Miracle-dz/UniFAR-FTUs huggingface dataset:
The Relationship between Host Lifespan and Pathogen Reservoir Potential: An Analysis in the System Arabidopsis thaliana-Cucumber mosaic virus

Identification of the determinants of pathogen reservoir potential is central to understand disease emergence. It has been proposed that host lifespan is one such determinant: short-lived hosts will invest less in costly defenses against pathogens, so that they will be more susceptible to infection, more competent as sources of infection and/or will sustain larger vector populations, thus being effective reservoirs for the infection of long-lived hosts. This hypothesis is sustained by analyses of different hosts of multihost pathogens, but not of different genotypes of the same host species. Here we examined this hypothesis by comparing two genotypes of the plant Arabidopsis thaliana that differ largely both in life-span and in tolerance to its natural pathogen Cucumber mosaic virus (CMV). Experiments with the aphid vector Myzus persicae showed that both genotypes were similarly competent as sources for virus transmission, but the short-lived genotype was more susceptible to infection and was able to sustain larger vector populations. To explore how differences in defense against CMV and its vector relate to reservoir potential, we developed a model that was run for a set of experimentally-determined parameters, and for a realistic range of host plant and vector population densities. Model simulations showed that the less efficient defenses of the short-lived genotype resulted in higher reservoir potential, which in heterogeneous host populations may be balanced by the longer infectious period of the long-lived genotype. This balance was modulated by the demography of both host and vector populations, and by the genetic composition of the host population. Thus, within-species genetic diversity for lifespan and defenses against pathogens will result in polymorphisms for pathogen reservoir potential, which will condition within-population infection dynamics. These results are relevant for a better understanding of host-pathogen co-evolution, and of the dynamics of pathogen emergence.
Plasma tau in Alzheimer disease

Objective: To test whether plasma tau is altered in Alzheimer disease (AD) and whether it is related to changes in cognition, CSF biomarkers of AD pathology (including β-amyloid [Aβ] and tau), brain atrophy, and brain metabolism. Methods: This was a study of plasma tau in prospectively followed patients with AD (n = 179), patients with mild cognitive impairment (n = 195), and cognitive healthy controls (n = 189) from the Alzheimer's Disease Neuroimaging Initiative (ADNI) and cross-sectionally studied patients with AD (n = 61), mild cognitive impairment (n = 212), and subjective cognitive decline (n = 174) and controls (n = 274) from the Biomarkers for Identifying Neurodegenerative Disorders Early and Reliably (BioFINDER) study at Lund University, Sweden. A total of 1284 participants were studied. Associations were tested between plasma tau and diagnosis, CSF biomarkers, MRI measures, 18fluorodeoxyglucose-PET, and cognition. Results: Higher plasma tau was associated with AD dementia, higher CSF tau, and lower CSF Aβ42, but the correlations were weak and differed between ADNI and BioFINDER. Longitudinal analysis in ADNI showed significant associations between plasma tau and worse cognition, more atrophy, and more hypometabolism during follow-up. Conclusions: Plasma tau partly reflects AD pathology, but the overlap between normal aging and AD is large, especially in patients without dementia. Despite group-level differences, these results do not support plasma tau as an AD biomarker in individual people. Future studies may test longitudinal plasma tau measurements in AD.
TouchRing: subtle and always-available input using a multi-touch ring

We propose a finger-worn touch device TouchRing to provide subtle and multi-touch input. TouchRing leverages printed electrodes and the capacitive sensing technique to detect touch input. It allows users to perform multi-touch gestures in one hand to increase input modality. TouchRing worn on the index finger allows multi-touch using the thumb and middle finger. Ten multi-touch gestures are designed in this paper. We also propose touch detection and gesture recognition approaches in TouchRing. Gesture Recognition accuracy is evaluated in the user study. Applications for TouchRing are also proposed to make controlling smart glasses more convenient.
On the dynamic management of chemica l engineering knowledge using an ontology-based approach

