Miracle-dz/UniFAR-FTUs huggingface dataset:
A portable instrument for measuring macular pigment with central fixation

Purpose. To evaluate the reliability and validity of a portable instrument for measuring macular pigment optical density. Methods. The instrument is small, uses light emitting diodes as light sources and the principles of heterochromatic flicker photometry of comparing foveal and extra-foveal minimum flicker matches. It uses central fixation for the extra-foveal matches, which subjects found easier than eccentric fixation. Subjects with healthy eyes used the instrument to measure their pigment density in a number of eye clinics. Results. The mean pigment density in 124 eyes in 124 individuals was 0.41 ± 0.16 (mean ± SD), there was no significant change with age but the density was less in females, those with light irides, smokers, subjects on diets low in precursor carotenoids and in those exposed to several hours of daylight every day or who used sun beds. Conclusions. The portable instrument gave valid and reliable data that confirmed published values for macular pigment. It was convenient to use in the clinic and has potential as a screening tool.
Repetition of self-harm and suicide following self-harm in children and adolescents: findings from the Multicentre Study of Self-harm in England.

BACKGROUND Self-harm (intentional self-poisoning and self-injury) in children and adolescents is often repeated and is associated with increased risk of future suicide. We have investigated factors associated with these outcomes. METHOD We used data collected in the Multicentre Study of Self-harm in England on all self-harm hospital presentations by individuals aged 10-18 years between 2000 and 2007, and national death information on these individuals to the end of 2010. Cox hazard proportional models were used to identify independent and multivariable predictors of repetition of self-harm and of suicide. RESULTS Repetition of self-harm occurred in 27.3% of individuals (N = 3920) who presented between 2000 and 2005 and were followed up until 2007. Multivariate analysis showed that repetition was associated with age, self-cutting, and previous self-harm and psychiatric treatment. Of 51 deaths in individuals who presented between 2000 and 2007 and were followed up to 2010 (N = 5133) half (49.0%) were suicides. The method used was usually different to that used for self-harm. Multivariate analysis showed that suicide was associated with male gender [Hazard ratio (HR) = 2.4, 95% CI 1.2-4.8], self-cutting (HR = 2.1, 95% CI 1.1-3.7) and prior psychiatric treatment at initial presentation (HR = 4.2, 95% CI 1.7-10.5). It was also associated with self-cutting and history of psychiatric treatment at the last episode before death, and history of previous self harm. CONCLUSIONS Self-cutting as a method of self-harm in children and adolescents conveys greater risk of suicide (and repetition) than self-poisoning although different methods are usually used for suicide. The findings underline the need for psychosocial assessment in all cases.
Communication and quality of life outcomes from an interprofessional intensive, comprehensive, aphasia program (ICAP)

Background: Intensive Comprehensive Aphasia Programs (ICAPs) have developed in response to a growing need for treatments which produce changes in language function in people with aphasia, especially in the chronic phase of recovery. ICAPs are growing in number and several papers have presented preliminary results of their use, but little data exist about their efficacy or effectiveness. Objective: This paper explores the communication effects of an ICAP program that incorporated evidenced-based individual and group treatment in an interprofessional program. Method: Twenty-seven individuals with chronic aphasia were provided with 30 h of interprofessional treatment a week for a four-week period in both individual and group formats. A delayed treatment, within-participant research protocol was used. Language measures were taken at two intervals pre- and two intervals post treatment. Functional, narrative, and quality of life measures were taken once pre and once post treatment. Results: Significant change was observed on targeted language functions post treatment. Significant treatment effects were also observed on functional and quality of life measures as well as on all impairment-based language measures for the group. Conclusion: The results provide evidence of linguistic and quality of life change in individuals with chronic aphasia who were treated in an interprofessional ICAP.
Epigenetic Therapy: Novel Translational Implications for Arrest of Environmental Dioxin-Induced Disease in Females

Increased toxicant exposure and resultant environmentally induced diseases are a tradeoff of industrial productivity. Dioxin [2,3,7,8 tetrachlorodibenzo-p-dioxin (TCDD)], a ubiquitous byproduct, is associated with a spectrum of diseases including endometriosis, a common, chronic disease in women. TCDD activates cytochrome (CYP) p450 metabolic enzymes that alter organ function to cause disease. In contrast, the transcription factor, Krüppel-like factor (KLF) 11, represses these enzymes via epigenetic mechanisms. In this study, we characterized these opposing mechanisms in vitro and in vivo as well as determining potential translational implications of epigenetic inhibitor therapy. KLF11 antagonized TCDD-mediated activation of CYP3A4 gene expression and function in endometrial cells. The repression was pharmacologically replicated by selective use of an epigenetic histone acetyltransferase inhibitor (HATI). We further showed phenotypic relevance of this mechanism using an animal model for endometriosis. Fibrotic extent in TCDD-exposed wild-type animals was similar to that previously observed in Klf11-/- animals. When TCDD-exposed animals were treated with a HATI, Cyp3 messenger RNA levels and protein expression decreased along with disease progression. Fibrotic progression is ubiquitous in environmentally induced chronic, untreatable diseases; this report shows that relentless disease progression can be arrested through targeted epigenetic modulation of protective mechanisms.
The occurrence and impact of bacterial organisms complicating critical care illness associated with 2009 influenza A(H1N1) infection.

