Miracle-dz/UniFAR-FTUs huggingface dataset:
Correlating the Transcriptome, Proteome, and Metabolome in the Environmental Adaptation of a Hyperthermophile

We have performed a comprehensive characterization of global molecular changes for a model organism Pyrococcus furiosus using transcriptomic (DNA microarray), proteomic, and metabolomic analysis as it undergoes a cold adaptation response from its optimal 95 to 72 °C. Metabolic profiling on the same set of samples shows the down-regulation of many metabolites. However, some metabolites are found to be strongly up-regulated. An approach using accurate mass, isotopic pattern, database searching, and retention time is used to putatively identify several metabolites of interest. Many of the up-regulated metabolites are part of an alternative polyamine biosynthesis pathway previously established in a thermophilic bacterium Thermus thermophilus. Arginine, agmatine, spermidine, and branched polyamines N 4-aminopropylspermidine and N 4-(N-acetylaminopropyl)spermidine were unambiguously identified based on their accurate mass, isotopic pattern, and matching of MS/MS data acquired under identical conditions for the natural metabolite and a high purity standard. Both DNA microarray and semiquantitative proteomic analysis using a label-free spectral counting approach indicate the down-regulation of a large majority of genes with diverse predicted functions related to growth such as transcription, amino acid biosynthesis, and translation. Some genes are, however, found to be up-regulated through the measurement of their relative mRNA and protein levels. The complimentary information obtained by the various " omics " techniques is used to catalogue and correlate the overall molecular changes.
Treatment Guided by an Online Course

This article describes the successful treatment of a 16-year-old female presenting with chronic posttraumatic stress disorder (PTSD) related to alleged childhood sexual abuse using trauma-focused cognitive behavioral therapy (TF-CBT). Treatment was delivered by a graduate student who learned the treatment through the completion of an online training course and was supervised by a licensed clinical psychologist. Both the student and the supervisor had extensive training and experience in the delivery of cognitive behavioral therapy (CBT) interventions for adolescents. Several challenges were encountered, most notably the reemergence of legal proceedings related to the alleged abuse during the course of treatment. Treatment implications are discussed, including the need to tailor manualized treatments for particular clients and the utility of online training courses. Overall, this case study adds to the limited literature on the treatment of chronic PTSD in adolescents and provides support for the transportability of TF-CBT to practice settings, as well as the dissemination potential of an online course.
Oxidation state governs structural transitions in peroxiredoxin II that correlate with cell cycle arrest and recovery

Inactivation of eukaryotic 2-Cys peroxiredoxins (Prxs) by hyperoxidation has been proposed to promote accumulation of hydrogen peroxide (H2O2) for redox-dependent signaling events. We examined the oxidation and oligomeric states of PrxI and -II in epithelial cells during mitogenic signaling and in response to fluxes of H2O2. During normal mitogenic signaling, hyperoxidation of PrxI and -II was not detected. In contrast, H2O2-dependent cell cycle arrest was correlated with hyperoxidation of PrxII, which resulted in quantitative recruitment of ∼66- and ∼140-kD PrxII complexes into large filamentous oligomers. Expression of cyclin D1 and cell proliferation did not resume until PrxII-SO2H was reduced and native PrxII complexes were regenerated. Ectopic expression of PrxI or -II increased Prx-SO2H levels in response to oxidant exposure and failed to protect cells from arrest. We propose a model in which Prxs function as peroxide dosimeters in subcellular processes that involve redox cycling, with hyperoxidation controlling structural transitions that alert cells of perturbations in peroxide homeostasis.
Extensions of the regenerative method to new functionals

This paper briefly reviews the regenerative method for steady-state simulation, and then shows how regenerative structure can be used computationally to develop new estimators for the spectral density, moments of hitting times, and both discounted and average reward value functions. All our estimators typically exhibit the Monte Carlo method's usual “square root” convergence rate. This is in contrast to the usual sub-square root rate exhibited by, for example, spectral density estimators in the absence of regenerative structure.
Essential role for Abi1 in embryonic survival and WAVE2 complex integrity