The paper presents an ontology-based approach to monitor and assess changes and trends of technology intensive domains. The research, produced in collaboration with a variety of chemical engineering users of knowledge, promotes ontologies and semantically enriched models to enable knowledge sharing, classification, monitoring and reuse. Ontologies are deployed to search, retrieve and analyze technical structured and unstructured context from heterogeneous sources of information. The environment integrates models, language processing tools, knowledge engineering tools (crawlers, tokenizers), and agents. Besides the search and the management of information, the approach can be used to validate the suitability of ontologies and their relevance to the particular application, suggesting modifications and alterations when appropriate.
Managing wicked policy problems: A case for deliberative practices

Demanding policy issues require responses that are both effective and legitimate. Wicked problems are examples of such demanding issues. In contrast to tame policy issues, wicked problems can be distinguished when levels of uncertainty, value divergence, and complexity reach high levels. Examples of wicked problems include issues such as climate change, illicit drug use, and indigenous disadvantage. This thesis puts forward the case for using deliberative democratic practices (in conjunction with typical policy development methods) when working with wicked problems. Deliberative democracy aims to promote greater legitimacy in decisions as a result of public consultation. Deliberative democracy can create better outcomes as a result of rigorous engagement and deliberation over a topic, and more inclusion in the political process for those groups who have typically found themselves alienated from politics. Such aims and principles lend themselves to good policy development. Typical policy development methods may not be sufficiently flexible to devise effective and long lasting solutions to wicked problems. By using deliberative practices in conjunction with typical policy development methods, the policy process becomes more flexible and adaptive to work with the ever-changing nature of a wicked problem. The principles and aims of deliberative democracy can make wicked problems appear more manageable by creating legitimacy in decisions as a result of public consultation, bridge the gap between different parties’ value divergence, and possibly even change the mind of participants in the deliberation by invoking thought and reason.
Explaining CDS Prices Before and After the Lehman Default with a Simple Structural Model

We examine what determines CDS prices over 2005-2012. To do this, we calibrate Merton's model in a novel way that allows for deviations from lognormality. The model works well in cross-section and time-series, both within and out-of sample. It confirms that systematic equity volatility is the major determinant of CDS prices. Before the Lehman default, all firms have CDS prices that are close to those set by the model (with small variations due to illiquidity and earnings-uncertainty). After the default, some firms continue to have CDS prices at model-predicted levels, but others are now more-strongly influenced by idiosyncratic factors and have much higher prices.
Change of the Expression of Human Telomerase Reverse Transcriptase mRNA and Human Telomerase RNA after Cisplatin and 5-Fluorouracil Exposure in Head and Neck Squamous Cell Carcinoma Cell Lines

Telomerase activity appears to be associated with cell immortalization and malignant progression. Understanding how telomerase activity is regulated in vivo is important not only for understanding the molecular biology of telomerase but also for the potential clinical application of anticancer drugs. This study evaluated telomerase activity and quantified the expression of human telomerase reverse transcriptase (hTERT) mRNA and human telomerase RNA (hTR) using a real-time reverse transcriptase-polymerase chain reaction (RT-PCR) method before and after the exposure of cisplatin and 5-fluorouracil (5-FU) in two head and neck squamous cell carcinoma (HNSCC) cell lines. Two human HNSCC cell lines (PNUH-12 and SNU-899) were studied. Cell cytotoxicity, the change of telomerase activity, and hTERT mRNA and hTR expression by 5-FU and cisplatin exposure were assessed by MTT assay, TRAP assay, and real-time RT-PCR, respectively. In two cell lines, after cisplatin exposure, the telomerase activity and hTERT mRNA expression decreased, but hTR expression increased according to the concentration of drug. However, in both cell lines, the telomerase activity and hTR did not show any significant change after 5-FU treatment, but the expression of hTERT mRNA decreased. These results suggest that there may be other important regulating mechanism except hTERT mRNA as the regulation factor of telomerase activity in HNSCC cell lines.
Characterization of the Promoter Region of an Arabidopsis Gene for 9-cis-Epoxycarotenoid Dioxygenase Involved in Dehydration-Inducible Transcription

