Miracle-dz/UniFAR-FTUs huggingface dataset:
Fe-phyllosilicate redox cycling organisms from a redox transition zone in Hanford 300 Area sediments

Microorganisms capable of reducing or oxidizing structural iron (Fe) in Fe-bearing phyllosilicate minerals were enriched and isolated from a subsurface redox transition zone at the Hanford 300 Area site in eastern Washington, USA. Both conventional and in situ “i-chip” enrichment strategies were employed. One Fe(III)-reducing Geobacter (G. bremensis strain R1, Deltaproteobacteria) and six Fe(II) phyllosilicate-oxidizing isolates from the Alphaproteobacteria (Bradyrhizobium japonicum strains 22, is5, and in8p8), Betaproteobacteria (Cupriavidus necator strain A5-1, Dechloromonas agitata strain is5), and Actinobacteria (Nocardioides sp. strain in31) were recovered. The G. bremensis isolate grew by oxidizing acetate with the oxidized form of NAu-2 smectite as the electron acceptor. The Fe(II)-oxidizers grew by oxidation of chemically reduced smectite as the energy source with nitrate as the electron acceptor. The Bradyrhizobium isolates could also carry out aerobic oxidation of biotite. This is the first report of the recovery of a Fe(II)-oxidizing Nocardioides, and to date only one other Fe(II)-oxidizing Bradyrhizobium is known. The 16S rRNA gene sequences of the isolates were similar to ones found in clone libraries from Hanford 300 sediments and groundwater, suggesting that such organisms may be present and active in situ. Whole genome sequencing of the isolates is underway, the results of which will enable comparative genomic analysis of mechanisms of extracellular phyllosilicate Fe redox metabolism, and facilitate development of techniques to detect the presence and expression of genes associated with microbial phyllosilicate Fe redox cycling in sediments.
Exposition of a New Theory on the Measurement of Risk

EVER SINCE mathematicians first began to study the measurement of risk there has been general agreement on the following proposition: Expected values are computed by multiplying each possible gain by the number of ways in which it can occur, and then dividing the sum of these products by the total number of possible cases where, in this theory, the consideration of cases which are all of the same probability is insisted upon. If this rule be accepted, what remains to be done within the framework of this theory amounts to the enumeration of all alternatives, their breakdown into equi-probable cases and, finally, their insertion into corresponding classifications…
SFBC and ICI Cancellation Method Comparison in the MISO DFT-Spread OFDM System with Frequency Offset and Phase Noise

In this paper, frequency offset and phase noise influence in the MISO SFBC DFT-Spread OFDM system is analyzed theoretically, then, ICI cancellation methods are applied to minimize interference. Simulation results show that in the 2×1 SFBC DFT-Spread OFDM system, ICI and SCI can not be neglected because the system even intensifies interference due to the simultaneous generation of more SCI and ICI than 2×1 DFT-Spread OFDM only. This phenomenon can be resolved by using ICI self-cancellation methods, especially, considerable performance improvement can be achieved by using data-conjugate method.
TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype trees

SUMMARY We present the software implementation of the tree scanning method to detect associations between genetic haplotypes and quantitative traits, utilizing the evolutionary history of the haplotypes, in samples of unrelated individuals. AVAILABILITY The program is available free of charge, under the GNU General Public License. A package including C source code, a Makefile, and Windows (DOS) and Macintosh binaries, can be downloaded from http://darwin.uvigo. es
Online gambling participation and problem gambling severity: is there a causal relationship?