Abl interactor 1 (Abi1) plays a critical function in actin cytoskeleton dynamics through participation in the WAVE2 complex. To gain a better understanding of the specific role of Abi1, we generated a conditional Abi1-KO mouse model and MEFs lacking Abi1 expression. Abi1-KO cells displayed defective regulation of the actin cytoskeleton, and this dysregulation was ascribed to altered activity of the WAVE2 complex. Changes in motility of Abi1-KO cells were manifested by a decreased migration rate and distance but increased directional persistence. Although these phenotypes did not correlate with peripheral ruffling, which was unaffected, Abi1-KO cells exhibited decreased dorsal ruffling. Western blotting analysis of Abi1-KO cell lysates indicated reduced levels of the WAVE complex components WAVE1 and WAVE2, Nap1, and Sra-1/PIR121. Although relative Abi2 levels were more than doubled in Abi1-KO cells, the absolute Abi2 expression in these cells amounted only to a fifth of Abi1 levels in the control cell line. This finding suggests that the presence of Abi1 is critical for the integrity and stability of WAVE complex and that Abi2 levels are not sufficiently increased to compensate fully for the loss of Abi1 in KO cells and to restore the integrity and function of the WAVE complex. The essential function of Abi1 in WAVE complexes and their regulation might explain the observed embryonic lethality of Abi1-deficient embryos, which survived until approximately embryonic day 11.5 and displayed malformations in the developing heart and brain. Cells lacking Abi1 and the conditional Abi1-KO mouse will serve as critical models for defining Abi1 function.
MR Imaging of Neoplastic Central Nervous System Lesions: Review and Recommendations for Current Practice

SUMMARY: MR imaging is the preferred technique for the diagnosis, treatment planning, and monitoring of patients with neoplastic CNS lesions. Conventional MR imaging, with gadolinium-based contrast enhancement, is increasingly combined with advanced, functional MR imaging techniques to offer morphologic, metabolic, and physiologic information. This article provides updated recommendations to neuroradiologists, neuro-oncologists, neurosurgeons, and radiation oncologists on the practical applications of MR imaging of neoplastic CNS lesions in adults, with particular focus on gliomas, based on a review of the clinical trial evidence and personal experiences shared at a recent international meeting of experts in neuroradiology, neuro-oncology, neurosurgery, and radio-oncology.
Family Environment and Pediatric Major Depressive Disorder

Background: The risks for depression broadly include biological and environmental factors. Furthermore, having a family member suffering from major depression is also likely to have consequences for the family environment. Further research aimed at understanding the effects of having a child with major depression on family interaction patterns is warranted. Methods: We studied 31 families with an 8- to 17-year-old child (mean age ± SD = 12.9 ± 2.7 years) who met the DSM-IV criteria for major depressive disorder (MDD) and 34 families with no mentally ill children (mean age ± SD = 12.6 ± 2.9 years) or parents. Children and their parents were assessed with the K-SADS-PL (Kiddie Schedule for Affective Disorders and Schizophrenia – Present and Lifetime Version) interview. Parents completed the Moos Family Environment Scale (FES) to assess their perceptions of current family functioning. Data were analyzed using the nonparametric Wilcoxon-Mann-Whitney test. Results: Families of MDD children showed significantly different patterns of family functioning on FES subscales representing relationships and personal growth dimensions. The families with MDD children showed higher levels of conflict (p < 0.001) and lower levels of cohesion (p < 0.001), expressiveness (p = 0.003) and active-recreational orientation (p = 0.02) compared to the families without mentally ill children. Conclusion: Families with MDD children show a lower degree of commitment, provide less support to one another, provide less encouragement to express feelings and have more conflicts compared to families with no mentally ill children or parents. Interventions aimed at improving family dynamics may be beneficial to MDD children and their families.
Assessing agreement between measurements recorded on a ratio scale in sports medicine and sports science.

