Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of a Novel Strategy of Engineering Conditional Alleles to a Single Exon Gene, Sox2

Background The Conditional by Inversion (COIN) method for engineering conditional alleles relies on an invertible optimized gene trap-like element, the COIN module, for imparting conditionality. The COIN module contains an optimized 3′ splice site-polyadenylation signal pair, but is inserted antisense to the target gene and therefore does not alter transcription, until it is inverted by Cre recombinase. In order to make COIN applicable to all protein-coding genes, the COIN module has been engineered within an artificial intron, enabling insertion into an exon. Methodology/Principal Findings Therefore, theoretically, the COIN method should be applicable to single exon genes, and to test this idea we engineered a COIN allele of Sox2. This single exon gene presents additional design challenges, in that its proximal promoter and coding region are entirely contained within a CpG island, and are also spanned by an overlapping transcript, Sox2Ot, which contains mmu-miR1897. Here, we show that despite disruption of the CpG island by the COIN module intron, the COIN allele of Sox2 (Sox2COIN) is phenotypically wild type, and also does not interfere with expression of Sox2Ot and miR1897. Furthermore, the inverted COIN allele of Sox2, Sox2INV is functionally null, as homozygotes recapitulate the phenotype of Sox2ßgeo/ßgeo mice, a well-characterized Sox2 null. Lastly, the benefit of the eGFP marker embedded in the COIN allele is demonstrated as it mirrors the expression pattern of Sox2. Conclusions/Significance Our results demonstrate the applicability of the COIN technology as a method of choice for targeting single exon genes.
Methods of critical paths delay faults testing in digital systems

The dissertation thesis is aimed at automatic delay faults test generation methods for digital systems. Path delay faults are tested via selected critical paths in a tested digital circuit. The critical paths can be specified e.g. by static timing analysis (STA), statistical static timing analysis (SSTA) and others. Signal delay propagation is also affected by many factors such as power supply noise, multiple input switching, temperature and others during test. The impact of each factor to the path delay faults has been individually solved and published in some papers but their joint effects should be also investigated. A new method for evaluation of critical paths and a general system for critical paths selection, named PaCGen, are presented in the dissertation thesis. The method is based on STA and influences of multiple factors used in the new technique for path criticality calculation. Some critical paths can be found as untestable based on structure of the circuit. The proposed system PaCGen includes also more effective DFT (design-for-testability) technique to change untestable critical paths to testable. Evaluation of the proposed method, system and used techniques has been done over selected benchmark circuits and compared with published results.
IpgD, a protein secreted by the type III secretion machinery of Shigella flexneri, is chaperoned by IpgE and implicated in entry focus formation

Invasion of epithelial cells by Shigella flexneri involves entry and intercellular dissemination. Entry of bacteria into non‐phagocytic cells requires the IpaA–D proteins that are secreted by the Mxi–Spa type III secretion machinery. Type III secretion systems are found in several Gram‐negative pathogens and serve to inject bacterial effector proteins directly into the cytoplasm of host cells. In this study, we have analysed the IpgD protein of S. flexneri, the gene of which is located on the virulence plasmid at the 5′ end of the mxi–spa locus. We have shown that IpgD (i) is stored in the bacterial cytoplasm in association with a specific chaperone, IpgE; (ii) is secreted by the Mxi–Spa type III secretion system in amounts similar to those of the IpaA–D proteins; (iii) is associated with IpaA in the extracellular medium; and (iv) is involved in the modulation of the host cell response after contact of the bacterium with epithelial cells. This suggests that IpgD is an effector that might be injected into host cells to manipulate cellular processes during infection.
A Working Memory Deficit among Dyslexic Readers with No Phonological Impairment as Measured Using the N-Back Task: An fNIR Study

Data indicated that dyslexic individuals exhibited difficulties on tasks involving Working Memory (WM). Previous studies have suggested that these deficits stem from impaired processing in the Phonological Loop (PL). The PL impairment was connected to poor phonological processing. However, recent data has pointed to the Central Executive (CE) system as another source of WM deficit in dyslexic readers. This opened a debate whether the WM deficit stems solely from PL or can also be seen as an outcome of poor CE processing. In an attempt to verify this question, the current study compared adult skilled and compensated dyslexic readers with no impairment of phonological skills. The participants’ PL and CE processing were tested by using the fNIR device attached to the frontal lobe and measured the changes in brain oxygen values when performing N-back task. As it was previously suggested, the N = 0 represented PL and N = 1 to 3 represent CE processing. It was hypothesized that dyslexic readers who show non-impaired phonological skills will exhibit deficits mainly in the CE subsystem and to a lesser extent in the PL. Results indicated that the two reading level groups did not differ in their accuracy and reaction times in any of the N-Back conditions. However, the dyslexic readers demonstrated significant lower maximum oxyHb values in the upper left frontal lobe, mainly caused due to a significant lower activity under the N = 1 condition. Significant task effects were found in the medial left hemisphere, and the high medial right hemisphere. In addition, significant correlations between fNIR-features, reading performance and speed of processing were found. The higher oxyHb values, the better reading and speed of processing performance obtained. The results of the current study support the hypothesis that at least for the group of dyslexics with non-impaired PL, WM deficit stems from poor CE activity.
Asymptotic normality of plug-in level set estimates.