Studies of Internet gambling have consistently shown that online gamblers are more likely to report disordered gambling behaviour than offline gamblers. However, little research has focused on whether this is a causal relationship or whether this risk factor is capturing a relationship with one or more missing variables. To address whether there is a strong causal argument for the effect of online gambling participation on problem gambling severity, we use a secondary data method that corrects for potential omitted variable bias. Once this issue is addressed, we find that past-year participation in online gambling is related to a decrease in problem gambling severity, which is the opposite of the popular view in current literature. The estimates in this study are found to be robust to various forms of online gambling, control variables and problem gambling measurement instruments. The findings were also consistent when using a representative sample from the United Kingdom and when using an online research panel from Ontario, Canada. As a primary force against the widespread adoption of Internet gambling has been public health concern over problem gambling, this study provides evidence that such decisions should be more closely considered by policymakers.
An approach to model the risk in the second-stage cost is to use a convex nondecreasing disutility function

We propose a semidefinite optimization (SDP) model for the class of minimax two-stage stochastic linear optimization problems with risk aversion. The distribution of second-stage random variables belongs to a set of multivariate distributions with known first and second moments. For the minimax stochastic problem with random objective, we provide a tight SDP formulation. The problem with random right-hand side is NP-hard in general. In a special case, the problem can be solved in polynomial time. Explicit constructions of the worst-case distributions are provided. Applications in a productiontransportation problem and a single facility minimax distance problem are provided to demonstrate our approach. In our experiments, the performance of minimax solutions is close to that of data-driven solutions under the multivariate normal distribution and better under extremal distributions. The minimax solutions thus guarantee to hedge against these worst possible distributions and provide a natural distribution to stress test stochastic optimization problems under distributional ambiguity.
Dependency oriented complexity metrics to detect rippling related design defects

Even though object oriented software development has gained popularity due to its inherent features, it also throws challenges in early detection of defects during design phase. Detection of design defects helps in performing appropriate refactorings in improving the quality of design. Literature indicates that active research is going on in detecting design defects using metrics. The present paper introduces a set of metrics for detecting defects in object oriented designs caused by the presence of shotgun surgery and divergent change bad smells. These metrics are, dependency oriented complexity metric for structure (DOCMS(R)), dependen-cy oriented complexity metric for an artifact causing ripples (DOCMA(CR)), and dependency oriented complexity metric for an artifact affected by ripples (DOCMA(AR)). The proposed me-trics have been computed for four cases. These metrics are used successfully in detecting design defects and complexity. In the present study DOCMA(CR) metric value indicated the presence of shotgun surgery bad smell, whereas DOCMA(AR) metric value indicated the presence of divergent change bad smell. DOCMS(R) metric value indicated the increase in complexity of structure (ar-chitecture) when the design defects are present. Detecting bad smells helps in performing appropriate refactorings to make the software maintainable and to improve the quality of software.
Detecting public sentiment over PM2.5 pollution hazards through analysis of Chinese microblog

Decision-making in crisis management can benefit from routine monitoring of the (social) media to discover the mass opinion on highly sensitive crisis events. We present an experiment that analyzes Chinese microblog data (extracted from Weibo.cn) to measure sentiment strength and its change in relation to the recent PM 2.5 air pollution events. The data were analyzed using SentiStrength algorithm together with a special sentiment words dictionary tailored and refined for Chinese language. The results of time series analysis on detected sentiment strength showed that less than one percent of the posts are strong-positive or strong negative. Weekly sentiment strength measures show symmetric changes in positive and negative strength, but overall trend moved towards more positive opinions. Special attention was given to sharp bursts of sentiment strength that coincide temporally with the occurrence of extreme social events. These findings suggest that sentiment strength analysis may generate useful alert and awareness of pending extreme social events.
CD8+ T cell‐mediated protection against an intracellular bacterium by perforin‐dependent cytotoxicity