OBJECTIVE: The consensus of opinion suggests that when assessing measurement agreement, the most appropriate statistic to report is the "95% limits of agreement". The precise form that this interval takes depends on whether a positive relation exists between the differences in measurement methods (errors) and the size of the measurements--that is, heteroscedastic errors. If a positive and significant relation exists, the recommended procedure is to report "the ratio limits of agreement" using log transformed measurements. This study assessed the prevalence of heteroscedastic errors when investigating measurement agreement of variables recorded on a ratio scale in sports medicine and sports science. METHODS: Measurement agreement (or repeatability) was assessed in 13 studies (providing 23 examples) conducted in the Centre for Sport and Exercise Sciences at Liverpool John Moores University over the past five years. RESULTS: The correlation between the absolute differences and the mean was positive in all 23 examples (median r = 0.37), eight being significant (P < 0.05). In 21 of 23 examples analysed, the correlation was greater than the equivalent correlation using log transformed measurements (median r = 0.01). Based on a simple meta-analysis, the assumption that no relation exists between the measurement differences and the size of measurement must be rejected (P < 0.001). CONCLUSIONS: When assessing measurement agreement of variables recorded on a ratio scale in sports medicine and sports science, this study (23 examples) provides strong evidence that heteroscedastic errors are the norm. If the correlation between the absolute measurement differences and the means is positive (but not necessarily significant) and greater than the equivalent correlation using log transformed measurements, the authors recommend reporting the "ratio limits of agreement".
Implementation of load transportation using multiple quadcopters

This paper studies a load transportation problem using two and three quadcopters for outdoor applications. We construct a transportation controller, that consists of a formation controller to track a desired trajectory and a load sharing controller to share the load effects, in a distributed way. Specifically, based on the displacement-based formation and consensus approaches, the formation and load sharing controllers are constructed using only local information, measured by own measurement units and received from neighbors. Experimental results show the validity and the effectiveness of the proposed controller.
Transformation of Social Care Services for the Elderly in Slovakia

ABSTRACT The main objective of this article is to present a theoretical framework for the relevant historical, economic, demographic, and political factors influencing the transformation of social care services for the elderly in Slovakia. A major restructuring of the social care services for the elderly is necessitated by the aging of the Slovak population (demographic reason), the path dependency of the current Slovak elderly care system (historical reason), the growing purchasing power of older people and the general population (economic reason), and new requirements formulated by the European Union and the general public (political reason). Historical documents, legislative acts, strategic documents, international project documents, and statistics were reviewed, and 34 open-ended interviews within the framework of two case studies were carried out in order to obtain qualitative and quantitative data. The theoretical framework and the results based on those interviews indicate that the Slovak social care service for the elderly may turn out to become more similar to the advanced Central European systems, but also that prompt legislative and financial changes are required. Nevertheless, the future direction can only be more precisely identified when more case studies can be compared with one another.
On Non-automatizability in PAC-Semantics

We consider the proof search (“automatizability”) problem for integrated learning and reasoning, a problem modeling certain kinds of data mining and common sense reasoning [14]. In such a problem, the approximate validity (i.e., under Valiant’s PAC-Semantics [24]) of an input query formula over a background probability distribution is verified using incomplete examples from the distribution; queries featuring a proof from some learnable premises are distinguished from queries that are falsified with moderately high probability under the distribution. The introduction of tolerance for some approximation and examples from the target distribution raise the possibility that this problem may be easier than classical automatizability in many circumstances. In particular, for certain restricted distributions and information-masking processes, the automatizability problem for resolution can be solved in quasipolynomial time [15]. Nevertheless, we argue here that the known cryptographic non-automatizability results [18, 8, 7] carry over to even the highly restricted kinds of distributions considered in that work.
'Pure' constructional apraxia - a cognitive analysis of a single case.