Plants respond to dehydration stress and tolerate water-deficit status through complex physiological and cellular processes. Many genes are induced by water deficit. Abscisic acid (ABA) plays important roles in tolerance to dehydration stress by inducing many stress genes. ABA is synthesized de novo in response to dehydration. Most of the genes involved in ABA biosynthesis have been identified, and they are expressed mainly in leaf vascular tissues. Of the products of such genes, 9-cis-epoxycarotenoid dioxygenase (NCED) is a key enzyme in ABA biosynthesis. One of the five NCED genes in Arabidopsis, AtNCED3, is significantly induced by dehydration. To understand the regulatory mechanism of the early stages of the dehydration stress response, it is important to analyse the transcriptional regulatory systems of AtNCED3. In the present study, we found that an overlapping G-box recognition sequence (5′-CACGTG-3′) at −2248 bp from the transcriptional start site of AtNCED3 is an important cis-acting element in the induction of the dehydration response. We discuss the possible transcriptional regulatory system of dehydration-responsive AtNCED3 expression, and how this may control the level of ABA under water-deficit conditions.
"Toru": a game that reverses the wisdom of age using mosquito sound

We propose "Toru," a game that reverses the game skills developed as a person ages using ultra-high-frequency (mosquito) sound. The game has its origin in the computer game Simon (1978), which we interpret from visual to auditory form using the mosquito sound (i.e., ultra-high-frequency sound) for its difficulty settings. Because of individual variations in hearing, the Toru game transforms its character from Mimicry (simulation) to Alea (chance), and provides an opportunity to reverse the wisdom of age (i.e., game skills advantage) developed by adults over the years.
Evaluation of the COPD Assessment Test and GOLD patient types: a cross-sectional analysis

Background The COPD Assessment Test (CAT) has been recently developed to quantify COPD impact in routine practice. However, no relationship with other measures in the Global Initiative for Obstructive Lung Disease (GOLD) strategy has been evaluated. The present study aimed to evaluate the relationship of the CAT with other GOLD multidimensional axes, patient types, and the number of comorbidities. Methods This was a cross-sectional analysis of the Clinical presentation, diagnosis, and course of chronic obstructive pulmonary disease (On-Sint) study. The CAT score was administered to all participants at the inclusion visit. A GOLD 2011 strategy consisting of modified Medical Research Council scale (MRC) scores was devised to study the relationship between the CAT, and GOLD 2011 axes and patient types. The relationship with comorbidities was assessed using the Charlson comorbidity index, grouped as zero, one to two, and three or more. Results The CAT questionnaire was completed by 1,212 patients with COPD. The CAT maintained a relationship with all the three axes, with a ceiling effect for dyspnea and no distinction between mild and moderate functional impairment. The CAT score increased across GOLD 2011 patient types A–D, with similar scores for types B and C. Within each GOLD 2011 patient type, there was a considerably wide distribution of CAT values. Conclusion Our study indicates a correlation between CAT and the GOLD 2011 classification axes as well as the number of comorbidities. The CAT score can help clinicians, as a complementary tool to evaluate patients with COPD within the different GOLD patient types.
Cerchiamo : a collaborative exploratory search tool

We describe Cerchiamo, a collaborative exploratory search system that allows teams of searchers to explore document collections synchronously. Working with Cerchiamo, team members use independent interfaces to run queries, browse results, and make relevance judgments. The system mediates the team members’ search activity by passing and reordering search results and suggested query terms based on the teams’ actions. The combination of synchronous influence with independent interaction allows team members to be more effective and efficient in performing search tasks. Author
Frequency-aware reconstruction of forwarding tables in name-based routing

In the future Internet, routing on contents or resources is anticipated as the post-Internet Protocol (IP) routing. The final goal of our research is to realize routing based on the name of a resource in the network layer. Towards this purpose, we use the 'name' for routing, particularly the 'fully qualified domain name (FQDN)' to show the feasibility of name-based routing and to generalize it to resource-based routing. When writing the routing information of hierarchically structured FQDN into a hierarchical virtual topology, mismatch between the virtual topology and physical topology can occur if the virtual topology lacks the physical topology's information. In addition, routing tables should be reorganized to reflect the different access frequency among the FQDNs. In this paper, we propose an algorithm for reconstructing routing tables to better map a virtual topology to the physical topology. As a result, we show that using the access frequency and physical topology's information increases the efficiency for searching FQDN.
A general Hua-type matrix equality and its applications

