Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Poly(ADP-Ribose) Polymerases in Arabidopsis Telomere Biology

Maintaining the length of the telomere tract at chromosome ends is a complex process vital to normal cell division. Telomere length is controlled through the action of telomerase as well as a cadre of telomere-associated proteins that facilitate replication of the chromosome end and protect it from eliciting a DNA damage response. In vertebrates, multiple poly(ADP-ribose) polymerases (PARPs) have been implicated in the regulation of telomere length, telomerase activity and chromosome end protection. Here we investigate the role of PARPs in plant telomere biology. We analyzed Arabidopsis thaliana mutants null for PARP1 and PARP2 as well as plants treated with the PARP competitive inhibitor 3-AB. Plants deficient in PARP were hypersensitive to genotoxic stress, and expression of PARP1 and PARP2 mRNA was elevated in response to MMS or zeocin treatment or by the loss of telomerase. Additionally, PARP1 mRNA was induced in parp2 mutants, and conversely, PARP2 mRNA was induced in parp1 mutants. PARP3 mRNA, by contrast, was elevated in both parp1 and parp2 mutants, but not in seedlings treated with 3-AB or zeocin. PARP mutants and 3-AB treated plants displayed robust telomerase activity, no significant changes in telomere length, and no end-to-end chromosome fusions. Although there remains a possibility that PARPs play a role in Arabidopsis telomere biology, these findings argue that the contribution is a minor one.
Handbook of Brief Cognitive Behaviour Therapy

In this unique handbook, Frank Bond and Windy Dryden, have brought together a prominent cast of authors, to discuss issues concerning the definition, assessment and, in particular, the practice of brief Cognitive Behaviour Therapy (CBT). Contents include: * the difference between brief and regular CBT and evidence for its effectiveness * How to use brief CBT in your own area of practice * Applying brief CBT to emotional disorders, anxiety, workplace stress and more This handbook is accessible to a wide range of readers, including academics, practitioners, psychotherapists, counsellors, and students training in CBT.
A New Closed-Form Solution to Light Scattering by Spherical Nanoshells

Light or electromagnetic wave scattered by a single sphere or a coated sphere has been considered as a classic Mie theory. There have been some further extensions that were made further based on the Mie theory. Recently, a closed-form analytical model of the scattering cross section of a single nanoshell has been considered. The present paper is documented further, based on the work in 2006 by Alam and Massoud, to derive another different closed-form solution to the problem of light scattered by the nanoshells using polynomials of up to order 6. Validation is made by comparing the present closed-form solution to the exact Mie scattering solution and also to the other closed-form solution by Alam and Massoud. This study is found to be, however, more generalized and also more accurate for the coated spheres of either tiny/small or medium sizes than that of Alam and Massoud. Therefore, the derived formulas can be used for accurately characterizing both surface plasmon resonances of nanoparticles (of small sizes) or nanoantenna near-field properties (of medium sizes comparable with half wavelength).
Truths about the NINDS study: setting the record straight.

Thrombolysis for acute ischemic stroke has been studied for more than adecade, but its efficacy remains controversial. The first study to claim thattissue plasminogen activator (tPA) is effective in the treatment of acuteischemic stroke was a multicenter clinical trial coordinated by the NationalInstitute of Neurological Disorders and Stroke (NINDS) Study Group. The NINDSstudy's conclusions, published in1995,1 were that“treatment with intravenous tPA within 3 hours of the onset of ischemicstroke improved clinical outcome at 3 months. [A]s compared with patientsgiven placebo, patients treated with tPA were at least 30% more likely to haveminimal or no disability at 3months. ”1(p1586)The NINDS study was widely perceived to be a well-executed and analyzedrandomized controlled trial, and its results were well received by manymedical professionals and thepublic. ​thepublic. Table 1 Percentage of patients (N = 320) in the 91 to 180-minute subgroups witha specific baseline National Institutes of Health Stroke Scale (NIHSS)score* Over the past 5 years, tPA therapy for acute ischemic stroke has enteredthe mainstream of emergency medical practice in the United States. When theAmerican Heart Association revised its advanced cardiac life support (ACLS)guidelines for the 2000 ACLS handbook, Guidelines 2000 for CardiopulmonaryResuscitation and Emergency Cardiovascular Care, it gave tPA a class Irecommendation for the therapy of acute ischemic stroke. The American HeartAssociation gives a drug a class I recommendation if the evidence in supportof its effectiveness is considered homogeneous, consistently positive, androbust. Are the NINDS study's results sufficiently robust to withstandrigorous analysis, and is tPA, therefore, fully deserving of a class Irecommendation for the treatment of acute ischemic stroke?
Residual auditory function in persistent vegetative state: a combined pet and fmri study