We establish the asymptotic normality of the $G$-measure of the symmetric difference between the level set and a plug-in-type estimator of it formed by replacing the density in the definition of the level set by a kernel density estimator. Our proof will highlight the efficacy of Poissonization methods in the treatment of large sample theory problems of this kind.
CV-SLAM using line and point features

Simultaneous Localization and Mapping (SLAM) is a fundamental problem in the mobile robotics. As SLAM is usually utilized in an indoor environment, we select the ceiling view (CV) as a stable source of features. In this research, three types of features are extracted from CV and constitute a single map. The landmarks detected from ceilings are ceiling boundaries, electric lamps, and circles. Each of them is very robustly detected from CV and the combination of them yields more stable and accurate localization performance. Multiple kinds of features are integrated into an EKF-SLAM framework. We demonstrated the SLAM system in an indoor environment and proved its high performance.
Bioactivity of the Murex Homeopathic Remedy and of Extracts from an Australian Muricid Mollusc against Human Cancer Cells

Marine molluscs from the family Muricidae are the source of a homeopathic remedy Murex, which is used to treat a range of conditions, including cancer. The aim of this study was to evaluate the in vitro bioactivity of egg mass extracts of the Australian muricid Dicathais orbita, in comparison to the Murex remedy, against human carcinoma and lymphoma cells. Liquid chromatography coupled with mass spectrometry (LC-MS) was used to characterize the chemical composition of the extracts and homeopathic remedy, focusing on biologically active brominated indoles. The MTS (tetrazolium salt) colorimetric assay was used to determine effects on cell viability, while necrosis and apoptosis induction were investigated using flow cytometry (propidium iodide and Annexin-V staining, resp.). Cells were treated with varying concentrations (1–0.01 mg/mL) of crude and semi-purified extracts or preparations (dilute 1 M and concentrated 4 mg/mL) from the Murex remedy (4 h). The Murex remedy showed little biological activity against the majority of cell lines tested. In contrast, the D. orbita egg extracts significantly decreased cell viability in the majority of carcinoma cell lines. Flow cytometry revealed these extracts induce necrosis in HT29 colorectal cancer cells, whereas apoptosis was induced in Jurkat cells. These findings highlight the biomedical potential of Muricidae extracts in the development of a natural therapy for the treatment of neoplastic tumors and lymphomas.
The Tasmanian River Catchment Water Quality Initiative Pesticide Impact Rating Index (PIRI) risk indicator for minimising off-site migration of pesticides

CSIRO advises that the information contained in this publication comprises general statements based on scientific research. The reader is advised and needs to be aware that such information may be incomplete or unable to be used in any specific situation. No reliance or actions must therefore be made on that information without seeking prior expert professional, scientific and technical advice. To the extent permitted by law, CSIRO (including its employees and consultants) excludes all liability to any person for any consequences, including but not limited to all losses, damages, costs, expenses and any other compensation, arising directly or indirectly from using this publication (in part or in whole) and any information or material contained in it. Acknowledgements We are grateful to the following agencies and colleagues for their help and support during the project: EC50 Effective dose required to reduce a biological function by 50% as determined in a laboratory test under specified conditions FT Forestry Tasmania K d A partition coefficient representing the distribution of a pesticide between soil and a solution. In PIRI K d is estimated as mass fraction of organic carbon × K oc K oc Partition coefficient between soil organic carbon and water. Pesticides with a low K oc are less strongly bound to soil and are considered more likely to move with surface water than pesticides with a high K oc K ow Octanol-water partition coefficient (a measure of hydrophobicity of a pesticide). KSDI Keetch-Byram Soil Dryness Index (Keetch and Byram 1968) k 1 Estimate of pH at which original K oc values were determined k 2 Scale parameter used to moderate the effect of pKa and pH on K oc LC50 Concentration required to cause mortality to 50% of animals (expressed as mg/L in this report) as determined in a laboratory test under specified conditions. LD50 p Dosage required to kill 50% of animals (expressed as mg/kg in this report) as determined in a laboratory test under specified conditions.
Evaluating Parent Education Groups: Effects on Sense of Competence and Social Isolation