Let Mm×n be the set of all complex matrices of size m × n with Mn = Mn×n. For A ∈ Mm×n, we denote the conjugate transpose of A by A ∗ and call A strictly contractive if I − A∗A is positive definite, where I is the identity matrix of appropriate size. If A ∈ Mn is Hermitian positive (semi)definite, then we write A(≥) > 0. Also, we identify A > (≥)B with A−B > (≥)0, called the Löwner partial order. The starting point of this paper is the following Hua matrix equality, which arises in studying the theory of functions of several variables.
The Detectability of Orphan Afterglows

The realization that gamma-ray bursts (GRBs) release a constant amount of energy implies that post-jet-break afterglow evolution is largely universal. For a given redshift, all afterglows should be detected up to a fixed observer angle. We estimate the observed magnitude and the implied detectability of orphan afterglows. We show that for reasonable limiting magnitudes (mlim = 25), orphan afterglows will typically be detected from small (~10°) angles away from the GRB jet axis. A detected orphan afterglow generally corresponds to a "near miss" of a GRB whose jet is pointing just slightly away from us. With our most optimistic parameters, we expect that 15 orphan afterglows will be recorded in the Sloan Digital Sky Survey, and 35 transients will be recorded in a dedicated 2 m class telescope operating full time for a year in an orphan afterglow search. The rate is smaller by a factor of 15 for our "canonical" parameters. We show that for a given facility, an optimal survey should be shallower, covering a larger area, rather than deeper. The limiting magnitude should not be, however, lower than ~23, as in this case, more transients from on-axis GRBs will be discovered than orphan afterglows. About 15% of the transients could be discovered with a second exposure of the same area provided that it follows after 3, 4, and 8 days for mlim = 23, 25, and 27, respectively.
MIMO / Smart Antenna Development Platform

Smart Antennas (SA) and Multiple Input Multiple Output (MIMO) systems are considered as one of the key technologies for the third generation mobile communication systems and are now even being included in the UMTS standard [1]. With those technologies it is possible to improve the signal-to-noise ratio at the receiver and increase capacity in mobile radio systems. To test and evaluate new algorithms for those systems a MIMO/SA development platform has been developed. It comprises a MIMO real-time channel simulator and a receiver unit. The real-time channel simulator uses a geometry based stochastic channel model (GSCM) proposed by COST 259 [2] to simulate MIMO channels accurately and in real-time. The MIMO/SA receiver allows rapid prototyping and real-time evaluation of MIMO/SA algorithms. The hardware of the development platform is made up of an expandable architecture of up to ten parallel processing boards. The DSP-boards combine the versatility of a DSP with the raw power of a FPGA and offer a performance of up to 12000 MIPS. Together with an analog I/O board for RF and IF signals, the DSP-board is ideally suited for software defined radios (SDR).
Identification of Genia Events using Multiple Classifiers

We describe our system to extract genia events that was developed for the BioNLP 2013 Shared Task. Our system uses a supervised information extraction platform based on Support Vector Machines (SVM) and separates the process of event classification into multiple stages. For each event type the SVM parameters are adjusted and feature selection carried out. We find that this optimisation improves the performance of our approach. Overall our system achieved the highest precision score of all systems and was ranked 6th of 10 participating systems on F-measure (strict matching).
Use of Electrocardiography to Predict Future Development of Hypertension in the General Population