We report on a patient affected by selective drawing disabilities. The patient could correctly reproduce and draw simple geometric figures on request, but when he tried to reproduce more complex drawings or to draw common objects he performed very poorly. To identify the cognitive impairment in this patient, we adopted two test batteries based on recent information-processing models of drawing. Results showed that the patient's drawing disabilities were independent of visuo-perceptual and executive impairments. These findings support recent cognitive models of drawing abilities: some intermediate stages of drawing exist at which information is processed to prepare and guide motor output, and which may be selectively disrupted after discrete cerebral lesions.
Antiaggregative Aspirin Dosage at the Affected Vessel Wall

The present study, using patients with Thkayasu's disease (pulseless disease), characterized by segmentally affected arterial lesions and stenotic conditions with a nonspecific inflammatory morbid condition, was designed to assess whether or not a low dose of aspirin can practically exert its preventive effect against the aggregation of platelets that have just passed along a rough-surfaced arterial wall. Twenty Japanese women with Takayasu's disease were selected under the following criteria: (1) A unilateral upper extremity was angiographi cally confirmed to be affected with the disease, while the contralateral limb was almost normal. (2) Systolic blood pressure on the affected side was almost half that on the nonaffected side. (3) The patients showed neither a positive CRP nor an accentuated ESR. In these patients, mean plasma levels of TXB2 and 3 μM ADP-induced platelet aggregation in blood obtained from the affected side were 156.5±17.7 pg/ml, and 59.5 ±6.0%, respectively, which were significantly high as compared with 104.5±17.6 and 41.7±8.8%, respectively, in samples from the nonaffected side. Forty and eighty mg of aspirin per day administered to two randomly composed groups, respectively, showed an improvement in plate let aggregability and TXB2 levels on the nonaffected side. In the affected limbs, though 80 mg/day led to significant decreases in TXB2 levels (108.0 ±7.8 pg/ml, p < 0.05) and platelet aggregability (21.3±7.6%), the 40-mg regimen showed no significant reductions (134.6±9.4 pg/ml, 35.6±17.1%). Plasma levels of 6-keto PGF1α revealed no differences between 40- and 80-mg regimens, or between before and after treatment. These data suggest that a dosage of 80 mg of aspirin per day is effective for long-term treatment in preventing thrombus formation in surface-damaged blood vessels.
Bayesian Network Models for Web Effort Prediction: A Comparative Study

The objective of this paper is to compare, using a cross-company dataset, several Bayesian network (BN) models for Web effort estimation. Eight BNs were built; four automatically using Hugin and PowerSoft tools with two training sets, each with 130 Web projects from the Tukutuku database; four using a causal graph elicited by a domain expert, with parameters automatically fit using the same training sets used in the automated elicitation (hybrid models). Their accuracy was measured using two validation sets, each containing data on 65 projects, and point estimates. As a benchmark, the BN-based estimates were also compared to estimates obtained using manual stepwise regression (MSWR), case-based reasoning (CBR), mean- and median-based effort models. MSWR presented significantly better predictions than any of the BN models built herein, and in addition was the only technique to provide significantly superior predictions to a median-based effort model. This paper investigated data-driven and hybrid BN models using project data from the Tukutuku database. Our results suggest that the use of simpler models, such as the median effort, can outperform more complex models, such as BNs. In addition, MSWR seemed to be the only effective technique for Web effort estimation.
Designing a Clinical Framework to Guide Gross Motor Intervention Decisions for Infants and Young Children With Hypotonia

Clinical practice frameworks are a valuable component of clinical education, promoting informed clinical decision making based on the best available evidence and/or clinical experience. They encourage standardized intervention approaches and evaluation of practice. Based on an international project to support the development of an enhanced service system for infants and young children with neuromotor disabilities in Guangzhou, China, this article describes the processes used to develop a practice framework to guide therapists' intervention choices to encourage the gross motor abilities of infants and children (0–3 years of age) exhibiting hypotonia and gross motor delays. The goal was to provide a practice framework that aligns with contemporary interest in activity-focused intervention approaches and that considers both a child's abilities and the influence of environmental context in the achievement of gross motor skills. The final product, the Hypotonia Wheel, is presented. It may be useful for therapists and early intervention providers who work with infants and young children with hypotonia. The process used to design the Hypotonia Wheel also could be used as a template to develop intervention guidelines for other clinical conditions.
Mitigation of mitochondrial dysfunction and regulation of eNOS expression during experimental myocardial necrosis by alpha-mangostin, a xanthonic derivative from Garcinia mangostana

