Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptive psychophysical procedures and Ulam's game

The problem of finding the threshold of a psychometric function is of major interest to researchers in the field of psychophysics, and has applications in many areas of medical diagnosis, particularly those dealing with perception, such as optometry and hearing tests. This problem is closely related to other problems in computer science, such as search with errors, however most existing literature does not make this link. This thesis provides a review of existing algorithms for finding the threshold, with an emphasis on identifying the types of problems for which each algorithm is useful. We also address a number of issues which are not adequately covered in the literature. These include choosing an appropriate loss function to evaluate the performance of an algorithm for a given problem, as well as relating the problem of finding the threshold to binary search with errors problems in computer science. Finally, this research presents a new algorithm for finding the threshold of a psychometric function, EntFirst, which results in improved performance compared to many existing algorithms.
Cigarette Smoke Modulates Vascular Smooth Muscle Phenotype: Implications for Carotid and Cerebrovascular Disease

Background The role of smooth muscle cell (SMC) phenotypic modulation in the cerebral circulation and pathogenesis of stroke has not been determined. Cigarette smoke is a major risk factor for atherosclerosis, but potential mechanisms are unclear, and its role in SMC phenotypic modulation has not been established. Methods and Results In cultured cerebral vascular SMCs, exposure to cigarette smoke extract (CSE) resulted in decreased promoter activity and mRNA expression of key SMC contractile genes (SM-α-actin, SM-22α, SM-MHC) and the transcription factor myocardin in a dose-dependent manner. CSE also induced pro-inflammatory/matrix remodeling genes (MCP-1, MMPs, TNF-α, IL-1β, NF-κB). CSE increased expression of KLF4, a known regulator of SMC differentiation, and siKLF4 inhibited CSE induced suppression of SMC contractile genes and myocardin and activation of inflammatory genes. These mechanisms were confirmed in vivo following exposure of rat carotid arteries to CSE. Chromatin immune-precipitation assays in vivo and in vitro demonstrated that CSE promotes epigenetic changes with binding of KLF4 to the promoter regions of myocardin and SMC marker genes and alterations in promoter acetylation and methylation. Conclusion CSE exposure results in phenotypic modulation of cerebral SMC through myocardin and KLF4 dependent mechanisms. These results provides a mechanism by which cigarette smoke induces a pro-inflammatory/matrix remodeling phenotype in SMC and an important pathway for cigarette smoke to contribute to atherosclerosis and stroke.
Obstructive sleep apnea and objective short sleep duration are independently associated with the risk of serum vitamin D deficiency

Background Studies demonstrate an association between vitamin D (25(OH)D) deficiency and sleep disturbances, such as obstructive sleep apnea (OSA) and short sleep duration. However, to date, no studies have concurrently and objectively evaluated the effect of these factors on 25(OH)D. Objectives To evaluate whether OSA and objective short sleep duration are independently associated with reduced 25(OH)D in an adult population sample. Methods A cross-sectional study included 657 individuals from the city of Sao Paulo, Brazil, as part of the ERA project. Participants fulfilled questionnaires and underwent clinical evaluation, polysomnography and blood sample collection for 25(OH)D quantification. OSA was classified into three categories (mild, moderate and severe). The risk of 25(OH)D deficiency was considered as levels<30 ng/mL. Short sleep duration was defined as total sleep time<6 hours. Results The risk of 25(OH)D deficiency was observed in 59.5% of the sample, affecting more individuals of the female gender, obese, with African American ethnicity, and those that were smokers, sedentary and presented hypertension and diabetes. In the final logistic model adjusted for age, gender, ethnicity, obesity, smoking, hypertension, diabetes, sedentary lifestyle, seasonality and creatinine serum levels, both OSA and short sleep duration showed significant independent associations with the risk of 25(OH)D deficiency (moderate OSA: OR for 25(OH)D<30 = 2.21, 95% CI: 1.35–3.64, p<0.01; severe OSA: OR for 25(OH)D<30 = 1.78, 95% CI: 1.06–3.00, p = 0.03; short sleep duration: OR for 25(OH)D<30 = 1.61, 95% CI: 1.15–2.26, p = 0.01). After a subgroup analysis, similar results were observed only in participants ≥50 years. Conclusion OSA and short sleep duration are independently associated with the risk of 25(OH)D deficiency in an adult population. Age-related changes in vitamin D metabolism and the frequency of sleep disorders may be involved in these associations. Future studies exploring whether 25(OH)D levels may modulate OSA and sleep curtailment-related outcomes are needed.
Understanding how Deep Belief Networks perform acoustic modelling

