Miracle-dz/UniFAR-FTUs huggingface dataset:
Removal of Mn(II) ions from aqueous neutral media by manganese‐oxidizing fungus in the presence of carbon fiber

A manganese‐oxidizing fungus was isolated from a hot spring in Japan. The fungus was increasingly effective at oxidizing Mn(II) ions as the concentration of organic carbon sources in the growth medium was decreased. The fungus oxidized 50 ppm of Mn(II) ions within 160 h in a pH 7.3 medium at 25°C. The presence of carbon fiber shortened the time to 80 h, and promoted steady oxidation. The oxidation products were identified by XPS and XRD to be poorly crystallized and amorphous MnO2, both with and without the fiber. These results suggest that the fiber participates in kinetically limited oxidation. The fungus was entangled with and clung to the fibers, and the oxidized Mn species accumulated on the fungus. Similarly shaped polyethylene telephthalate fiber did not enhance the oxidation, nor was adhesion of the fungus observed. Although the mechanism is still unknown, the present work shows that removal of Mn from solution through the precipitation and accumulation of Mn‐oxides on the fungus in the presence of carbon fiber is a promising improvement for water treatment. © 2004 Wiley Periodicals, Inc.
Reliable Reporting for Massive M2M Communications With Periodic Resource Pooling

This letter considers a wireless M2M communication scenario with a massive number of M2M devices. Each device needs to send its reports within a given deadline and with certain reliability, e.g., 99.99%. A pool of resources available to all M2M devices is periodically available for transmission. The number of transmissions required by an M2M device within the pool is random due to two reasons-random number of arrived reports since the last reporting opportunity and requests for retransmission due to random channel errors. We show how to dimension the pool of M2M-dedicated resources in order to guarantee the desired reliability of the report delivery within the deadline. The fact that the pool of resources is used by a massive number of devices allows basing the dimensioning on the central limit theorem. The results are interpreted in the context of LTE, but they are applicable to any M2M communication system.
Local Effects on Strain Seismogram at Matsushiro Seismological Observatory-1. Love Waves

We proposed a simple method to evaluate local effects on a strain seismogram, and applied the method to investigation of the effects at Matsushiro Seismological Observatory, Japan Meteorological Agency, central Japan, for a Love wave in a period range of 170-400 sec. First, we took a ratio of EW to NS component strain for a Love wave on a time-frequency plane. Although NS and EW component strain for a Love wave travelling in any direction have the same amplitude theoretically, the ratio of observed EW to NS component strain was 0.7. Next, we compared the strain seismogram with a velocity seismogram recorded with STS-1 broadband seismometer. A ratio of a partial derivative of a displacement field with respect to time to that with respect to wave propagation direction equals a phase velocity of the wave theoretically. Utilizing the fact, we estimated the phase velocity of a Love wave using the observed velocity and strain seismogram, after NS component strain had been multiplied by 0.7. The result was 24% smaller than the theoretical phase velocity. Finally, we compared the velocity seismogram with other velocity seismograms recorded by STS-1 seismometers at F-net observation stations near Matsushiro and by STS-2 seismometer at Matsushiro, and found that the every deviation from Matsushiro was less than 10%. From these results, we conclude that the EW and NS component strain seismograms have been amplified by factors of 1.32 and 1.88 for a Love wave, respectively. This fact, which may be because of local geology and/or topography effects, must be taken into account when the strain seismogram is used for seismological applications such as the CMT inversion and research on earth's free oscillations.
Oracle and storage IOs, explanations and experience at CERN

The Oracle database system is used extensively in the High Energy Physics community. Critical to the efficient running of these databases is the storage subsystem, and over the years Oracle has introduced new ways to access and manage this storage, e.g. ASM (Oracle database version 10.1), Direct NFS (Oracle database version 11.1), and Exadata (Oracle database version 11.1). This paper presents CERN's experience over the past few years with the different storage access and management features, and gives a comparison of each functionality. Also compared are the different solutions used at CERN, and the Tier 1 sites for storing Oracle databases.
Using Change Impact Analysis to Select Tests for Extended Finite State Machines

A formal approach to select tests for regression testing of changes performed in a system evolution step is proposed. Systems are modeled as extended finite state machines (EFSMs) supporting several commonly used data types including booleans, numbers, arrays, queues and records. Tests are described using a sequence of input and expected output messages with concrete parameter values. Changes add/delete/replace one or more EFSM transitions. Transitions potentially executed by a test are automatically identified from its description. A simple structural invariant for a test description based on these transitions is introduced. It is shown that for a test description satisfying the invariant it can be accurately determined if a given change affects the test. Affected tests are selected for regression testing of the change. Failure of a description to meet the invariant is analyzed to identify non-observable regions in the description, which are then further analyzed using other system transitions to identify affected tests. We also describe a novel approach based on substitutability of tests to reduce the size of a regression test suite without affecting coverage. The effectiveness of the proposed approach is illustrated by applying it to several examples. Our experiments based on a well-known cost model for regression testing show that the proposed approach is economical for selective re-testing in these examples.
Dissolution and mass transfer of multiple organics under field conditions: The Borden emplaced source