One-hundred twenty-four mothers from eight community service regions in the Australian state of Tasmania participated in a study of parent education services provided in a small group format. Using a no-treatment control group design, it was predicted that participation in parent education groups would enhance the mother's sense of competence as a parent, reduce parental social isolation, and improve child comportment. These hypotheses were partially supported. Participation in parent education groups did enhance the mother's sense of competence immediately posttreatment, but reductions in social isolation and child difficulty were not found until the 3-month follow-up. Although a variety of parent education group formats were employed, there were no appreciable differences among them in terms of effectiveness. Further applications for social work practice are discussed.
Psychometric Properties of the Chinese Cultural Beliefs About Adversity Scale

Objective: The purpose of the study was to examine the psychometric properties of the Chinese Cultural Beliefs about Adversity scale (CBA). Methods: The CBA was administered in a sample of 275 Chinese parents experiencing economic disadvantage. Results: The CBA was found to be internally consistent. Consistent with the conceptual framework, factor analyses showed that two stables factors were abstracted from the scale. The scale and subscale scores of the CBA showed correlation with parental attributional beliefs of children’s success and failure to effort and luck, respectively, thus supporting the construct validity of the measures. Conclusions: The CBA is a reliable and valid measurement tool to measure Chinese cultural beliefs about adversity from the perspective of parents in the context of poverty.
Forensic usefulness of a 25 X‐chromosome single‐nucleotide polymorphism marker set

BACKGROUND: The analysis of X‐chromosome markers can be valuable in particular situations, for example, deficiency kinship cases, where the putative father cannot be typed. X‐chromosome short‐tandem repeats (X‐STRs) are widely used in forensic genetics, while the use of X‐chromosome single‐nucleotide polymorphisms (X‐SNPs) is still limited.
Examining Spirituality Over Time: Latent Growth Curve and Individual Growth Curve Analyses

SUMMARY Research on spirituality and religiousness has gained growing attention in recent years; however, most studies have used cross-sectional designs. As research on this topic evolves, there has been increasing recognition of the need to examine these constructs and their effects through the use of longitudinal designs. Beyond repeated-measures ANOVA and OLS regression models, what tools are available to examine these constructs over time? The purpose of this paper is to provide an overview of two cutting-edge statistical techniques that will facilitate longitudinal investigations of spirituality and religiousness: latent growth curve analysis using structural equation modeling (SEM) and individual growth curve models. The SEM growth curve approach examines change at the group level, with change over time expressed as a single latent growth factor. In contrast, individual growth curve models consider longitudinal change at the level of the person. While similar results may be obtained using either method, researchers may opt for one over the other due to the strengths and weaknesses associated with these methods. Examples of applications of both approaches to longitudinal studies of spirituality and religiousness are presented and discussed, along with design and data considerations when employing these modeling techniques.
Resource allocation for HARQ-IR systems with QoS constraints and limited feedback

This paper investigates power allocation for reliable downlink transmission in cellular networks subject to quality-of-service (QoS) constraints. The reliability of data transmissions is assured by hybrid automatic repeat request protocol with incremental redundancy (HARQ-IR). By evaluating the effective throughput of the HARQ-IR protocol for the downlink transmission under QoS constraints, we propose a novel power allocation policy to efficiently exploit the available resources. Furthermore, based on the derived effective throughput, optimization problem is formulated and solved, in which all channels are effectively allocated to all users. Finally, numerical results are provided to support theoretical findings.
Brain activation patterns resulting from learning letter forms through active self-production and passive observation in young children

Although previous literature suggests that writing practice facilitates neural specialization for letters, it is unclear if this facilitation is driven by the perceptual feedback from the act of writing or the actual execution of the motor act. The present study addresses this issue by measuring the change in BOLD signal in response to hand-printed letters, unlearned cursive letters, and cursive letters that 7-year-old children learned actively, by writing, and passively, by observing an experimenter write. Brain activation was assessed using fMRI while perceiving letters—in both cursive and manuscript forms. Results showed that active training led to increased recruitment of the sensori-motor network associated with letter perception as well as the insula and claustrum, but passive observation did not. This suggests that perceptual networks for newly learned cursive letters are driven by motor execution rather than by perceptual feedback.
Finding care for the caregiver? Active participation in online health forums attenuates the negative effect of caregiver strain on wellbeing

Abstract This paper focuses on how online health forums may benefit the wellbeing of caregivers. An online questionnaire of caregivers assessed caregiver strain, forum use, and mental and physical wellbeing. Results show a positive relation between caregiver strain and using online health forums to seek emotional support. Furthermore, we find that caregivers with higher levels of caregiver strain report lower mental and physical wellbeing. This relation is however moderated by using online health forums. While the amount of time spent on the online forums did not moderate the relation between caregiver strain and wellbeing, the amount of activity (i. e. the number of messages posted per week) did: Active participation in online health forums attenuates the negative effect of caregiver strain on wellbeing.These findings suggest that online forums are valuable for caregivers and that it is active contribution that matters, rather than simply visiting the online health groups.
Chlorophyll Binding to Monomeric Light-harvesting Complex

