Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing the utility of AFLP for determining mutational changes in coral

Introduction Degradation of the world's coral reefs is one of the most vivid examples of the effects of global environmental damage of marine ecosystems. The major stressors responsible for coral reef decline have been attributed to coastal urban and industrial development, agricultural activity, sedimentation, overharvesting, marine pollution, disease and climate change Reef species experiencing persistent environmental disturbances (e.g., coastal development and land‐based pollution) may exhibit acute mortality leading to a seemingly rapid loss of coral‐ reef diversity and abundance, but may also display non‐acute, sub‐lethal effects. These effects are often present as increased incidence of disease, altered growth and regeneration rates, reduced reproductive effort and reduced recruitment, which can ultimately result in a cascading effect of The ecological consequences to coral and coral reefs of exposures to increasing amounts and types of pollutants are difficult or impossible to assess in short‐ term (less than five years) studies. One of the most informative endpoints to measure
To clip or not to clip? Noseclips for spirometry

The use of noseclips for open-circuit spirometry is sporadic, despite guidelines encouraging their use. The authors aimed to evaluate whether noseclips significantly affected measurements of forced vital capacity (FVC) and forced expiratory volume in one second (FEV1) in children attending a tertiary, paediatric respiratory centre. Children attending the asthma and cystic fibrosis (CF) clinics were asked to perform two sets of spirometry, one with and one without noseclips in random order, 20-min apart. Paired data was obtained on 62 patients (32 asthma, 30 CF) with a median age of 11.4 yrs (range 7.2–17.2 yrs). There were no systematic differences in FEV1 or FVC measured with and without noseclips, although seven children (11%) had clinically significant differences in FEV1 of >190 mL. There is no clear advantage to wearing noseclips when performing open-circuit spirometry. Individuals should be assessed to ascertain their optimal technique, which should then be used consistently in clinical practice. Noseclips should probably be retained for research protocols.
Investigating the Consequences of Interference between Multiple CD8+ T Cell Escape Mutations in Early HIV Infection

During early human immunodeficiency virus (HIV) infection multiple CD8+ T cell responses are elicited almost simultaneously. These responses exert strong selective pressures on different parts of HIV’s genome, and select for mutations that escape recognition and are thus beneficial to the virus. Some studies reveal that the later these escape mutations emerge, the more slowly they go to fixation. This pattern of escape rate decrease(ERD) can arise by distinct mechanisms. In particular, in large populations with high beneficial mutation rates interference among different escape strains –an effect that can emerge in evolution with asexual reproduction and results in delayed fixation times of beneficial mutations compared to sexual reproduction– could significantly impact the escape rates of mutations. In this paper, we investigated how interference between these concurrent escape mutations affects their escape rates in systems with multiple epitopes, and whether it could be a source of the ERD pattern. To address these issues, we developed a multilocus Wright-Fisher model of HIV dynamics with selection, mutation and recombination, serving as a null-model for interference. We also derived an interference-free null model assuming initial neutral evolution before immune response elicitation. We found that interference between several equally selectively advantageous mutations can generate the observed ERD pattern. We also found that the number of loci, as well as recombination rates substantially affect ERD. These effects can be explained by the underexponential decline of escape rates over time. Lastly, we found that the observed ERD pattern in HIV infected individuals is consistent with both independent, interference-free mutations as well as interference effects. Our results confirm that interference effects should be considered when analyzing HIV escape mutations. The challenge in estimating escape rates and mutation-associated selective coefficients posed by interference effects cannot simply be overcome by improved sampling frequencies or sizes. This problem is a consequence of the fundamental shortcomings of current estimation techniques under interference regimes. Hence, accounting for the stochastic nature of competition between mutations demands novel estimation methodologies based on the analysis of HIV strains, rather than mutation frequencies.
Analysing Object−Capability Security