The process that transfers mass from a subsurface source zone of residual dense nonaqueous phase liquid (DNAPL) to the flowing groundwater is a controlling factor in determining the time required to dissolve the source by noninvasive means. While mass transfer can be kinetic or equilibrium under laboratory conditions, aqueous concentrations in the field are generally found to be below equilibrium levels. To gain insight into the mass transfer process under field conditions, we simulated the dissolution of the emplaced DNAPL source at the Canadian Forces Base Borden, Ontario, which contains a mixture of three DNAPLs. The simulations clearly show that mass transfer at this site is equilibrium‐controlled during the 1000‐day observation period and that apparent tailing of one of the organic components is due to its declining solubility, rather than mass transfer kinetics. Flow lines passing through the source are focused in a narrow streamtube downstream of the source, and equilibrium concentrations are therefore observed only at the center of the effluent plume. Since the concentration peaks can be easily missed in the sampling, streamline focusing can explain the low concentrations observed in the field.
Clinical outcomes and Quality of Life in Elderly Patients on Peritoneal Dialysis versus Hemodialysis

♦ Objective To compare clinical outcomes and quality of life (QOL) in elderly patients on peritoneal dialysis (PD) and hemodialysis (HD) in the North Thames Dialysis Study. ♦ Design A 12-month prospective cohort study. ♦ Setting Four hospital-based renal units in London, UK. ♦ Patients 174 patients that were 70 years or older at the start of dialysis, separated into two cohorts: 78 new patients (36 PD, 42 HD) that were recruited after 90 days of chronic dialysis; and 96 stock patients (42 PD, 54 HD) that were already on dialysis during the recruitment period. ♦ Main Outcome Measures 12-month survival and hospitalization rate, and QOL assessed at baseline and at 6 and 12 months by the SF-36 and the Symptoms/Problems scale of the Kidney Disease Quality of Life Questionnaire (KDQOL). ♦ Results Peritoneal dialysis and HD patients were similar for sociodemographic and clinical characteristics. Annual mortality and hospitalization rates in PD versus HD patients were 26.1 versus 26.4 deaths/100 person–years and 1.9 versus 2.0 admissions/person–year, respectively. Adjusted relative risks showed no effect of modality on clinical outcomes. Multiple linear regression analyses of QOL at baseline showed similar SF-36 scores between PD and HD patients, but higher KDQOL scores in PD patients (3.5 points higher, 95% confidence interval 0.3 – 6.6). There was, however, no effect of dialysis modality on QOL at 6 or 12 months. ♦ Conclusions Clinical outcomes and QOL are similar in elderly people on PD and HD. Peritoneal dialysis is a viable option for more than a carefully selected minority of elderly people requiring dialysis.
Detecting Interactions in Association Studies by Using Simple Allele Recoding

This paper aims to describe the benefits of using data recoding methods for the analysis of genetic interactions. By changing the representation of the input data it is possible to model non-additive genetic effects in association analysis software, which has been primarily designed to analyse only additive genetic effects. Similar treatment can be applied also for general-purpose statistical search algorithms available in general statistical packages. Data recoding is illustrated for several interaction models using hypothetical examples and by presenting gene-gene interaction analysis in a real cystic fibrosis dataset using the BAMA software.
Quantitative relaxation templates for the human brain at 3T

The development of brain Magentic Resonance Imaging (MRI) is driving increasing demand for quantitative measurements. Quantitative MRI (qMRI) templates of relaxation times and proton density can be of particular interest for dedicated clinical applications such as characterizing brain tissue abnormalities, as well as general research purposes. In this paper, we have developed 3D qMRI statistical templates consisting of T1, T2, T2* and ρ* maps from the human brain at 3T. The qMRI templates were built from a population of 20 normal controls, for which individual maps were estimated in a robust manner, accounting for acquisition artifacts and expected relationships between the relaxometry parameters. For validation, we fed the qMRI templates into a realistic MRI simulator to synthesize MR-weighted images, and compared these images with the real MR acquisitions. High correlation coefficients (>0.80) show that the developed qMRI templates can be used as input dataset for MRI simulation community, which may be of great interest to clinical neuroscience field.
Different approaches of visibility analyses applied on hilly urban environment