Growth of Listeria monocytogenes is mainly controlled by macrophages, which are activated by specific T cells. A potential role of CD8+ T cells by direct lysis of infected cells was investigated in perforin‐deficient mice generated by homologous recombination. The absence of perforin‐mediated cytotoxicity resulted in delayed clearance of Listeria from the spleen but not the liver after primary infection, overall susceptibility to Listeria however was not increased. Protection against a secondary infection was drastically impaired in perforin‐deficient mice. Adoptive transfer of immune spleen cells to recipients revealed that anti‐Listeria protection by CD8+ T cells from perforin‐deficient versus normal mice was about 10‐fold reduced in livers and about 100‐fold reduced in the spleen of recipients. CD4+ T cells from immune control and perforin‐deficient mice conferred comparable protection. These results indicate that the protective effect of CD8+ T cells against an intracellular bacterium mainly evident in secondary infection is mediated by a perforin‐dependent pathway, presumably cytotoxicity, and less by other direct or indirect effector mechanisms.
Hybrid prism/chirped mirror compressor for multi-mJ, kHz, sub-30 fs, CEP stabilized Ti:Sa laser

We achieve pulse compression down to 24 fs with 1.1 mJ energy and full carrier-envelope phase (CEP) stabilisation at 1 kHz using a compressor combining prisms and chirped mirrors. We demonstrate that this hybrid compression scheme can be scaled in order to produce CEP-stabilized sub-30 fs pulses at the multi-mJ level.
Insurance Telematics: Opportunities and Challenges with the Smartphone Solution

Smartphone-based insurance telematics or usage based insurance is a disruptive technology which relies on insurance premiums that reflect the risk profile of the driver; measured via smartphones with appropriate installed software. A survey of smartphone-based insurance telematics is presented, including definitions; Figure-of-Merits (FoMs), describing the behavior of the driver and the characteristics of the trip; and risk profiling of the driver based on different sets of FoMs. The data quality provided by the smartphone is characterized in terms of Accuracy, Integrity, Availability, and Continuity of Service. The quality of the smartphone data is further compared with the quality of data from traditional in-car mounted devices for insurance telematics, revealing the obstacles that have to be combated for a successful smartphone-based installation, which are the poor integrity and low availability. Simply speaking, the reliability is lacking considering the smartphone measurements. Integrity enhancement of smartphone data is illustrated by both second-by-second lowlevel signal processing to combat outliers and perform integrity monitoring, and by trip-based map-matching for robustification of the recorded trip data. A plurality of FoMs are described, analyzed and categorized, including events and properties like harsh braking, speeding, and location. The categorization of the FoMs in terms of Observability, Stationarity, Driver influence, and Actuarial relevance are tools for robust risk profiling of the driver and the trip. Proper driver feedback is briefly discussed, and rule-of-thumbs for feedback design are included. The work is supported by experimental validation, statistical analysis, and experiences from a recent insurance telematics pilot run in Sweden.
Single-Trial Extraction of Pure Somatosensory Evoked Potential Based on Expectation Maximization Approach

It is of great importance for intraoperative monitoring to accurately extract somatosensory evoked potentials (SEPs) and track its changes fast. Currently, multi-trial averaging is widely adopted for SEP signal extraction. However, because of the loss of variations related to SEP features across different trials, the estimated SEPs in such a way are not suitable for the purpose of real-time monitoring of every single trial of SEP. In order to handle this issue, a number of single-trial SEP extraction approaches have been developed in the literature, such as ARX and SOBI, but most of them have their performance limited due to not sufficient utilization of multi-trial and multi-condition structures of the signals. In this paper, a novel Bayesian model of SEP signals is proposed to make systemic use of multi-trial and multi-condition priors and other structural information in the signal by integrating both a cortical source propagation model and a SEP basis components model, and an Expectation Maximization (EM) algorithm is developed for single-trial SEP estimation under this model. Numerical simulations demonstrate that the developed method can provide reasonably good single-trial estimations of SEP as long as signal-to-noise ratio (SNR) of the measurements is no worse than -25 dB. The effectiveness of the proposed method is further verified by its application to real SEP measurements of a number of different subjects during spinal surgeries. It is observed that using the proposed approach the main SEP features (i.e., latencies) can be reliably estimated at single-trial basis, and thus the variation of latencies in different trials can be traced, which provides a solid support for surgical intraoperative monitoring.
A Moral-Existential Account of the Psychological Factors Fostering Intergroup Conflict