Much of the power and utility of modern computing arises in the different forms of cooperation that it enables. However, today this power comes with great risk because those engaged in cooperation are left vulnerable to one another. The Object-Capability (OCap) Model is a promising remedy, because it enables the creation of security-enforcing abstractions, or patterns, that can be composed with other code to buildions, or patterns, that can be composed with other code to build systems that enable cooperation whilst minimising vulnerability. Unfortunately, little work has been done to adequately formally analyse standard OCap patterns. In particular, their analysis requires frameworks that are capable of reasoning about their, often novel, security properties whilst taking into account the variation that exists across different OCap systems, particularly in concurrency semantics. We use the process algebra CSP to examine the implementations of a number of OCap patterns and their security properties in various kinds of OCap system. CSP allows us to not only reason about security properties beyond the reach of previous approaches, such as revocation, but also to consider different models of concurrency that various kinds of OCap system exhibit. We find that while some implementations function correctly when moved from one kind of system to another, others exhibit subtle differences or fail to preserve their security properties altogether.
Tone of voice in emotional expression and its implications for the affective character of musical mode

•Correspondence: Daniel Bowling, Department of Cognitive Biology, University of Vienna. tel: +431427776101; email: dan.bowling@univie.ac. at • Received: 02 October 2013; Revised: 25 April 2014; Accepted: 19 May 2014 • Available online: 22 June 2014 • doi: 10.4407/jims.2014. 06.002 ARTICLE IN PRESS Please cite this article as: D. Bowling, B. Gingras, S. Han, J. Sundararajan, and E. Opitz, Tone of voice in emotional expression and its implications for the affective character of musical mode, Journal of Interdisciplinary Music Studies (2013), doi: 10.4407/jims.2014. 06.002 Tone of voice in emotional expression and its implications for the affective character of musical mode
A rapid voltage detection method for low voltage ride through under distorted voltage conditions

This paper deals with a novel voltage detection method for low voltage ride through under distorted voltage conditions. According to the new Grid Codes, the photovoltaic (PV) system should keep connected with the grid and inject the acquired reactive power as soon as possible when the grid voltage sags. So the voltage detection is important to the PV system. The principle of voltage detection is analyzed in detail. Then, by comparing with T/4 delay detection method and single vector detection method, the double vectors detection method is designed to suppress the harmonic voltage. Finally, the simulation results are carried out to validate the proposed voltage detection method.
Detecting Paper Fibre Cross Sections in Microtomy Images

The goal of this work is the fully-automated detection of cellulose fibre cross sections in microtomy images. A lack of significant appearance information makes edges the only reliable cue for detection. We present a novel and highly discriminative edge fragment descriptor that represents angular relations between fragment points. We train a Random Forest with a plurality of these descriptors including their respective center votes. In such a way, the Random Forest exploits the knowledge about the object centroid for detection using a generalized Hough voting scheme. In the experiments we found that our method is able to robustly detect fibre cross sections in microtomy images and can therefore serve as initialization for successive fibre segmentation or tracking algorithms.
Experience and Behavior: How Negative Feedback in New Versus Experienced Domains Affects Firm Action and Subsequent Performance

How organizations respond to failure (negative feedback) has important implications for subsequent organizational performance. This study focuses on theoretical and empirical distinctions between the different potential organizational reactions to failure (in this case around new product development) and how those feedback-driven choices aggregate to affect firm performance. To understand when and why negative feedback is organizationally beneficial, we focus on how possession of domain-specific experience affects the way in which firms interpret and respond to negative feedback, offering both organization- and mechanism-level theories. In particular, we distinguish between conditions that should lead to different behavioral responses to negative feedback: retreat, local search, or distant search. We find support for our theory using data on all U.S. mutual fund companies from 1962 to 2002 and testing both aggregated and mechanism-level theories. Our results show that negative feedback on new funds launch.
UTILIZING AIRBORNE LASER INTENSITY FOR TREE SPECIES CLASSIFICATION

