Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Demographic Expansions From Pairwise Comparisons of Linked Microsatellite Haplotypes

This work extends the methods of demographic inference based on the distribution of pairwise genetic differences between individuals (mismatch distribution) to the case of linked microsatellite data. Population genetics theory describes the distribution of mutations among a sample of genes under different demographic scenarios. However, the actual number of mutations can rarely be deduced from DNA polymorphisms. The inclusion of mutation models in theoretical predictions can improve the performance of statistical methods. We have developed a maximum-pseudolikelihood estimator for the parameters that characterize a demographic expansion for a series of linked loci evolving under a stepwise mutation model. Those loci would correspond to DNA polymorphisms of linked microsatellites (such as those found on the Y chromosome or the chloroplast genome). The proposed method was evaluated with simulated data sets and with a data set of chloroplast microsatellites that showed signal for demographic expansion in a previous study. The results show that inclusion of a mutational model in the analysis improves the estimates of the age of expansion in the case of older expansions.
Presence and emotions in virtual environments: the influence of stereoscopy.

ABSTRACT This study investigates how stereoscopy (the illusion of depth and 3D imaging) affects the sense of presence and the intensity of the positive mood that users feel in virtual environments (VEs). A between-group design was used, and 40 volunteers were randomly assigned to one of two experimental conditions (stereoscopy vs. no stereoscopy) and to one of two emotional VEs (relaxation or joy). The participants' emotions were assessed before and after the VR experience. Presence was measured with two postexperiment questionnaires (ITC-SOPI and SUS). Results show that there were no differences between stereoscopic and monoscopic presentations in VEs (neither subjective sense of presence nor emotional reactions). Practical and theoretical implications of these findings are discussed herein.
Flow for Exercise Adherence: Testing an Intrinsic Model of Health Behavior

Background: Health behavior theory generally does not include intrinsic motivation as a determinate of health practices. Purpose: The purpose of this study was to test the flow theory of exercise adherence. Flow theory posits that exercise can be intrinsically rewarding if the experiences of self/time transcendence and control/mastery are achieved during performance. It was hypothesized that higher levels of flow during exercise would be associated with exercise adherence rates. Methods: Expert panel review, test–retest, and factor analysis were used to establish the reliability and validity of a Flow for Exercise Adherence Scale. Free-living exercise among 445 young adults (age range 19–29) was tracked for 4 weeks to test the scale. Results: Flow scale scores differentiated between stages of change for exercise as theorized. Flow scale scores were significantly correlated with days of vigorous physical activity for subjects in the maintenance (r = 0.52) and action (r = 0.31) stages. Discussion: The results of this study are consistent with flow theory. Intrinsic motivation can be an important factor in free-living exercise adherence. Translation to Health Education Practice: Health educators may enhance program effectiveness by using flow theory to focus on intrinsic motivations for the target health behavior.
The Discomfort of Strangers: Racism, Incivility and Ontological Security in a Relaxed and Comfortable Nation

This paper explores the increasing experience of discomfort amongst migrant Australians and their children, drawing on two sets of empirical data—one about a sense of home amongst migrants and the other about incidents of racism towards Arabs and Muslims since 2001. The idea of comfort captures what Giddens calls ontological security, or the trust we have in our surroundings, both human and non-human. This sense of security, built on mutual recognition, is fundamental to our capacity for social agency. Migrant home-building constantly negotiates the displacement thrown up by the act of migration as migrants attempt to settle in a new country. Experiences of racism, especially since 2001, however, undermine the ability of migrants to feel ‘at home’, and hence their capacity to exist as citizens.
Prepositions retain aspects of spatial meaning in abstract contexts