AbstractCardiac muscle responds to increased afterload by developing hypertrophy. During the early stages of hypertension, the heart can be transiently, but frequently, exposed to increased afterload. This study was designed to test the hypothesis that left ventricular hypertrophy (LVH) assessed by electrocardiography (ECG) can be used to predict future development of hypertension.Sokolow–Lyon voltage and Cornell product were calculated using ECG in 5770 normotensive participants who visited our hospital for a physical checkup (age 52.7 ± 11.3 years). LVH was defined as a Sokolow–Lyon voltage of >3.8 mV or a Cornell product of >2440 mm × ms. After baseline examination, participants were followed up with the endpoint being the development of hypertension.During the median follow-up period of 1089 days (15,789 person-years), hypertension developed in 1029 participants (65.2/1000 person-years). A Kaplan–Meier analysis demonstrated a significantly higher incidence of hypertension in participants with LVH than in those without LVH as assessed by Sokolow–Lyon voltage or Cornell product (P < 0.0001 for both). The hazard ratios for incident hypertension in participants with LVH defined by Sokolow–Lyon voltage and Cornell product were 1.49 (95% confidence interval [CI] 1.16–1.90, P < 0.01) and 1.34 (95% CI 1.09–1.65, P < 0.01), respectively, after adjustment for possible risk factors. Furthermore, in multivariable Cox hazard analysis, where Sokolow–Lyon voltage and Cornell product were taken as continuous variables, both indices were independent predictors of future hypertension (P < 0.0001). Both Sokolow–Lyon voltage and Cornell product are novel predictors of future development of hypertension in the general population.
Altered colonic function and microbiota profile in a mouse model of chronic depression

Depression often coexists with the irritable bowel syndrome (IBS) which is characterized by alterations in gut function. There is emerging evidence that the microbial composition (microbiota) of the gut is altered in IBS, but the basis for this is poorly understood. The aim of this study was to determine whether the induction of chronic depression results in changes in the colonic function and in its microbial community, and to explore underlying mechanisms.
Targeted Capture Sequencing in Whitebark Pine Reveals Range-Wide Demographic and Adaptive Patterns Despite Challenges of a Large, Repetitive Genome

Whitebark pine (Pinus albicaulis) inhabits an expansive range in western North America, and it is a keystone species of subalpine environments. Whitebark is susceptible to multiple threats – climate change, white pine blister rust, mountain pine beetle, and fire exclusion – and it is suffering significant mortality range-wide, prompting the tree to be listed as ‘globally endangered’ by the International Union for Conservation of Nature and ‘endangered’ by the Canadian government. Conservation collections (in situ and ex situ) are being initiated to preserve the genetic legacy of the species. Reliable, transferrable, and highly variable genetic markers are essential for quantifying the genetic profiles of seed collections relative to natural stands, and ensuring the completeness of conservation collections. We evaluated the use of hybridization-based target capture to enrich specific genomic regions from the 27 GB genome of whitebark pine, and to evaluate genetic variation across loci, trees, and geography. Probes were designed to capture 7,849 distinct genes, and screening was performed on 48 trees. Despite the inclusion of repetitive elements in the probe pool, the resulting dataset provided information on 4,452 genes and 32% of targeted positions (528,873 bp), and we were able to identify 12,390 segregating sites from 47 trees. Variations reveal strong geographic trends in heterozygosity and allelic richness, with trees from the southern Cascade and Sierra Range showing the greatest distinctiveness and differentiation. Our results show that even under non-optimal conditions (low enrichment efficiency; inclusion of repetitive elements in baits), targeted enrichment produces high quality, codominant genotypes from large genomes. The resulting data can be readily integrated into management and gene conservation activities for whitebark pine, and have the potential to be applied to other members of 5-needle pine group (Pinus subsect. Quinquefolia) due to their limited genetic divergence.
Gender Wage Differentials in Greece

The paper studies the existence of wage differentials between male and female employees in Greece employing quantile regession analysis techniques and applying a variant of the selection-adjusted Oaxaca and Ransom (1994) decomposition method to explain the components of the wage differentials. The results suggest that, in Greece, differences in wages between men and women can be identified. Decomposing the wage gap between genders, the results show that the difference in wages is attributed mainly to the unexplained part and to a lesser extent to the employee’s characteristics. In all deciles of the wage distribution, wage differentials between genders are not explained by differences in the productive characteristics of the employed but rather they constitute the unexplained part of the wage differential.