High-resolution datasets from Airborne Laser Scanning (ALS) provide information to extract the outline of single tree crowns. Laser echoes with spatial coordinates inside these single-tree crowns give the ability of measuring biophysical properties and to classify species of these single-trees. Species classification by ALS-data is based on differences in crown shape, crown density, reflectivity and distribution of foliage and branches between tree species. All of these parameters may be express ed by spatial coordinates of the point cloud or by the intensity of the backscattered signal measured by ALS. In this study we investigate mean intensity and standard deviation of intensity computed for single trees by explorative data analysis and linear discriminant analysis. We explore differences in spruce, birch, and aspen trees for different echo categories from a multiple return ALS system. We found that intensity could assist species discrimination. The overall classification accuracies obtained were from 68 to 74 %, depending on number of variables considered. In spite of the heterogeneous structure of the forest studied, the classification accuracy was fairly high. Intensity metrics computed from different echo categories influence overall accuracies by 3 to 4 %, depending on the intensity metric used in the classification. Both species reflectivity and structural characteristics within the tree crown will influence intensity recorded by ALS.
The roles of input and output modalities on user interaction in mobile augmented reality application

Current interaction that make use of touchscreen displays have now become the de-facto standard especially in smartphones. Very few works have been done on interaction modalities in mobile AR application. This paper presents the results of a study that investigates the effect of different combinations of input and output modalities on user interaction experience. Participants were given a mobile AR application and they needed to perform a certain task in specific time. Results showed interaction modalities mostly preferred by the participants is GAV_HS and certain combinations of interaction modalities that could improve user interaction experience in terms of ease of use.
Daytona : A User-Level TCP Stack

This paper presents Daytona, a user-level TCP stack for Linux. A user-level TCP stack can be an invaluable tool for TCP performance research, network performance diagnosis, rapid prototyping and testing of new optimizations and enhancements to the TCP protocol, and as a tool for creating adaptive application-level overlays. We present the design and implementation of Daytona, and also describe several projects that are using Daytona in a rich variety of contexts, indicating its suitability as an open-source project.
Wafer-scale W-band power amplifiers using on-chip antennas

This paper presents, for the first time, a W-band SiGe power amplifier designed and fabricated together with a high-efficiency on-chip microstrip antenna. The antenna/amplifier results in an effective radiated power (ERP=PtGt) ≫ 10 dBm from 88 to 98 GHz, with a peak of 14.6 dBm at 92 GHz. The chip consumes 120 mA from a 1.7 V supply. The antenna/amplifier approach can be extended to a large number of elements (8×8) and allows for efficient wafer-scale power combining and phased-array scanning.
Botnet Detection Based on Degree Distributions of Node Using Data Mining Scheme

Botnet is most widespread and occurs commonly in today's cyber attacks and they become one of the most serious threats on the Internet. Most of the existing Botnet detection approaches concentrate only on particular Botnet command and control (C&C) protocols and structures, and can become ineffective as Botnets change their structure and C&C techniques. In this paper, we proposed a new general detection strategy. This proposed strategy was based on degree distributions of node and anomaly net flows, and combined data mining technology. In this scheme, we first constructed accurate traffic profile based on packet behavioral mode, and then introduced dialog flow to draw traffic profile of node. Finally we set up degree distributions of node and group and applied the degree distributions of node as input of data mining, which were then classified and distinguished to obtain reliable results with acceptable accuracy. The advantages of our proposed detection method is that there is no need for prior knowledge of Botnets such as Botnet signature and the accuracy of the experiment results is as much as 99%. The FP rate and the FN rate can be controlled within 3%, the best is almost 0.
ON THE NUMBER OF LIMIT CYCLES OF SOME LIÉNARD SYSTEMS