In recent years, a number of studies have demonstrated an important role for functional neuroimaging in the identification of residual cognitive function in persistent vegetative state. Such studies, when successful, may be particularly useful where there is concern about the accuracy of the diagnosis and the possibility that residual cognitive function has remained undetected. Unfortunately, functional neuroimaging in persistent vegetative state is extremely complex and subject to numerous methodological, clinical and theoretical difficulties. Here, we describe the strategy used to study residual auditory and speech processing in a single patient with a clinical diagnosis of persistent vegetative state. Identical positron emission tomography studies, conducted nine months apart, revealed preserved and consistent responses in predicted regions of auditory cortex in response to intelligible speech stimuli. Moreover, a preliminary functional magnetic resonance imaging examination at the time of the second session revealed partially intact responses to semantically ambiguous stimuli, which are known to tap higher aspects of speech comprehension. In spite of the multiple logistic and procedural problems involved, these results have major clinical and theoretical implications and provide a strong basis for the systematic study of possible residual cognitive function in patients diagnosed as being in a persistent vegetative state.
MicroRNA Genes and Their Target 3′-Untranslated Regions Are Infrequently Somatically Mutated in Ovarian Cancers

MicroRNAs are key regulators of gene expression and have been shown to have altered expression in a variety of cancer types, including epithelial ovarian cancer. MiRNA function is most often achieved through binding to the 3′-untranslated region of the target protein coding gene. Mutation screening using massively-parallel sequencing of 712 miRNA genes in 86 ovarian cancer cases identified only 5 mutated miRNA genes, each in a different case. One mutation was located in the mature miRNA, and three mutations were predicted to alter the secondary structure of the miRNA transcript. Screening of the 3′-untranslated region of 18 candidate cancer genes identified one mutation in each of AKT2, EGFR, ERRB2 and CTNNB1. The functional effect of these mutations is unclear, as expression data available for AKT2 and EGFR showed no increase in gene transcript. Mutations in miRNA genes and 3′-untranslated regions are thus uncommon in ovarian cancer.
The Haemophilus ducreyi Fis Protein Is Involved in Controlling Expression of the lspB-lspA2 Operon and Other Virulence Factors

ABSTRACT Expression of the lspB-lspA2 operon encoding a virulence-related two-partner secretion system in Haemophilus ducreyi 35000HP is directly regulated by the CpxRA regulatory system (M. Labandeira-Rey, J. R. Mock, and E. J. Hansen, Infect. Immun. 77:3402–3411, 2009). In the present study, we show that this secretion system is also regulated by the small nucleoid-associated protein Fis. Inactivation of the H. ducreyi fis gene resulted in a reduction in expression of both the H. ducreyi LspB and LspA2 proteins. DNA microarray experiments showed that a H. ducreyi fis deletion mutant exhibited altered expression levels of genes encoding other important H. ducreyi virulence factors, including DsrA and Flp1, suggesting a possible global role for Fis in the control of virulence in this obligate human pathogen. While the H. ducreyi Fis protein has a high degree of sequence and structural similarity to the Fis proteins of other bacteria, its temporal pattern of expression was very different from that of enterobacterial Fis proteins. The use of a lacZ-based transcriptional reporter provided evidence which indicated that the H. ducreyi Fis homolog is a positive regulator of gyrB, a gene that is negatively regulated by Fis in enteric bacteria. Taken together, the Fis protein expression data and the observed regulatory effects of Fis in H. ducreyi suggest that this small DNA binding protein has a regulatory role in H. ducreyi which may differ in substantial ways from that of other Fis proteins.
Mutation of a putative protein degradation gene LITAF/SIMPLE in Charcot-Marie-Tooth disease 1C