We combine ideas from terror management and moral foundations theories to analyze the role of existential and moral concerns in the creation and escalation of intergroup conflict. We argue that moral values, as important components of cultural worldviews, serve to buffer existential anxiety. Perceived threats to one’s moral values thus are capable of inducing existential anxiety and unleashing strong moral emotions, creating the psychological impetus for intergroup conflict and violence. We review evidence that threats to the five core moral intuitions posited by moral foundations theory (harm/care, fairness/reciprocity, ingroup/loyalty, authority/respect, and purity/sanctity) are associated with existential anxiety and that this contributes to intergroup strife and violence. Moral and existential concerns combine to create a vicious feedback loop that leads to self-perpetuating spirals of violence, which helps explain the intractability of many real-life conflicts.
PARK10 is a major locus for sporadic neuropathologically confirmed Parkinson disease

Objective: To minimize pathologic heterogeneity in genetic studies of Parkinson disease (PD), the Autopsy-Confirmed Parkinson Disease Genetics Consortium conducted a genome-wide association study using both patients with neuropathologically confirmed PD and controls. Methods: Four hundred eighty-four cases and 1,145 controls met neuropathologic diagnostic criteria, were genotyped, and then imputed to 3,922,209 variants for genome-wide association study analysis. Results: A small region on chromosome 1 was strongly associated with PD (rs10788972; p = 6.2 × 10−8). The association peak lies within and very close to the maximum linkage peaks of 2 prior positive linkage studies defining the PARK10 locus. We demonstrate that rs10788972 is in strong linkage disequilibrium with rs914722, the single nucleotide polymorphism defining the PARK10 haplotype previously shown to be significantly associated with age at onset in PD. The region containing the PARK10 locus was significantly reduced from 10.6 megabases to 100 kilobases and contains 4 known genes: TCEANC2, TMEM59, miR-4781, and LDLRAD1. Conclusions: We confirm the association of a PARK10 haplotype with the risk of developing idiopathic PD. Furthermore, we significantly reduce the size of the PARK10 region. None of the candidate genes in the new PARK10 region have been previously implicated in the biology of PD, suggesting new areas of potential research. This study strongly suggests that reducing pathologic heterogeneity may enhance the application of genetic association studies to PD.
Use of triaxial accelerometers to assess terrestrial mammal behaviour in the wild Journal Article

The Open University's repository of research publications and other research outputs Use of tri-axial accelerometers to assess terrestrial mammal behaviour in the wild Journal Article Copyright and Moral Rights for the articles on this site are retained by the individual authors and/or other copyright owners. For more information on Open Research Online's data policy on reuse of materials please consult the policies page. 1 Title Page 1 Use of tri-axial accelerometers to assess terrestrial mammal behaviour in the wild 2 Running title 3 AcTags used to assess terrestrial mammal behaviour 4 5 Author names and affiliations 6 Abstract 28 Tri-axial accelerometer tags provide quantitative data on body movement that can be 29 used to characterise behaviour and understand species ecology in ways that would 30 otherwise be impossible. Using tags on wild terrestrial mammals, especially smaller 31 species, in natural settings has been limited. Poor battery power also reduced the 32 amount of data collected, which limits what can be derived about animal behaviour. 33 Another challenge using wild animals, is acquiring observations of actual behaviours 34 with which to compare tag data and create an adequate training set to reliably identify 35 behavioural states. 36 Brown hares were fitted with accelerometers for five weeks to evaluate their use in 37 collecting detailed behaviour data and activity levels. Collared hares were filmed to 38 associate actual behaviours with tag data. Observed behaviours were classified using 39 Random Forests (ensemble learning method) to create a supervised model and then used 40 to classify hare behaviour from the tags. 41 Increased tag longevity allowed acquisition of large quantities of data from each 42 individual and direct observation of tagged hare's behaviour. Random Forests 43 accurately classified observed behaviours from tag data with an 11 % error rate. 44 Individual accuracy of behaviours varied with running (100 % accuracy), feeding (94.7 45 %) and vigilance (98.3 %) having the highest classification accuracy. Hares spent 46 % 46 of their time being vigilant and 25 % feeding when active. 47 The combination of our tags and Random Forests facilitated large amounts of 48 behavioural data to be collected on animals where observational studies could be 49 limited, or impossible. The same method could be used on a range of terrestrial 50 mammals to create models to investigate behaviour from tag data, to learn more about 51 their behaviour and be used to answer many …
A qualitative study of perceptions of bullying in Irish primary schools