In this paper, we are concerned with the problem of limit cycle bifurcations of some polynomial Liénard systems whose unperturbed system is a system of degree four having a double homoclinic loop and a homoclinic loop. By using the expansion of Melnikov functions and homoclinic bifurcation methods we investigate the number of limit cycles and present some new results.
Phylogeny and Characterization of Three nifH-Homologous Genes from Paenibacillus azotofixans

ABSTRACT In this paper, we report the cloning and characterization of three Paenibacillus azotofixans DNA regions containing genes involved in nitrogen fixation. Sequencing analysis revealed the presence of nifB1H1D1K1 gene organization in the 4,607-bp SacI DNA fragment. This is the first report of linkage of a nifB open reading frame upstream of the structural nif genes. The second (nifB2H2) and third (nifH3) nif homologues are confined within the 6,350-bp HindIII and 2,840-bp EcoRI DNA fragments, respectively. Phylogenetic analysis demonstrated that NifH1 and NifH2 form a monophyletic group among cyanobacterial NifH proteins. NifH3, on the other hand, clusters among NifH proteins of the highly divergent methanogenic archaea.
The impact of frailty and delirium on mortality in older inpatients.

BACKGROUND delirium and frailty are common among hospitalised older people but delirium is often missed and frailty considered difficult to measure in clinical practice. OBJECTIVE to explore the relationship between delirium and frailty in older inpatients and determine their impact on survival. DESIGN AND SETTING the prospective cohort study of 273 patients aged ≥75 years. MEASURES patients were screened for delirium at presentation and on alternate days throughout their hospital stay. Frailty status was measured by an index of accumulated deficits (FI), giving a potential score from 0 (no deficits) to 1.0 (all 33 deficits), with 0.25 used as the cut-off between 'fit' and 'frail'. RESULTS delirium was detected in 102 patients (mean FI: 0.33) and excluded in 171 (mean FI: 0.18) (P < 0.005); 111 patients were frail. Among patients with delirium, the median survival in fit patients was 359 days (95% CI: 118-600) compared with 88 days for those who were frail (95% CI: 5-171; P < 0.05). CONCLUSION delirium was associated with higher levels of frailty: the identification of frail patients may help to target those at a greatest risk of delirium. Survival following delirium was poor with the combination of frailty and delirium conferring a particularly bleak prognosis.
A study examining women's sexual function in twelve months postpartum

The postpartum period has physical, psychological, and social effects on womenÂ’s health, two of which include sexual function and dysfunction. The aim of this study was to identify womenÂ’s sexual function in twelve months postpartum. This descriptive study was conducted between January and May 2018 at the Well-Child Outpatient Service at Giresun UniversityÂ’s WomenÂ’s Obstetrics and Gynaecology Training and Research Hospital. The sample of the study consisted of all women who applied to the clinic and who met the inclusion criteria. The research population consisted of 236 women with 0 to 12 month-old children. The Â‘Identification Features Specification FormÂ’ and Â‘Turkish Version of the Sexual Distress Scale-Revised (Tr-FSDS-R)Â’ were used in order to collect data. The Mann Whitney U and Kruskal-Wallis tests, as well as Spearman correlation analysis were used in the analyses because the data did not show any normal distribution features. The age average of the participants was 28.68 ± 5.43. The mean Tr-FSDS-R score was determined as 7.50 ± 9.45 (min0- max52). SD was found in 24.6% (n:59) of women when the cut point of the scale (>11.5) was taken into consideration. A positive weak correlation was seen between the mean Tr-FSDS-R score of women and the average of marital year points. The mean Tr-FSDS-R score significantly differed depending on the time of sexual intercourse (z: -2.61, p:0.009), the use of contraception (z:-2.20, p:0.028), and current sexual activeness (x2:64.798, p:0.000) (p
Examining robotic systems with shape-adjustable manipulators under dynamic environments: From simulation to verification