Deep Belief Networks (DBNs) are a very competitive alternative to Gaussian mixture models for relating states of a hidden Markov model to frames of coefficients derived from the acoustic input. They are competitive for three reasons: DBNs can be fine-tuned as neural networks; DBNs have many non-linear hidden layers; and DBNs are generatively pre-trained. This paper illustrates how each of these three aspects contributes to the DBN's good recognition performance using both phone recognition performance on the TIMIT corpus and a dimensionally reduced visualization of the relationships between the feature vectors learned by the DBNs that preserves the similarity structure of the feature vectors at multiple scales. The same two methods are also used to investigate the most suitable type of input representation for a DBN.
Determination of Fracture Strength in Orthotropic Graphite-Epoxy Laminates

A fracture test program performed on orthotropic graphite-epoxy laminates is reported. The test data are used to evaluate the effects of specimen size and specimen configuration on the measured value of laminate fracture strength. It is shown that apparent fracture strength is independent of specimen configuration and specimen thickness, but varies significantly with respect to crack length. As crack length increases, however, the apparent fracture strength is found to asymptotically approach a limiting value, taken to be the valid laminate fracture toughness. The test data are also used to evaluate two analytical models for predicting laminate fracture toughness. The first model links basic ply properties and the fracture toughness of angle-ply laminates, while the second model relates the fracture toughness of an arbitrary orthotropic laminate to the fracture properties of its angle-ply components. Both models show good agreement with the test data. It is concluded that linear elastic fracture mechanics does provide a meaningful characterization of crack growth in orthotropic composite laminates, if some specified conditions are met. Study of cases which do not meet these conditions is recommended for future work.
The Fur Transcription Regulator and Fur-Regulated Genes in Clostridium botulinum A ATCC 3502

Clostridium botulinum is a spore-forming bacterium that can produce a very powerful neurotoxin that causes botulism. In this study, we have investigated the Fur transcription regulators in Clostridium botulinum and Fur-regulated genes in Clostridium botulinum A ATCC 3502. We found that gene loss may be the main cause leading to the different numbers of Fur transcription regulators in different Clostridium botulinum strains. Meanwhile, 46 operons were found to be regulated by the Fur transcription regulator in Clostridium botulinum A ATCC 3502, involved in several functional classifications, including iron acquisition, iron utilization, iron transport, and transcription regulator. Under an iron-restricted medium, we experimentally found that a Fur transcription regulator (CBO1372) and two operons (DedA, CBO2610–CBO2614 and ABC transporter, CBO0845–CBO0847) are shown to be differentially expressed in Clostridium botulinum A ATCC 3502. This study has provided-us novel insights into the diversity of Fur transcription regulators in different Clostridium botulinum strains and diversity of Fur-targeted genes, as well as a better understanding of the dynamic changes in iron restriction occurring in response to this stress.
A Randomized Controlled Pilot Study of Home-Based Step Training in Older People Using Videogame Technology

