraction. Two types of classifier (namely k-means and classification expectation-maximization) were incorporated within the spike sorting algorithms, in order to find a suitable classifier for the feature sets. Simulated data sets and in-vivo tetrode multichannel recordings were employed to assess the performance of the spike sorting algorithms. The results show that the proposed algorithm yields significantly improved performance with mean sorting accuracy of 73% and sorting error of 10% compared to PCA which combined with k-means had a sorting accuracy of 58% and sorting error of 10%. A correction was made to this article on 22 February 2011. The spacing of the title was amended on the abstract page. No changes were made to the article PDF and the print version was unaffected.
Variabilidade mineralógica de latossolos da área da Embrapa Cerrados em relação aos do bioma cerrado.

A multiplicidade de levantamentos de solos na regiao do Cerrado, em escalas as mais variadas possiveis, bem como a heterogeneidade das condicoes ambientais do Cerrado pode tornar bastante dificeis as extrapolacoes em resultados na pesquisa agropecuaria. Este estudo teve como objetivo analisar as caracteristicas morfologicas, fisicas, quimicas e mineralogicas dos solos da area da Embrapa Cerrados, relacionando-as com as de outros solos dos diferentes ambientes do Cerrado. Foram tabulados os dados dos levantamentos de solo existentes nas mais variadas escalas de trabalho: 1:1.000. 000, envolvendo toda area de Cerrado descontinuo (Distrito Federal, Minas Gerais, Mato Grosso, Mato Grosso do Sul, Goias, Maranhao, Sao Paulo, Amapa Bahia e Piaui); 1:500.000 (regiao Geoeconomica de Brasilia); 1:100.000 (Distrito Federal e Rio Verde); 1:50.000 (Bacia do rio Jardim, DF); 1:20.000 (Embrapa Cerrados). Aplicou-se uma metodologia para semiquantificacao dos minerais na fracao argila de Latossolos, baseados nos dados de ataque sulfurico e cor (matiz-valor-croma), obtendo-se os teores de caulinita (Ct), hematita (Hm), goethita (Gt), gibbsita (Gb) e anatasio (An). De posse dos resultados mineralogicos, verificou-se a similaridade dos Latossolos da Embrapa Cerrados com os da regiao do Cerrado. Somente o LATOSSOLO VERMELHO Distrofico (LVd) caulinitico da Embrapa Cerrados e representativo dessa regiao; nao se observou LV oxidico-gibbsitico na Embrapa Cerrados; o LV oxidico-hematitico e tipico de solos resultantes de material de origem basalto; alguns LV classificados em oxidico-gibbsitico, segundo criterios da Soil Taxonomy, seriam mais bem reenquadrados como caulinitico-oxidico ao apresentarem razao caulinita-gibbsita (RCGb) superior a 0,50 e valores medios de Ct superiores a 40%; os LV cauliniticos, derivados de metarritmito da Embrapa Cerrados, possuem similaridade com os seguintes materiais de origem: argilito, TQDl, quartzito, arenito, Formacao Cachoeirinha, ardosia, xisto, granito e arenito/basalto. Os LATOSSOLOS VERMELHO-AMARELOS Distroficos (LVA) caulinitico e oxidico-gibbsitico da Embrapa Cerrados sao representativos da regiao do Cerrado; nao se observou LVA gibbsitico na Embrapa Cerrados; alguns LVAs classificados em oxidico-gibbsiticos, segundo criterios da Soil Taxonomy, seriam mais bem reenquadrados como caulinitico-oxidicos ao apresentarem razao caulinita-gibbsita (RCGb) superior a 0,50 e valores medios de Ct superiores a 40%. Os LVAs cauliniticos derivados de metarritmito argiloso e arenoso e sedimentos/quartzito na Embrapa Cerrados sao similares aos LVAs cauliniticos da regiao do Cerrado derivados da cobertura Detrito-lateritica do Terciario-Quaternario (TQDl), mica-clorita-xisto, arenito, ardosia e Formacao Barreiras. Os LVAs oxidico-gibbsiticos derivados da TQDl na Embrapa Cerrados sao similares aos LVAs oxidico-gibbsiticos dessa regiao derivados de quartzito, gnaisse, Formacao Cachoeirinha e arenito.
Anomaly detection from linguistic summaries

Linguistic summaries of sensor data have been shown to be valuable as a communication tool with health care providers in an eldercare environment. Additionally, we have developed a metric distance for our particular form of linguistic protoform summaries (LPS). This has allowed the creation of linguistic prototypes from clusters of summaries over some temporal range. Using that, we present a method for detecting anomalies, as observations considerably different from the linguistic prototypes in a moving temporal window. Two case studies from an eldercare environment demonstrate the utility of this approach.
Large Angle based Skeleton Extraction for 3D Animation