In this paper, we present our preliminary report in applying formal verification to the design process of robotic systems under dynamic environments; the goal is to complement existing testing or simulation techniques by experimenting an adaptable framework, where verification models with tamable complexity are generated from the simulation model. Our targets are robotic systems with shape-adjustable manipulators (e.g., robot arms), which in essence bring different challenges compared to existing research. By investigating the problem structure, we propose ingredients for successful verification of such systems, conduct experiments, and outline future studies.
Modeling and Simulation of Gun Barrel's Lateral Vibration

Gun's vibration during its shooting makes projectile impact bore much more fiercely, which cause projectile's initial disturbance and affect gun's firing accuracy. Among gun's multiform vibrations, lateral vibration has the maximal influence to firing accuracy. The paper builds simulation model of gun barrel's lateral vibration based on finite element method and ascertain the equations of gun barrel's lateral vibration under multi-load. Using some type gun as the example of simulation test, displacement response curves of gun barrel's lateral vibration are obtained. It can be found that simulation results are accordant with measured response curve of muzzle's displacement. Therefore, the simulation results can be used for trajectory's correction of this type gun, while those results can help us estimate initial disturbance's influence to gun's firing accuracy.
Using Object Oriented Design Patterns to Develop an Interactive Command System for a CAD Software with Undo and Redo Support

Although little time has passed since its introduction, object oriented design patterns have had a worldwide interest. This paper presents the use of design patterns to develop a flexible and undoable interactive command system for a CAD software, explaining in detail the design issues and specific cases where the need for tuning and modification of patterns has been observed.
Aberrant TRPV1 Expression in Heat Hyperalgesia Associated with Trigeminal Neuropathic Pain

Trigeminal neuropathic pain is a facial pain syndrome associated with trigeminal nerve injury. However, the mechanism of trigeminal neuropathic pain is poorly understood. This study aimed to determine the role of transient receptor potential vanilloid 1 (TRPV1) in heat hyperalgesia in a trigeminal neuropathic pain model. We evaluated nociceptive responses to mechanical and heat stimuli using a partial infraorbital nerve ligation (pIONL) model. Withdrawal responses to mechanical and heat stimuli to vibrissal pads (VP) were assessed using von Frey filaments and a thermal stimulator equipped with a heat probe, respectively. Changes in withdrawal responses were measured after subcutaneous injection of the TRP channel antagonist capsazepine. In addition, the expression of TRPV1 in the trigeminal ganglia was examined. Mechanical allodynia and heat hyperalgesia were observed in VP by pIONL. Capsazepine suppressed heat hyperalgesia but not mechanical allodynia. The number of TRPV1-positive neurons in the trigeminal ganglia was significantly increased in the large-diameter-cell group. These results suggest that TRPV1 plays an important role in the heat hyperalgesia observed in the pIONL model.
An analysis of psychological endurance and personality traits of individuals doing sports and not doing sports by various variables

Purpose : The aim was to examine the psychological endurance and personality levels of the students studying at Faculty of Education and students studying at Faculty of Sports Sciences. Material and Method: Target population of the study was composed of students studying at Sakarya University in the academic year 2015-2016. The sample of the research consisted of a total of 365 (n = 197 males, n = 168 females) participants. They were educated at Faculty of Education (n=166) and Faculty of Sports Sciences (n=199) at Sakarya University. *Personal Information Form* by the researcher, Turkish adapted version of *Personality Inventory* were implemented. Also, Turkish adapted version of *Psychological Endurance Scale for Adults* were implemented. T-test was used for paired comparisons. Pearson Product-Moment Correlation (r) Coefficient was employed to determine the relationship between psychological endurance and five factor personality traits of the participants. Result : There was a significant difference between sporting situations, sporting year, sports branches of students in terms of total scores of psychological endurances. There was also a significant difference between gender, sporting situation, sporting year and socio-economic situations in terms of the personality traits of the students. Conclusion : The results show that the psychological endurance levels of those who do not play sports are lower than those who do any of the individual sport branches or team sports. In short, it can be said that doing sports affects psychological endurance positively.