Background Stepping impairments are associated with physical and cognitive decline in older adults and increased fall risk. Exercise interventions can reduce fall risk, but adherence is often low. A new exergame involving step training may provide an enjoyable exercise alternative for preventing falls in older people. Purpose To assess the feasibility and safety of unsupervised, home-based step pad training and determine the effectiveness of this intervention on stepping performance and associated fall risk in older people. Design Single-blinded two-arm randomized controlled trial comparing step pad training with control (no-intervention). Setting/Participants Thirty-seven older adults residing in independent-living units of a retirement village in Sydney, Australia. Intervention Intervention group (IG) participants were provided with a computerized step pad system connected to their TVs and played a step game as often as they liked (with a recommended dose of 2–3 sessions per week for 15–20 minutes each) for eight weeks. In addition, IG participants were asked to complete a choice stepping reaction time (CSRT) task once each week. Main Outcome Measures CSRT, the Physiological Profile Assessment (PPA), neuropsychological and functional mobility measures were assessed at baseline and eight week follow-up. Results Thirty-two participants completed the study (86.5%). IG participants played a median 2.75 sessions/week and no adverse events were reported. Compared to the control group, the IG significantly improved their CSRT (F31,1 = 18.203, p<.001), PPA composite scores (F31,1 = 12.706, p = 0.001), as well as the postural sway (F31,1 = 4.226, p = 0.049) and contrast sensitivity (F31,1 = 4.415, p = 0.044) PPA sub-component scores. In addition, the IG improved significantly in their dual-task ability as assessed by a timed up and go test/verbal fluency task (F31,1 = 4.226, p = 0.049). Conclusions Step pad training can be safely undertaken at home to improve physical and cognitive parameters of fall risk in older people without major cognitive and physical impairments. Trial Registration Australian New Zealand Clinical Trials Registry ACTRN12611001081909.
Rapid antimicrobial susceptibility testing of isolates from blood cultures by direct inoculation and early reading of disk diffusion tests

Disk diffusion tests, inoculated directly from positive blood cultures, were evaluated for accuracy of reading zone diameters after 4- and 6-h and overnight incubation. In comparisons with results from standard disk diffusion tests, the 4-h results were in agreement for 83% of tests with gram-positive organisms and 64% of tests with gram-negative organisms. When minor discrepancies were ignored, the 4-h readings were in agreement for 98% of the tests with gram-positive organisms and 95% of the tests with gram-negative organisms. After 6 h of incubation, 91% of the tests with gram-positive organisms and 86% of the tests with gram-negative organisms agreed with standard results. The agreement was 99% for tests with both gram-positive and gram-negative organisms when minor discrepancies were excluded. Very major discrepancies occurred in two tests (0.1%) with gram-positive organisms and were not observed in tests with gram-negative organisms. The frequencies of major discrepancies were 3.5% after 4 h, 0.6% after 6 h, and 0.7% after overnight incubation. Ampicillin and cephalothin tests with Escherichia coli and Klebsiella spp. accounted for 81% of the major discrepancies in tests with gram-negative organisms. Oxacillin tests accounted for more than half of the major discrepancies in tests with staphylococci. The results of this study, which did not include the newer antibiotics, indicate that direct susceptibility tests from blood cultures read after 6 h of incubation are more reliable than 4-h results and produce less than 1% major errors in comparisons with standard susceptibility tests.
Algorithms for data streams Camil Demetrescu

Data stream processing has gained increasing popularity in the last few years as an effective paradigm for processing massive data sets. A wide range of applications in computational sciences generate huge and rapidly changing data streams that need to be continuously monitored in order to support exploratory analyses and to detect correlations, rare events, fraud, intrusion, unusual or anomalous activities. Relevant examples include monitoring network traffic, online auctions, transaction logs, telephone call records, automated bank machine operations, atmospheric and astronomical events. Due to the high sequential access rates of modern disks, streaming algorithms can also be effectively deployed for processing massive files on secondary storage, providing new insights into the solution of several computational problems in external memory. Streaming models constrain algorithms to access the input data in one or few sequential passes, using only a small amount of working memory and processing each input item quickly. Solving computational problems under these restrictions poses several algorithmic challenges. This chapter is intended as an overview and survey of the main models and techniques for processing data streams and their applications. Dipartimento di Informatica e Sistemistica, Università di Roma “La Sapienza”, Roma, Italy. Email: demetres@dis.uniroma1.it. URL: http://www.dis.uniroma1.it/~demetres. Dipartimento di Informatica, Università di Roma “La Sapienza”, Roma, Italy. Email: finocchi@di.uniroma1.it. URL: http://www.dsi. uniroma1.it/~finocchi.
Inter-twin Relationships and Mental Health