Prepositions such as in and on convey not only spatial relationships between objects, but also abstract relationships, such as ‘Mary is in love’ and ‘Tim’s on a roll’. Although such uses are often thought to be purely idiomatic, we hypothesized that these abstract, non-spatial relationships might preserve one specific aspect of prepositions’ spatial meaning: the degree to which the figure or the ground controls the figure-ground relationship (Coventry, 1992; Coventry, Carmichael & Garrod, 1994; Feist & Gentner, 1997, 1998, 2003). We found that locus of control distinguishes in and on in common abstract metaphorical contexts (e.g., in love/on a roll), matched abstract contexts (e.g., in/on time), and novel abstract contexts. These findings suggest that prepositions retain aspects of their spatial meaning when used abstractly.
Expression and prognostic significance of the autoimmune regulator gene in breast cancer cells

ABSTRACT The autoimmune regulator gene (AIRE) plays a fundamental role in tolerance by promoting the expression of tissue-specific antigens in medullary thymic epithelial cells (mTECs). Recently, AIRE expression was detected also in human keratinocytes and in tumors originating in stratified epithelia. Here, we tested whether AIRE is expressed in cancer cells. We analyzed AIRE expression in cancer cases from The Cancer Genome Atlas (TCGA) RNA-seq dataset and we found association with better outcome. AIRE protein expression was verified by immunohistochemistry in a cohort of 39 human breast cancer specimens and its prognostic relevance was confirmed in microarray-based gene expression data set NKI-295 and KM-Plotter. Both in the RNA-seq and gene expression datasets analyzed, AIRE expression was an independent strong prognostic factor for relapse-free survival (RFS), particularly in estrogen receptor-positive tumors. Enrichment of translation-related pathways was observed in AIRE-expressing tumors by Ingenuity Pathway Analysis and a significant increase of cells in G1 phase and activation of caspase cascades was induced by AIRE transfection in breast cancer luminal cell lines, suggesting that AIRE-induced over-translation of proteins lead to cycle arrest and apoptosis. These data are the first to identify AIRE expression in breast cancer and an association with prognosis.
Enhanced electrospray ionization mass spectrometric detection of hexamethylene triperoxide diamine (HMTD) after oxidation to tetramethylene diperoxide diamine dialdehyde (TMDDD).

RATIONALE Hexamethylene triperoxide diamine (HMTD) is one of the peroxide-based explosives that are difficult to detect using standard analytical methodologies. METHODS It was analyzed by electrospray ionization mass spectrometry (ESI-MS) on a UPLC-TOF instrument. Alkali metal salts were used to promote the formation of ions. RESULTS In the full scan positive ion mode a 3 ng (13 pmol) limit of detection was achieved if [HMTD + Me](+) ions (Me = Li, Na, K) were detected. It was found that HMTD easily undergoes oxidation to tetramethylene diperoxide diamine dialdehyde (TMDDD) in the source as well as in the samples. TMDDD can be detected as [TMDDD + Me](+) ions, but better ionization efficiency leads to the detection limit of TMDDD at the 2 pg (0.01 pmol) level. In butyl acetate the yield of oxidation of HMTD to TMDDD reaches 25% within 20 min at 120 °C, which offers a simple way of improving the detection limit of HMTD by two orders of magnitude. CONCLUSIONS A simple procedure of detection of HMTD that matches the most sensitive methods available was developed. It uses standard equipment available in many laboratories. It was shown that the frequently reported [HMTD-H](+) cation observed by various authors was in fact a misinterpretation of the results, and should be attributed to [TMDDD + H](+).
Characterization and crystallization of mouse Aldehyde Oxidase 3 (mAOX3): from mouse liver to E. coli heterologous protein expression