Background: Charcot-Marie-Tooth (CMT) neuropathy is a heterogeneous group of inherited disorders of the peripheral nervous system. The authors recently mapped an autosomal dominant demyelinating form of CMT type 1 (CMT1C) to chromosome 16p13.1-p12.3. Objective: To find the gene mutations underlying CMT1C. Methods: The authors used a combination of standard positional cloning and candidate gene approaches to identify the causal gene for CMT1C. Western blot analysis was used to determine relative protein levels in patient and control lymphocyte extracts. Northern blotting was used to characterize gene expression in 1) multiple tissues; 2) developing sciatic nerve; and 3) nerve-crush and nerve-transection experiments. Results: The authors identified missense mutations (G112S, T115N, W116G) in the LITAFgene (lipopolysaccharide-induced tumor necrosis factor-α factor) in three CMT1C pedigrees. LITAF, which is also referred to as SIMPLE, is a widely expressed gene encoding a 161-amino acid protein that may play a role in protein degradation pathways. The mutations associated with CMT1C were found to cluster, defining a domain of the LITAF protein having a critical role in peripheral nerve function. Western blot analysis suggested that the T115N and W116G mutations do not alter the level of LITAF protein in peripheral blood lymphocytes. The LITAF transcript is expressed in sciatic nerve, but its level of expression is not altered during development or in response to nerve injury. This finding is in stark contrast to that seen for other known genes that cause CMT1. Conclusions: Mutations in LITAF may account for a significant proportion of CMT1 patients with previously unknown molecular diagnosis and may define a new mechanism of peripheral nerve perturbation leading to demyelinating neuropathy.
Risk of cataract and glaucoma in patients with multiple sclerosis

Background: The aim of the study was to evaluate whether multiple sclerosis (MS) is associated with risk of cataract or glaucoma. Methods: We conducted a population-based cohort study utilizing the UK General Practice Research Database (1987–2009) linked to the national hospital registry of England (1997–2008). Incident MS patients (5576 cases) were identified and each was matched to six patients without MS (controls) by age, gender, and practice. Cox proportional hazard models were used to estimate hazard ratios (HRs) of incident cataract and glaucoma in MS. Time-dependent adjustments were made for age, history of diseases and drug use. Results: MS patients had no overall increased risk of cataract, adjusted (adj.) HR 1.15 (95% CI 0.94–1.41) or glaucoma, adj. HR 1.02 (95% CI 0.78–1.33). Risk of cataract (adj. HR 2.45 (95% CI 1.56–3.86)) and glaucoma (adj. HR 1.70 (95% CI 1.01–2.86)) was significantly greater in patients < 50 years, particularly in men < 50 years: cataract, adj. HR 4.23 (95% CI 2.22–8.05) and glaucoma, adj. HR 2.76 (95% CI 1.28–5.93). Conclusion: This is the first study which showed that the risk of cataract and glaucoma is elevated in MS patients younger than 50 years, particularly men.
Galaxy bimodality versus stellar mass and environment

We analyse a z < 0.1 galaxy sample from the Sloan Digital Sky Survey focusing on the variation in the galaxy colour bimodality with stellar mass M and projected neighbour density Σ, and on measurements of the galaxy stellar mass functions. The characteristic mass increases with environmental density from about 10 10. 6 to 10 10.9 M ⊙ (Kroupa initial mass function, H 0 = 70) for Σ in the range 0.1-10 Mpc -2 . The galaxy population naturally divides into a red and blue sequence with the locus of the sequences in colour-mass and colour-concentration indices not varying strongly with environment. The fraction of galaxies on the red sequence is determined in bins of 0.2 in log Σ and log M (12 x 13 bins). The red fraction f r generally increases continuously in both Σ and M such that there is a unified relation: f, = F(Σ, M). Two simple functions are proposed which provide good fits to the data. These data are compared with analogous quantities in semi-analytical models based on the Millennium N-body simulation: the Bower et al. and Croton et al. models that incorporate active galactic nucleus feedback. Both models predict a strong dependence of the red fraction on stellar mass and environment that is qualitatively similar to the observations. However, a quantitative comparison shows that the Bower et al. model is a significantly better match; this appears to be due to the different treatment of feedback in central galaxies.
On-line learning migration: from social learning theory to social presence theory in a CMC environment