Abstract We evaluated dominance-submissiveness between co-twins and its relationship to mental health in a cohort study of 419 twins followed from pregnancy to 22–30 years of age. Dominance-submissiveness between co-twins was assessed from three separate perspectives: physical dominance, psychological dominance, and verbal dominance. Depressive, nervous, and psychosomatic symptoms were analyzed in different twin groups. In the physical domain, males were more commonly dominant than females at school age and in adulthood. Before and at school age, girls were more dominant than boys in the psychological and verbal domains, as well as in total dominance. These differences disappeared in adulthood, and 81% of adult twins felt themselves equal to their co-twin in total dominance. Submissiveness in the psychological domain seemed to be associated with increased depressiveness, nervous complaints and psychosomatic symptoms in males of male-female twin pairs. Verbally submissive males in same-sex twin pairs had more depression and psychosomatic symptoms. Among females of same-sex twin pairs, submissiveness in the psychological domain was most clearly associated with depressive symptoms, whereas psychological or verbal dominance-submissiveness among females from male-female twin pairs was not associated with symptoms. Psychologically dominant males and females of same-sex twin pairs expressed greater nervousness than did their co-twins. We conclude that being submissive, especially in the psychological domain, to a female twin partner seems to be stressful, whereas it is easier, especially for females, to be submissive to a male twin partner.
Seasonality of Clostridium difficile infections in Southern Germany

SUMMARY Between 2000 and 2009, the total number of patients with Clostridium difficile infections increased considerably in Southeastern Germany. A clear seasonality was observed with a higher number of affected patients occurring in the winter months (January–March). Moxifloxacin and erythromycin-resistant C. difficile PCR ribotypes 001 (72%) and 027 (4·6%) were the most commonly isolated strains.
Examining the Impact of Skin Lighteners In Vitro

Three cosmetically important skin lightening agents, hydroquinone (HQ), kojic acid (KA), and niacinamide (NA), consume the bulk of successful skin lightening ingredients in cosmetic applications. However, the mechanisms by which these ingredients work are still unclear. In this study, melanocytes and keratinocytes were treated with high, nontoxic doses of HQ, KA, and NA and the cells were examined by human microarrays and protein assays for several important targets including cytotoxicity, melanin expression, tyrosinase gene (TYR) and protein expression, melanocortin-1 receptor (MC1R) gene and protein expression, cytochrome c oxidase-1 (COX1) gene and protein expression, and ferritin (FTH1) gene and protein expression. It was found that all the skin lighteners examined showed marked increases in TYR, COX1, and FTH1 gene and protein expression, but not in MC1R expression in melanocytes. Upregulation of COX1 and FTH1 genes and proteins was common across both cell lines, melanocytes and keratinocytes. The results of the tyrosinase expression were somewhat unexpected. The role of iron in the expression of melanin is somewhat unexplored, but common and strong upregulation of ferritin protein in both types of cells due to the treatments suggests that iron plays a more pivotal role in melanin synthesis than previously anticipated.
Constitutive modelling of municipal solid waste

Design of landfills must consider both stability and integrity of the lining system. Therefore, stresses and strains in both mineral and geosynthetic lining materials must be controlled. Interaction between waste and barrier system is of particular importance for assessing the stability and structural integrity of steep non-self supporting barrier systems. The most appropriate approach to assess the interaction is the use of numerical modelling techniques, and therefore an appropriate constitutive model for waste material is required to represent its mechanical behaviour. In a literature review the key aspects of mechanical behaviour of municipal solid waste (MSW) were investigated, including the influence of compressible and reinforcing particles on compression and shear behaviour of MSW were identified. Constitutive modelling of both MSW and soil material were reviewed, based on which the methodology for this study have been developed. In addition, requirements of an appropriate constitutive model for MSW have been suggested from the numerical modelling experience, and a framework to develop a constitutive model for MSW was produced. A one-dimensional compression model was developed by including the influence of compressible particles on MSW compression behaviour. One-dimensional compression tests on both real and synthetic waste samples were modelled and the results have shown that the compression model can reproduce the measured behaviour. A fibre reinforcing model was developed by including the influence of reinforcing particles on MSW shear behaviour. A triaxial compression test on fibre reinforced sand was modelled and the results have shown that the reinforcing model can predict its shear strength. A constitutive model for MSW has been developed by combining the Modified Cam-Clay with the one-dimensional compression and the fibre reinforcing models. Typical MSW triaxial compression tests have been modelled and the results have shown that the MSW model can reproduce the stress-strain behaviour in specific strain ranges. The constitutive model for MSW has been coded into a non-linear elasto-plastic finite element method program. Comparisons between the finite element analysis results and the analytical solutions have been performed and good agreements have been obtained.
Al-doped MgZnO/p-AlGaN heterojunction and their application in ultraviolet photodetectors