Abstract The work reported in this paper is a contribution to the search for reliable visibility evaluation method for the urban environment. We examine three analysis models: 1. Point based visibility graph of street network based on , 2. Voxel based volumetric visibility analysis (Fisher-Gewirtzman et. al., 2013) and 3. Line Of Sight (LOS) based visibility analysis (Fisher-Gewirtzman and Elber, 2013). We compare between these models to explore their suitability to a hilly urban spatial configurations. We describe the similarities and differences. In this study we carry out a test comparing the value of visibility degree centrality for street network to the assessments of 3D Voxel and LOS visibility analyses. Our results demonstrate that junctions with similar rankings in all three models were located in a fairly flat topography and all the junctions with different rank were located on the border of a sloping topography. Their visibility was influenced by the changing topography. This preliminary study will be followed by more comprehensive research looking at a variety of urban, architectural and topographic conditions. These findings may provide planners and designers with information about factors that affect the visibility of the urban environment and may put forward new ideas to improve the existing measurement tools.
From Electrical Switched Networks to Hybrid Automata ( Extended Version )

In this paper, we propose a novel symbolic approach to automatically synthesize a Hybrid Automaton (HA) from a switched electrical network. The input network consists of a set of physical components interconnected according to some reconfigurable network topology. The underlying model defines a local dynamics for each component in terms of a Differential-Algebraic Equation (DAE), and a set of network topologies by means of discrete switches. Each switch configuration induces a different topology, where the behavior of the system is a Hybrid Differential-Algebraic Equations. Two relevant problems for these networks are validation and reformulation. The first consists of determining if the network admits an Ordinary Differential Equations (ODE) that describes its dynamics; the second consists of obtaining such ODE from the initial DAE. This step is a key enabler to use existing formal verification tools that can cope with ODEs but not with DAEs. Since the number of network topologies is exponential in the number of switches, first, we propose a technique based on Satisfiability Modulo Theories (SMT) that can solve the validation problem symbolically, avoiding the explicit enumeration of the topologies. Then, we show an SMT-based algorithm that reformulates the network into a symbolic HA. The algorithm avoids to explicitly enumerate the topologies clustering them by equivalent continuous dynamics. We implemented the approach with several optimizations and we compared it with the explicit enumeration of configurations. The results demonstrate the scalability of our technique.
scc: cluster storage provisioning informed by application characteristics and SLAs

Storage for cluster applications is typically provisioned based on rough, qualitative characterizations of applications. Moreover, configurations are often selected based on rules of thumb and are usually homogeneous across a deployment; to handle increased load, the application is simply scaled out across additional machines and storage of the same type. As deployments grow larger and storage options (e.g., disks, SSDs, DRAM) diversify, however, current practices are becoming increasingly inefficient in trading off cost versus performance. To enable more cost-effective deployment of cluster applications, we develop scc--a storage configuration compiler for cluster applications. scc automates cluster configuration decisions based on formal specifications of application behavior and hardware properties. We study a range of storage configurations and identify specifications that succinctly capture the trade-offs offered by different types of hardware, as well as the varying demands of application components. We apply scc to three representative applications and find that scc is expressive enough to meet application Service Level Agreements (SLAs) while delivering 2-4.5× savings in cost on average compared to simple scale-out options. scc's advantage stems mainly from its ability to configure heterogeneous--rather than conventional, homogeneous--cluster architectures to optimize cost.
Additive models, boosting, and inference for generalized divergences

We present a framework for designing incremental learning algorithms derived from generalized entropy functionals. Our approach is based on the use of Bregman divergences together with the associated class of additive models constructed using the Legendre transform. A particular one-parameter family of Bregman divergences is shown to yield a family of loss functions that includes the log-likelihood criterion of logistic regression as a special case, and that closely approximates the exponential loss criterion used in the AdaBoost algorithms of Schapire et a/. , as the natural parameter of the family varies. We also show how the quadratic approximation of the gain in Bregman divergence results in a weighted least-squares criterion. This leads to a family of incremental learning algorithms that builds upon and extends the recent interpretation of boosting in terms of additive models proposed by Friedman, Hastie, and Tibshirani.
Source Code Retrieval Using Sequence Based Similarity

Duplicated code has a negative impact on the quality of software systems and should be detected at least. In this paper, we discuss an approach that improves source code retrieval using the structural information about the programs. We developed a lexical parser to extract control statements and method identifiers from Java programs. We propose a similarity measure that is defined by the ratio of the number of sequentially full matching statements to the number of sequentially partial matching ones. The similarity measure is considered to be an extension of a set based similarity index, e.g., Sorensen-Dice index. Our key contribution of this research is the development of a similarity retrieval algorithm that derives meaningful search conditions from a given sequence, and then performs retrieval using all of the derived conditions. Experiments show that our retrieval model outperforms the other retrieval models up to 90.9% in the number of retrieved methods.
On the Complexity of Discrete Feature Selection for Optimal Classification