Oxidative stress can play a key role in myocardial necrosis. The present study was designed to investigate the effect of alpha-mangostin (an antioxidant phytonutrient) on mitochondrial dysfunction and endothelial nitric oxide synthase (eNOS) expression during isoproterenol-induced myocardial necrosis in rats. Induction of rats with isoproterenol (ISO) (150 mg/kg body weight, intraperitoneally) for 2 days resulted in a significant decrease in the activities of respiratory chain enzymes (NADH dehydrogenase and cytochrome c oxidase), tricarboxylic acid cycle enzymes (isocitrate dehydrogenase, succinate dehydrogenase, malate dehydrogenase, and alpha-ketoglutarate dehydrogenase), mitochondrial antioxidants (GPx, GST, SOD, CAT, and GSH), mitochondrial cytochromes (b, c, c1, and aa3), and adenosine triphosphate level. A marked elevation in mitochondrial lipid peroxidation was also observed in ISO-intoxicated rats. Pretreatment with alpha-mangostin (200 mg/kg body weight) orally for 8 days significantly attenuated these functional abnormalities and restored normal mitochondrial function, when compared to the ISO-intoxicated group of rats. Cardiac eNOS expression was assessed by Western blot. Cardiac eNOS expression and NO level were significantly suppressed in ISO-intoxicated rats. Pretreatment with alpha-mangostin extenuated ISO-induced diminution of eNOS expression and NO level. Transmission electron microscopic observations also correlated with these biochemical parameters. Hence, these findings conclude the ameliorative potential of alpha-mangostin against ISO-induced biochemical and morphological changes in mitochondria, which might be mediated through the NO pathway and by its ability at quenching free radicals.
Parenting, Attachment Security and Adjustment Outcomes: The Role of Nonshared Environment

A great deal of research has focussed on uncovering the antecedents of human behaviour. Studies have implicated parenting as having a fundamental impact on the developmental trajectories of children from the moment they are born, through infancy, adolescence, and their journey to adulthood. This thesis will explore the relationship between parenting and outcomes for children through to adolescence. Part one is a review of the literature examining the evidence for the association between differential parenting and differential adjustment outcomes in externalizing behaviour, internalizing behaviour, temperament, social, and cognitive domains. The review addresses the key question, ‘is differential parenting associated with differential outcomes for children growing up in the same family? ’. Part two of the thesis presents the empirical paper for a cross-sectional study observing the association between relative differences in parenting and relative differences in attachment security in a sample of monozygotic twins. The study used a monozygotic twin difference design to also examine differences in parenting and differences in adjustment outcomes in the sample, as well as differences in attachment security and adjustment outcomes. Part three is a critical appraisal of the research, reflecting on the process of the preparation, formation and conducting of the study. The impact of the design and methods on the findings are considered, as well as the researchers’ subjectivity.
Auditory filter shape.

Threshold for a pulsed tone was measured as a function of its distance in frequency from the edge of a broad band of noise with very sharp skirts. Tone frequency was held constant at 0.5, 1.0, 2.0, 4.0, or 8.0 kHz while the position of the noise edge was varied about the frequency of the tone. The spectrum level of the noise was 40 dB. As expected, tone threshold decreased as the distance between the tone and the noise edge increased, and the rate of decrease was inversely related to tone frequency. The data were used in conjunction with a simple model of masking to derive an estimate of the shape of the auditory filter. A mathematical expression was found to describe the filter, and subsequently, this expression was used to predict the results reported by several other investigators.