Aldehyde oxidase (AOX) is characterized by a broad substrate specificity oxidizing aromatic aza-heterocycles, e.g. N 1 -methylnicotinamide and N-methylphthalazinium, or aldehydes, such as benzaldehyde, retinal and vanillin. In the past decade, AO has been increasingly recognized to play an important role in the metabolism of drugs through its complex cofactor content, tissue distribution and substrate recognition. In humans, only one AOX gene ( AOX1 ) is present, but in mouse and other mammals different AOX homologues were identified. The multiple AOX isoforms are expressed tissue-specifically in different organisms, and it is believed that they recognize distinct substrates and carry out different physiological tasks. AOX is a dimer of approximately 300 kDa, and each subunit of the homodimeric enzyme contains four different cofactors: the molybdenum cofactor (Moco), two distinct [2Fe-2S] clusters and one FAD. We purified the AOX homologue (mAOX3) from mouse liver and established a system for the heterologous expression of mAOX3 in Escherichia coli . The purified enzymes were compared. Both proteins show the same characteristics and catalytic properties, with the difference that the recombinant protein was expressed and purified in a 30% active form, while the native protein is 100% active. Spectroscopic characterizations showed that the FeSII is not completely assembled in mAOX3. Additionally, both proteins were crystallized. The best crystals were from the native mAOX3 and diffracted beyond 2. 9Å. The crystals belong to space group P1 and two dimers are present in the unit cell.
SuperLab LT: Evaluation and Uses in Teaching Experimental Psychology

I describe and evaluate SuperLab LT (Chase & Abboud, 1990), a software package that enables students to replicate classic experiments in cognitive psychology. I also discuss the package with respect to its uses in teaching an undergraduate course in Experimental Psychology. Although the package has minor flaws, SuperLab LT provides numerous pedagogical benefits.
Multilocus Sequence Typing and Antimicrobial Resistance of Campylobacter jejuni Isolated from Dairy Calves in Austria

Human campylobacteriosis is primarily associated with poultry but also cattle. In this study, 55 Campylobacter jejuni strains isolated from 382 dairy calves’ feces were differentiated by multilocus sequence typing and tested for antimicrobial resistance. The most prevalent sequence type (ST) was ST883 (20.0%), followed by ST48 (14.5%), and ST50 (9.1%). In contrast to ST48 and ST50, ST883 has rarely been described in cattle previously. Furthermore, risk factor analysis was performed for the presence of the most prevalent STs in these calves. Multiple regression analysis revealed that the type of farm (organic vs. conventional) and calf housing (place, and individual vs. group) were identified as significantly (p < 0.05) associated with the presence of ST883 in calves, and ST50 was associated with calf diarrhea. Antimicrobial resistance was detected in 58.2% of the isolates. Most of the resistant isolates (81.3%) were resistant to more than one antimicrobial. Most frequently, resistance to ciprofloxacin (49.1%), followed by nalidixic acid (42.8%), and tetracycline (14.5%) was observed. The results of the present study support the hypothesis that dairy calves may serve as a potential reservoir for C. jejuni and pose a risk for transmission, including antimicrobial resistant isolates to the environment and to humans.
Victims Speak: Comparing Child Sexual Abusers’ and Child Victims’ Accounts, Perceptions, and Interpretations of Sexual Abuse

Abstract This article presents findings from a longitudinal study 1 that sought to evaluate a treatment program for child sexual abusers. A triangulated methodological approach was adopted drawing upon quantitative and qualitative methodological techniques. The focus here is upon one element of this research. 2 Ninety-one in-depth interviews were conducted over a four-year period with a small, nonrandom sample of twenty-one male offenders who had been convicted of sexual offenses against children. All of the men were subject to probation orders with a psychiatric condition (Criminal Justice Act, 1991). One of the aims of this element of the research was to explore the extent to which evidence of denial could be found in offenders’ accounts of offense circumstance and also to explore the extent to which offenders minimized the nature and extent of abuse perpetrated. Offenders’ accounts of offense circumstances were compared to victim statements, and stark differences emerge. These findings have considerable implications for treatment practice with sex offenders, where victims’ perceptions could be used to directly confront offender denial and minimization. 1The research aimed to explore the effectiveness of a treatment program for offenders which lasted for three years. The research design was structured around the program with interviews and psychometric testing undertaken at key points in time with the same group of respondents. 2The quantitative element of this research will be published shortly but is referred to in the following reports Davidson 2000, 2003 [research funded by the National Probation Service]. Psychometric testing was undertaken over a four-year period with the men attending the treatment program to explore shifts in the extent of denial, blame attribution, and victim empathy over time. Offender cognitive distortions, general health, and self-esteem were also explored via psychometric testing. An interview-administered survey was undertaken with all sex offenders registered with the Probation Service (those on probation and in custody) in order to gather demographic data, and 117 of 150 offenders responded.
[Effects of vacuum drainage combined with heparin irrigation for treatment of scald burns with seawater immersion in rabbits].