Consider a classification problem involving only discrete features that are represented as random variables with some prescribed discrete sample space. In this paper, we study the complexity of two feature selection problems. The first problem consists in finding a feature subset of a given size k that has minimal Bayes risk. We show that for any increasing ordering of the Bayes risks of the feature subsets (consistent with an obvious monotonicity constraint), there exists a probability distribution that exhibits that ordering. This implies that solving the first problem requires an exhaustive search over the feature subsets of size k. The second problem consists of finding the minimal feature subset that has minimal Bayes risk. In the light of the complexity of the first problem, one may think that solving the second problem requires an exhaustive search over all of the feature subsets. We show that, under mild assumptions, this is not true. We also study the practical implications of our solutions to the second problem.
Evaluating the Performance of RPL and 6LoWPAN in TinyOS

Responding to the increasing interest to connect wireless sensor networks (WSN) to the Internet, the IETF has proposed standards that enable IPv6-based sensor networks. Specifically, the IETF 6LoWPAN and RoLL working groups developed standards for encapsulating IPv6 datagrams in 802.15. 4 frames, neighbor discovery, and routing that allow sensor networks to exchange IPv6 datagrams with Internet hosts. However, given that these standards, especially the RPL routing protocol, are relatively new, there has not yet been a study that measures the actual performance of these proposals using real implementations. In this work, we use the BLIP and TinyRPL implementations in TinyOS 2.x to evaluate the performance of the newly proposed standards and compare them with CTP, the de-facto routing protocol standard for TinyOS. Our results indicate that the performance of TinyRPL is comparable with CTP and at the same time, TinyRPL can provide additional functionalities that traditional WSN routing protocols could not provide. We also discovered several issues, relevant to system developers and the standardization groups, which can enhance the proposed standards’ performance.
Genome-Wide Association Studies in an Isolated Founder Population from the Pacific Island of Kosrae

It has been argued that the limited genetic diversity and reduced allelic heterogeneity observed in isolated founder populations facilitates discovery of loci contributing to both Mendelian and complex disease. A strong founder effect, severe isolation, and substantial inbreeding have dramatically reduced genetic diversity in natives from the island of Kosrae, Federated States of Micronesia, who exhibit a high prevalence of obesity and other metabolic disorders. We hypothesized that genetic drift and possibly natural selection on Kosrae might have increased the frequency of previously rare genetic variants with relatively large effects, making these alleles readily detectable in genome-wide association analysis. However, mapping in large, inbred cohorts introduces analytic challenges, as extensive relatedness between subjects violates the assumptions of independence upon which traditional association test statistics are based. We performed genome-wide association analysis for 15 quantitative traits in 2,906 members of the Kosrae population, using novel approaches to manage the extreme relatedness in the sample. As positive controls, we observe association to known loci for plasma cholesterol, triglycerides, and C-reactive protein and to a compelling candidate loci for thyroid stimulating hormone and fasting plasma glucose. We show that our study is well powered to detect common alleles explaining ≥5% phenotypic variance. However, no such large effects were observed with genome-wide significance, arguing that even in such a severely inbred population, common alleles typically have modest effects. Finally, we show that a majority of common variants discovered in Caucasians have indistinguishable effect sizes on Kosrae, despite the major differences in population genetics and environment.
Evaluation of use of reading comprehension strategies to improve reading comprehension of adult college students with acquired brain injury

Adults with mild to moderate acquired brain injury (ABI) often pursue post-secondary or professional education after their injuries in order to enter or re-enter the job market. An increasing number of these adults report problems with reading-to-learn. The problem is particularly concerning given the growing population of adult survivors of ABI. Despite the rising need, empirical evaluation of reading comprehension interventions for adults with ABI is scarce. This study used a within-subject design to evaluate whether adult college students with ABI with no more than moderate cognitive impairments benefited from using reading comprehension strategies to improve comprehension of expository text. Integrating empirical support from the cognitive rehabilitation and special education literature, the researchers designed a multi-component reading comprehension strategy package. Participants read chapters from an introductory-level college anthropology textbook in two different conditions: strategy and no-strategy. The results indicated that reading comprehension strategy use was associated with recall of more correct information units in immediate and delayed free recall tasks; more efficient recall in the delayed free recall task; and increased accuracy recognising statements from a sentence verification task designed to reflect the local and global coherence of the text. The findings support further research into using reading comprehension strategies as an intervention approach for the adult ABI population. Future research needs include identifying how to match particular reading comprehension strategies to individuals, examining whether reading comprehension performance improves further through the incorporation of systematic training, and evaluating texts from a range of disciplines and genres.