This small-scale research examined young children’s, aged six to seven (n = 8), perceptions and understanding of bullying in Irish primary schools. It also included the views of the children’s parents (n = 8) and teachers (n = 2) on bullying. The participants’ views were obtained through semi-structured interviews which were analysed using the constant comparative method as per grounded theory approach. The results revealed the complexity of young children’s interactions in school and the difficulty that the adults around them have in accurately defining and addressing bullying behaviour. The data indicate the need for parents and teachers to listen attentively and sensitively to children’s accounts of bullying and to provide consistent advice on how to address bullying.
The influence of music tempo and musical preference on restaurant patrons' behavior

The article reports research into the effect of music tempo and musical preference on consumer behavior in a restaurant. The research investigates the extent to which these two variables influence actual and perceived time spent dining, the amount of money spent, and outcomes in terms of enjoyment of the experience and future behavioral intentions. The results show that music preference provided a better explanation of actual time spent dining than tempo, although neither variable had a significant effect on perceived time. Time spent in the restaurant was the most powerful predictor of money spent in the restaurant. Finally, the outcomes of the restaurant encounter were found to be significantly related to musical preference, but the effects of music tempo were nonsignificant. © 2002 Wiley Periodicals, Inc.
Efficient network flooding and time synchronization with Glossy

This paper presents Glossy, a novel flooding architecture for wireless sensor networks. Glossy exploits constructive interference of IEEE 802.15. 4 symbols for fast network flooding and implicit time synchronization. We derive a timing requirement to make concurrent transmissions of the same packet interfere constructively, allowing a receiver to decode the packet even in the absence of capture effects. To satisfy this requirement, our design temporally decouples flooding from other network activities. We analyze Glossy using a mixture of statistical and worst-case models, and evaluate it through experiments under controlled settings and on three wireless sensor testbeds. Our results show that Glossy floods packets within a few milliseconds and achieves an average time synchronization error below one microsecond. In most cases, a node receives the flooding packet with a probability higher than 99.99 %, while having its radio turned on for only a few milliseconds during a flood. Moreover, unlike existing flooding schemes, Glossy's performance exhibits no noticeable dependency on node density, which facilitates its application in diverse real-world settings.
Activation of Wnt/β-Catenin Pathway in Monocytes Derived from Chronic Kidney Disease Patients

Patients with chronic kidney disease (CKD) have significantly increased morbidity and mortality resulting from infections and cardiovascular diseases. Since monocytes play an essential role in host immunity, this study was directed to explore the gene expression profile in order to identify differences in activated pathways in monocytes relevant to the pathophysiology of atherosclerosis and increased susceptibility to infections. Monocytes from CKD patients (stages 4 and 5, estimated GFR <20 ml/min/1.73 m2) and healthy donors were collected from peripheral blood. Microarray gene expression profile was performed and data were interpreted by GeneSpring software and by PANTHER tool. Western blot was done to validate the pathway members. The results demonstrated that 600 and 272 genes were differentially up- and down regulated respectively in the patient group. Pathways involved in the inflammatory response were highly expressed and the Wnt/β-catenin signaling pathway was the most significant pathway expressed in the patient group. Since this pathway has been attributed to a variety of inflammatory manifestations, the current findings may contribute to dysfunctional monocytes in CKD patients. Strategies to interfere with this pathway may improve host immunity and prevent cardiovascular complications in CKD patients.