OBJECTIVE To investigate the effect of closed vacuum drainage combined with heparin irrigation in the treatment of scald burns with seawater immersion in rabbits. METHODS Twenty New Zealand rabbits were subjected to deep partial-thickness scald burns in 4 regions on the bilateral skin of the spine. The wounds were managed with common dressing (group A), common dressing after seawater immersion (group B), closed vacuum drainage after seawater immersion (group C), or closed vacuum drainage combined with heparin irrigation after seawater immersion (group D). Wound effusion and tissue necrosis were observed at 1, 3, 5 and 7 days after the burns. Tissue samples were collected from the wounds for HE staining and immunohistochemistry for VEGF and CD31, and the changes of capillary endothelial cells in the wound were observed using electron microscopy. The water content in the wound tissues was determined, and the wound healing rate was calculated after the injury. RESULTS Sea water immersion of the wound results in earlier onset of edema and more extensive tissue necrosis in the scalded rabbits. The mean necrotic area in groups C and D was smaller than that in group B early after the burns, and vacuum drainage promoted necrotic tissue elimination and accelerated wound healing. Early after the burns, water content in the tissues increased with time in all the groups and reached the highest level at 3 days, and was significantly lower in groups C and D than in group B. Pathologically, vascular endothelial cell damage at the wound site was worsened after seawater immersion. In group D, the basement membrane damage was milder and the endothelial cell membrane remained intact at the wound site, where new blood vessels occurred at 3 days after the burns, a time earlier than that in the other 3 groups with also the highest vascular density. CONCLUSIONS Closed vacuum drainage combined with heparin irrigation can relieve edema at the scald wound with seawater immersion, improve microcirculation, accelerate the removal of necrotic tissue, and promote the growth of new blood vessels.
Elementary [Ca2+]i signals generated by electroporation functionally mimic those evoked by hormonal stimulation

The generation of oscillations and global Ca2+ waves relies on the spatio‐temporal recruitment of elementary Ca2+ signals, such as ‘Ca2+ puffs’. Each elementary signal contributes a small amount of Ca2+ into the cytoplasm, progressively promoting neighboring Ca2+ release sites into an excitable state. Previous studies have indicated that increases in frequency or amplitude of such hormone‐evoked elementary Ca2+ signals are necessary to initiate Ca2+ wave propagation. In the present study, an electroporation device was used to rapidly and reversibly permeabilize the plasma membrane of HeLa cells and to allow a limited influx of Ca2+. With low field intensities (100–500 V/cm), brief (50–100 µs) electroporation triggered localized Ca2+ signals that resembled hormone‐evoked Ca2+ puffs, but not global signals. With such low intensity electroporative pulses, the Ca2+ influx component was usually undetectable, confirming that the electroporation‐induced local signals represented Ca2+ puffs arising from the opening of intracellular Ca2+ release channels. Increasing either the frequency at which low‐intensity electroporative pulses were applied, or the intensity of a single electroporative pulse (>500 V/cm), resulted in caffeine‐sensitive regenerative Ca2+ waves. We suggest that Ca2+ puffs caused by electroporation functionally mimic hormone‐evoked elementary events and can activate global Ca2+ signals if they provide a sufficient trigger. —Bobanovic, F. , Bootman, M. D. , Berridge, M. J., Parkinson, N. A. Lipp, P. Elementary [Ca2+]i signals generated by electroporation functionally mimic those evoked by hormonal stimulation. FASEB J. 13, 365–376 (1999)
Locating hidden servers