The chromophore binding properties of the higher plant light-harvesting complex II have been studied by site-directed mutagenesis of pigment-binding residues. Mutant apoproteins were overexpressed in Escherichia coli and then refoldedin vitro with purified chromophores to yield holoproteins selectively affected in chlorophyll-binding sites. Biochemical and spectroscopic characterization showed a specific loss of pigments and absorption spectral forms for each mutant, thus allowing identification of the chromophores bound to most of the binding sites. On these bases a map for the occupancy of individual sites by chlorophyll a and chlorophyll b is proposed. In some cases a single mutation led to the loss of more than one chromophore indicating that four chlorophylls and one xanthophyll could be bound by pigment-pigment interactions. Differential absorption spectroscopy allowed identification of the Qy transition energy level for each chlorophyll within the complex. It is shown that not only site selectivity is largely conserved between light-harvesting complex II and CP29 but also the distribution of absorption forms among different protein domains, suggesting conservation of energy transfer pathways within the protein and outward to neighbor subunits of the photosystem.
Primed Lexical Decision: Combined Effects of the Proportion of Related Prime-Target Pairs and the Stimulus-Onset Asynchrony of Prime and Target

Lexical decisions to word targets preceded by associatively related word primes are generally faster than those to words following neutral primes, whereas, under certain circumstances, lexical decisions to words preceded by unassociated word primes are slower than those to words following neutral primes. An experiment is reported that investigates the influence of the proportion of related prime-target pairs in the set of materials and of the stimulus-onset asynchrony (SOA) of prime and target on these associative priming effects. Four levels of proportion and three levels of SOA are systematically varied. Both variables are found to affect the size of the associative priming effects. Furthermore, the data suggest interdependence between them. The magnitude of priming only varies with SOA if the proportion of related pairs is relatively large. In contrast, the amount of priming varies with proportion under all SOA conditions. The data are interpreted primarily in terms of two contextual processes, viz., “prime-induced attentional processing” and “post-lexical coherence checking”.
Maintaining global coherence during reading

Previous research demonstrated a contradiction effect: although text currently being processed was locally coherent, readers were aware of inconsistencies between a protagonist's actions and characteristics of the protagonists that were described earlier in the text and subsequently backgrounded. In the present experiments, not only the critical characteristics but also the protagonist were backgrounded. When the protagonist was reintroduced into the narrative in the context of carrying out an inconsistent action, the contradiction effect again occurred. In experiments 1-3, we examined the effects of several variables on the onset of the effect. In Experiment 4, we presented probes at various points in the passage with results tha supported he conclusion that the critical characteristics had been backgrounded before the sentence that contradicted them
Comparative Study of Static and Dynamic Artificial Neural Network Models in Forecasting of Tehran Stock Exchange

During the recent decades, neural network models have been focused upon by researchers due to their more real performance and on this basis, different types of these models have been used in forecasting. Now, there is a question that which kind of these models has more explanatory power in forecasting the future processes of the stock. In line with this, the present paper made a comparison between static and dynamic neural network models in forecasting (uninvariable) the return of Tehran Stock Exchange (TSE) index in order to find the best model to be used for forecasting this series. The data were collected daily from 26/11/2009 to 17/10/2014. The models examined in this study included two static models (Adaptive Neuro-Fuzzy Inference Systems "ANFIS" and Multi-layer Feed-forward Neural Network "MFNN") and a dynamic model (nonlinear neural network autoregressive model "NNAR"). The findings showed that based on the Mean Square Error and Root Mean Square Error criteria, ANFIS model had a much higher forecasting ability compared to other models.
Combining Acceptance and Commitment Therapy and Cognitive Behavioral Therapy for the Treatment of Chronic Pain in Older Adults

The article discusses a combination of cognitive-behavioral therapy (CBT) for chronic pain and acceptance and commitment therapy (ACT) that was applied to an older adult. Findings reveal that a brief intervention of 8 weeks was effective in producing a clinically significant change in pain experience, as well as an increase in sleep quality/sleep maintenance and acceptance of pain. It is suggested that a central ACT component such as mindfulness skills as well as the focus on values may contribute to efficacy of cognitive behavioral treatment for chronic pain.
The next generation of pregnant women: more freedom in the public sphere or just an illusion?

This article argues that, withstanding the liberating effects of the women's movement, the contraceptive revolution, the equal opportunities revolution, and the increase in equal access to information – which have all helped to increase women's mobility within society – is a serendipitous form of societal policing of women's actions that may be linked to ongoing patriarchal views. We attempt to explain our analysis by reviewing historical developments, such as women's movement from the private domain of domestic life to the more public domain of work as well as the many changes in the forms of mass media since the 1950s, and by presenting findings from research across generations of pregnant women who shared with us their experiences of being pregnant.