Social presence is one of the most significant factors to examine in distance education. The impact of social presence on learning must be examined because of the prevalence of CMC (computer-mediated communication) in education. Many of the studies dealing with social presence on CMC have been done in standard educational settings and organizational settings. None of them have redefined social presence for CMC. This theory must be operationally understood and clearly defined before knowledgeable studies occur. The relationship between social presence and the social learning theory is also examined in this paper. Social interaction is fundamental to the explanation of this relationship. Social learning requires cognitive and environmental determinants. Social presence is required to enhance and foster on-line social interaction, which is the major vehicle of social learning.
Workplace waste recycling behaviour: a meta-analytical review.

In order to increase waste recycling, many studies have been conducted to understand factors that may influence waste recycling behaviour. However, these studies have focused on household contexts rather than other waste generation contexts. As a result, this paper seeks to provide a detailed analysis of previous studies on workplace waste recycling behaviour. Drawing from different databases, 51 relevant studies on workplace waste recycling attitudes and behaviour were meta-analysed. Findings showed that the highest percentage of the existing studies were conducted in the USA, focused on a single waste stream, were often conducted within academic contexts, adopted (or modified) an existing theoretical framework and were based on questionnaires which elicited self-reported behaviour. Some of the factors identified include demographics, situational variables, past behaviour, incentives, prompts and/or information, attitudes and identity. The findings highlighted the scale of challenges confronting waste management practitioners in understanding the factors that may affect waste recycling behaviour due to the complexity and heterogeneity of human behaviours. However, the results from the reviewed studies in this research suggest that a combination of different factors may be required to influence workplace waste recycling behaviour. This may provide effective incentives to develop a framework that may assist waste management stakeholders when addressing workplace waste management.
Real-Time Variable Center of Mass Height Trajectory Planning for Humanoids Robots

This paper presents a trajectory planner for humanoid robots based on nonlinear model predictive control that can generate trajectories with variable center of mass (COM) heights and adaptive foot positions in real-time. This is done by analytically formulating the zero moment point constraint as a quadratic function that includes the vertical COM state. This constraint is then combined with linear foot position constraints, constraints on the vertical COM state and a quadratic goal function to form a quadratically constrained quadratic program. This program is then solved via sequential quadratic programing. It can be solved in less than 5 ms on average with a 3.4 GHz CPU by taking advantage of the fact that the analytic problem formulation allows the analytical gradients to be computed, thus time consuming numerical differentiation is avoided and the gradient computation time is reduced from 12.4 to 0.12 ms. An experiment on a 3.5 Kg robot is conducted to verify the effectiveness of this algorithm in walking on a terrain where the two feet are at different heights. Lastly it is shown via simulation that the proposed approach can improve disturbance recovery capacity by up to 7%.
Fragments of HdhQ150 Mutant Huntingtin Form a Soluble Oligomer Pool That Declines with Aggregate Deposition upon Aging

Cleavage of the full-length mutant huntingtin (mhtt) protein into smaller, soluble aggregation-prone mhtt fragments appears to be a key process in the neuropathophysiology of Huntington’s Disease (HD). Recent quantification studies using TR-FRET-based immunoassays showed decreasing levels of soluble mhtt correlating with an increased load of aggregated mhtt in the aging HdhQ150 mouse brain. To better characterize the nature of these changes at the level of native mhtt species, we developed a detection method that combines size exclusion chromatography (SEC) and time-resolved fluorescence resonance energy transfer (TR-FRET) that allowed us to resolve and define the formation, aggregation and temporal dynamics of native soluble mhtt species and insoluble aggregates in the brain of the HdhQ150 knock-in mouse. We found that mhtt fragments and not full-length mhtt form oligomers in the brains of one month-old mice long before disease phenotypes and mhtt aggregate histopathology occur. As the HdhQ150 mice age, brain levels of soluble full-length mhtt protein remain similar. In contrast, the soluble oligomeric pool of mhtt fragments slightly increases during the first two months before it declines between 3 and 8 months of age. This decline inversely correlates with the formation of insoluble mhtt aggregates. We also found that the pool-size of soluble mhtt oligomers is similar in age-matched heterozygous and homozygous HdhQ150 mouse brains whereas insoluble aggregate formation is greatly accelerated in the homozygous mutant brain. The capacity of the soluble mhtt oligomer pool therefore seems exhausted already in the heterozygous state and likely kept constant by changes in flux and, as a consequence, increased rate of insoluble aggregate formation. We demonstrate that our novel findings in mice translate to human HD brain but not HD patient fibroblasts.
An Industrial Case Study on the Automated Detection of Performance Regressions in Heterogeneous Environments