In this paper, we present a solution for arbitrary 3D character deformation by investigating rotation angle of decomposition and preserving the mesh topology structure. In computer graphics, skeleton extraction and skeleton-driven animation is an active areas and gains increasing interests from researchers. The accuracy is critical for realistic animation and related applications. There have been extensive studies on skeleton based 3D deformation. However for the scenarios of large angle rotation of different body parts, it has been relatively less addressed by the state-of-the-art, which often yield unsatisfactory results. Besides 3D animation problems, we also notice for many 3D skeleton detection or tracking applications from a video or depth streams, large angle rotation is also a critical factor in the regression accuracy and robustness. We introduced a distortion metric function to quantify the surface curviness before and after deformation, which is a major clue for large angle rotation detection. The intensive experimental results show that our method is suitable for 3D modeling, animation, skeleton based tracking applications.
An efficient compiler framework for cache bypassing on GPUs

Graphics Processing Units (GPUs) have become ubiquitous for general purpose applications due to their tremendous computing power. Initially, GPUs only employ scratchpad memory as on-chip memory. Though scratchpad memory benefits many applications, it is not ideal for those general purpose applications with irregular memory accesses. Hence, GPU vendors have introduced caches in conjunction with scratchpad memory in the recent generations of GPUs. The caches on GPUs are highly-configurable. The programmer or the compiler can explicitly control cache access or bypass for global load instructions. This highly-configurable feature of GPU caches opens up the opportunities for optimizing the cache performance. In this paper, we propose an efficient compiler framework for cache bypassing on GPUs. Our objective is to efficiently utilize the configurable cache and improve the overall performance for general purpose GPU applications. In order to achieve this goal, we first characterize GPU cache utilization and develop performance metrics to estimate the cache reuses and memory traffic. Next, we present efficient algorithms that judiciously select global load instructions for cache access or bypass. Finally, we integrate our techniques into an automatic compiler framework that leverages PTX instruction set architecture. Experiments evaluation demonstrates that compared to cache-all and bypass-all solutions, our techniques can achieve considerable performance improvement.
REGIONAL FRAMEWORKS APPLIED TO HYDROLOGY: CAN LANDSCAPE‐BASED FRAMEWORKS CAPTURE THE HYDROLOGIC VARIABILITY?

Regional frameworks have been used extensively in recent years to aid in broad‐scale management. Widely used landscape‐based regional frameworks, such as hydrologic landscape regions (HLRs) and physiographic provinces, may provide predictive tools of hydrologic variability. However, hydrologic‐based regional frameworks, created using only streamflow data, are also available and have been created at various scales; thus, relating frameworks that share a common purpose can be informative. In addition, identifying how the relative importance of variables change in governing streamflow with respect to scale can also be informative. The purpose of this study was to determine whether landscape‐based frameworks could explain variation in streamflow classifications and in the hydrologic variables used in their creation. We also evaluated how climate and watershed‐based variables govern the divergence of different flow classifications at two different scales. HLRs and physiographic provinces poorly predicted flow class affiliation within our study and for the entire USA, although physiographic provinces explained more variability. We also found that HLRs explained very little variation in individual hydrologic parameters. Using variables summarized at the watershed scale, we found that climate will play a larger role in influencing hydrology across the entire US, whereas soils may govern variation in hydrology at smaller scales. Our results suggest that predictor variables, developed at the watershed scale, may be the most appropriate at explaining hydrology and that the variables used in creating regional landscape‐based frameworks may be more useful than the frameworks themselves. In addition, managers should be careful when using landscape‐based regional classifications for stream management because the scale of their construction may be too broad to capture differences in flow variability. Copyright © 2011 John Wiley & Sons, Ltd.
Modeling document features for expert finding

We argue that expert finding is sensitive to multiple document features in an organization, and therefore, can benefit from the incorporation of these document features. We propose a unified language model, which integrates multiple document features, namely, multiple levels of associations, PageRank, indegree, internal document structure, and URL length. Our experiments on two TREC Enterprise Track collections, i.e., the W3C and CSIRO datasets, demonstrate that the natures of the two organizational intranets and two types of expert finding tasks, i.e., key contact finding for CSIRO and knowledgeable person finding for W3C, influence the effectiveness of different document features. Our work provides insights into which document features work for certain types of expert finding tasks, and helps design expert finding strategies that are effective for different scenarios.