Hidden services were deployed on the Tor anonymous communication network in 2004. Announced properties include server resistance to distributed DoS. Both the EFF and Reporters Without Borders have issued guides that describe using hidden services via Tor to protect the safety of dissidents as well as to resist censorship. We present fast and cheap attacks that reveal the location of a hidden server. Using a single hostile Tor node we have located deployed hidden servers in a matter of minutes. Although we examine hidden services over Tor, our results apply to any client using a variety of anonymity networks. In fact, these are the first actual intersection attacks on any deployed public network: thus confirming general expectations from prior theory and simulation. We recommend changes to route selection design and implementation for Tor. These changes require no operational increase in network overhead and are simple to make; but they prevent the attacks we have demonstrated. They have been implemented
A Generalized Algorithm for Blind Channel Identification with Linear Redundant Precoders

It is well known that redundant filter bank precoders can be used for blind identification as well as equalization of FIR channels. Several algorithms have been proposed in the literature exploiting trailing zeros in the transmitter. In this paper we propose a generalized algorithm of which the previous algorithms are special cases. By carefully choosing system parameters, we can jointly optimize the system performance and computational complexity. Both time domain and frequency domain approaches of channel identification algorithms are proposed. Simulation results show that the proposed algorithm outperforms the previous ones when the parameters are optimally chosen, especially in time-varying channel environments. A new concept of generalized signal richness for vector signals is introduced of which several properties are studied.
Inoculation with RNAs 1 and 2 of Cucumber Mosaic Virus Induces Viral RNA Replicase Activity in Tobacco Mesophyll Protoplasts

Summary The activity of membrane-bound RNA-dependent RNA polymerase in tobacco mesophyll protoplasts was measured and in vitro products were characterized after inoculation with cucumber mosaic virus (CMV) or with different combinations of the four virus RNAs and satellite RNA. Activity increased rapidly 4 to 6 h after inoculation with virus particles. When the inoculum contained RNA 1, RNA 2 and RNA 3, most of the in vitro products of the enzyme were full-length positive-sense RNAs (RNAs 1, 2, 3 and 4) that migrated as dsRNA; inoculation of RNA 1 or RNA 2 alone did not increase RNA polymerase activity and no virus RNA was produced. After inoculation with a mixture of RNA 1 and RNA 2, however, the enzyme activity increased and full-length positive-sense RNA 1 and RNA 2 were synthesized, and we speculate that the induced enzyme is CMV RNA replicase as a complex comprising the translation products of RNA 1 and RNA 2, membrane components of the host cell and CMV RNA templates. Protoplasts inoculated with RNA 1, RNA 2 and RNA 4 did not synthesize RNA 4 which suggests that positive-sense RNA 4 does not serve as a template for the replicase complex. Satellite RNA was synthesized in protoplasts inoculated with RNA 1, RNA 2 and satellite RNA which suggests that satellite RNA is replicated by the replicase complex.
Gender differences in work experiences and satisfactions of Norwegian oil rig workers

Purpose – The present study sets out to compare women (N=24) and men (N=613) working on Norwegian oil rigs in the North Sea on work experiences, work satisfaction, perception of safety attitudes and safety climate, and psychological health.Design/methodology/approach – Data were collected using questionnaires from 1,022 women and men, a 59 percent response rate. Only those respondents working in traditionally male‐dominated jobs were considered.Findings – Few differences were observed, suggesting that those women that continue in this occupation compare favorably with their male colleagues.Research limitations/implications – The findings should be considered tentative, given the small number of women taking part in the study.Practical implications – For the past three decades, women were encouraged and supported to enter non‐traditional occupations (NTOs). NTOs were occupations that have traditionally been male‐dominated. Only modest inroads have been made by females during this time. Women in NTOs typica.