A key goal of performance testing is the detection of performance degradations (i.e., regressions) compared to previous releases. Prior research has proposed the automation of such analysis through the mining of historical performance data (e.g., CPU and memory usage) from prior test runs. Nevertheless, such research has had limited adoption in practice. Working with a large industrial performance testing lab, we noted that a major hurdle in the adoption of prior work (including our own work) is the incorrect assumption that prior tests are always executed in the same environment (i.e., labs). All too often, tests are performed in heterogenous environments with each test being run in a possibly different lab with different hardware and software configurations. To make automated performance regression analysis techniques work in industry, we propose to model the global expected behaviour of a system as an ensemble (combination) of individual models, one for each successful previous test run (and hence configuration). The ensemble of models of prior test runs are used to flag performance deviations (e.g., CPU counters showing higher usage) in new tests. The deviations are then aggregated using simple voting or more advanced weighting to determine whether the counters really deviate from the expected behaviour or whether it was simply due to an environment-specific variation. Case studies on two open-source systems and a very large scale industrial application show that our weighting approach outperforms a state-of-the-art environment-agnostic approach. Feedback from practitioners who used our approach over a 4 year period (across several major versions) has been very positive.
Emerging microbiota during cold storage and temperature abuse of ready-to-eat salad

ABSTRACT Introduction: Ready-to-eat (RTE) leafy vegetables have a natural leaf microbiota that changes during different processing and handling steps from farm to fork. The objectives of this study were (i) to compare the microbiota of RTE baby spinach and mixed-ingredient salad before and after seven days of storage at 8°C or 15°C; (ii) to explore associations between bacterial communities and the foodborne pathogens Listeria monocytogenes, pathogenic Yersinia enterocolitica, and pathogen model organism Escherichia coli O157:H7 gfp+ when experimentally inoculated into the salads before storage; and (iii) to investigate if bacterial pathogens may be detected in the 16S rRNA amplicon dataset. Material and methods: The microbiota was studied by means of Illumina 16S rRNA amplicon sequencing. Subsets of samples were inoculated with low numbers (50–100 CFU g−1) of E. coli O157:H7 gfp+, pathogenic Y. enterocolitica or L. monocytogenes before storage. Results and discussion: The composition of bacterial communities changed during storage of RTE baby spinach and mixed-ingredient salad, with Pseudomonadales as the most abundant order across all samples. Although pathogens were present at high viable counts in some samples, they were only detected in the community-wide dataset in samples where they represented approximately 10% of total viable counts. Positive correlations were identified between viable counts of inoculated strains and the abundance of Lactobacillales, Enterobacteriales, and Bacillales, pointing to positive interactions or similar environmental driver variables that may make it feasible to use such bacterial lineages as indicators of microbial health hazards in leafy vegetables. The data from this study contribute to a better understanding of the bacteria present in RTE salads and may help when developing new types of biocontrol agents.
Increasing the Reliability of Human Operator by Combination of Music Therapy with Neurofeedback

The results of human functional state correction by music influences feedback controlled by narrow-band (0.4-0.6 Hz) electroencephalographic (EEG) oscillators of the patient are presented. It is established that the utilization of narrow-band oscillators from the theta (4-8 Hz) and alpha (8-13 Hz) EEG ranges causes a normalization of the EEG, reduction of stress sensations and positive shifts in mental and emotional state of the patient by the end of the first treatment procedure.