In this study, n-type Al-doped MgxZn1-xO (AMZO) films were deposited onto p-Al0.08Ga0. 92N by using radiofrequency magnetron sputtering followed by annealing at 800°C in nitrogen ambient for 60 s. The film was highly transparent and had transmittances exceeding 95% in the visible region and a sharp absorption edge visible in the ultraviolet region. A high leakage current was obtained in the current-voltage (I-V) characteristics of the GMZO/AlGaN n-p junction diode. The AMZO/AlGaN photodetector based on the AMZO film exhibited a dark current of 1.56 μA at Vbias = -3V. The peak responsivity of the photodetector was approximately 200 nm and a cutoff wavelength was observed at approximately 250 nm.
THE THIRD GRAVITATIONAL LENSING ACCURACY TESTING (GREAT3) CHALLENGE HANDBOOK

The GRavitational lEnsing Accuracy Testing 3 (GREAT3) challenge is the third in a series of image analysis challenges, with a goal of testing and facilitating the development of methods for analyzing astronomical images that will be used to measure weak gravitational lensing. This measurement requires extremely precise estimation of very small galaxy shape distortions, in the presence of far larger intrinsic galaxy shapes and distortions due to the blurring kernel caused by the atmosphere, telescope optics, and instrumental effects. The GREAT3 challenge is posed to the astronomy, machine learning, and statistics communities, and includes tests of three specific effects that are of immediate relevance to upcoming weak lensing surveys, two of which have never been tested in a community challenge before. These effects include many novel aspects including realistically complex galaxy models based on high-resolution imaging from space; a spatially varying, physically motivated blurring kernel; and a combination of multiple different exposures. To facilitate entry by people new to the field, and for use as a diagnostic tool, the simulation software for the challenge is publicly available, though the exact parameters used for the challenge are blinded. Sample scripts to analyze the challenge data using existing methods will also be provided. See http://great3challenge.info and http://great3.projects. phys.ucl. ac.uk/leaderboard/ for more information.
Value of therapeutic drug monitoring of MMF therapy in pediatric transplantation *

Abstract: Therapeutic drug monitoring (TDM) is desirable whenever the desired drug effect cannot be predicted from a given dose, or when it is necessary to find a balance between the efficacy and toxicity of the drug. Children and adolescents particularly benefit from TDM, because dosing requirements are often not studied in the same detail as in adults. Also, drug‐drug interactions are frequent. The gold standard for assessment of drug exposure is the area‐under‐the‐curve (AUC) for a full pharmacokinetic profile. TDM for mycophenolic acid (MPA) is less well established. Monitoring of trough levels does not suffice because of enterohepatic recirculation of MPA after formation of its main metabolite, a glucoronide termed MPA‐G. However, abbreviated sampling schemes specific to mycophenolate mofetil (MMF) correlate well with the AUC for MPA. Cyclosporine interacts with MPA by inhibiting the multidrug resistance‐associated protein 2 (MRP2). Higher MPA concentrations result in a decreased two h concentration of cyclosporine, while higher cyclosporine exposure results in a lower MPA exposure. There are no drug interactions between tacrolimus and MPA, and lower doses of MMF are required in combination with tacrolimus. Steroids may induce the clearance of MPA, which could account in part for the increasing MPA exposure following transplantation. TDM has allowed for dosing recommendations of MMF in children, which could lead to improved efficacy and minimization of toxicities. It is important that these provisional target levels are validated in prospective studies. The above points clearly indicate that there is a role for TDM of MPA in pediatric transplant recipients.