BACKGROUND Although secondary infections are recognized as a cause of morbidity and mortality in seasonal influenza, their frequency, characteristics, and associated clinical outcomes in 2009 influenza A(H1N1) (A[H1N1])-related critical illness are unknown. METHODS In a prospective cohort of adult patients admitted to Canadian ICUs with influenza A(H1N1) infection, the frequency and associated clinical outcomes of prevalent (culture taken within 72 h of ICU admission) and ICU-acquired (culture taken after 72 h from ICU admission) positive bacterial cultures were determined. RESULTS Among 681 patients, the mean age was 47.9 years (SD, 15.1), APACHE (Acute Physiology and Chronic Health Examination) II score was 21.0 (9.9), and 573 patients (84.0%) were invasively mechanically ventilated. Positive cultures were obtained in 259 patients (38.0%): 77 (29.7%) had prevalent, 115 (44.4%) had ICU-acquired, and 40 (15.4%) had both; culture date was unavailable in 27 (10.4%). The most common bacterial organisms isolated were coagulase-negative staphylococci, Staphylococcus aureus, Pseudomonas species, and Streptococcus pneumoniae. Antibiotics were prescribed in 661 (97.1%), with 3.8 (1.9) prescriptions per patient. Patients with any positive culture had longer days of mechanical ventilation (mean [SD], 15.2 [10.7] vs 10.7 [9.0]; P<.0001), ICU stay (median [interquartile range (IQR)], 18.2 [12.5] days vs 10.8 [9.0] days, P<. 0001), and hospitalization (median [IQR], 30.7 [20.7] days vs 19.2 [17.4] days, P<.0001) and a trend toward increased hospital mortality (25.1% vs 19.9%, P=.15). Patients with ICU-acquired positive cultures had worse outcomes compared with those with positive prevalent cultures or who were culture-negative. CONCLUSION Culture-based evidence of secondary infections commonly complicates A(H1N1)-related critical illness and is associated with worse clinical outcomes despite nearly ubiquitous antibiotic administration.
Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel disease

Objective An inadequate host response to the intestinal microbiota likely contributes to the manifestation and progression of human inflammatory bowel disease (IBD). However, molecular approaches to unravelling the nature of the defective crosstalk and its consequences for intestinal metabolic and immunological networks are lacking. We assessed the mucosal transcript levels, splicing architecture and mucosa-attached microbial communities of patients with IBD to obtain a comprehensive view of the underlying, hitherto poorly characterised interactions, and how these are altered in IBD. Design Mucosal biopsies from Crohn's disease and patients with UC, disease controls and healthy individuals (n=63) were subjected to microbiome, transcriptome and splicing analysis, employing next-generation sequencing. The three data levels were integrated by different bioinformatic approaches, including systems biology-inspired network and pathway analysis. Results Microbiota, host transcript levels and host splicing patterns were influenced most strongly by tissue differences, followed by the effect of inflammation. Both factors point towards a substantial disease-related alteration of metabolic processes. We also observed a strong enrichment of splicing events in inflamed tissues, accompanied by an alteration of the mucosa-attached bacterial taxa. Finally, we noted a striking uncoupling of the three molecular entities when moving from healthy individuals via disease controls to patients with IBD. Conclusions Our results provide strong evidence that the interplay between microbiome and host transcriptome, which normally characterises a state of intestinal homeostasis, is drastically perturbed in Crohn's disease and UC. Consequently, integrating multiple OMICs levels appears to be a promising approach to further disentangle the complexity of IBD.
Sleep Architecture and Mental Health Among Community-Dwelling Older Men.

OBJECTIVES To investigate the association of mood and anxiety symptoms with sleep architecture (the distribution of sleep stages) in community-dwelling older men. METHOD We used in-home unattended polysomnography to measure sleep architecture in older men. Men were categorized into 4 mental health categories: (a) significant depressive symptoms only (DEP+ only, Geriatric Depression Scale ≥ 6), (b) significant anxiety symptoms only (ANX+ only, Goldberg Anxiety Scale ≥ 5), (c) significant depressive and anxiety symptoms (DEP+/ANX+), or (d) no significant depressive or anxiety symptoms (DEP-/ANX-). RESULTS Compared with men without clinically significant symptomology, men with depressive symptoms spent a higher percentage of time in Stage 2 sleep (65.42% DEP+ only vs 62.47% DEP-/ANX-, p = .003) and a lower percentage of time in rapid eye movement sleep (17.05% DEP+ only vs 19.44% DEP-/ANX-, p = .0005). These differences persisted after adjustment for demographic/lifestyle characteristics, medical conditions, medications, and sleep disturbances, and after excluding participants using psychotropic medications. The sleep architecture of ANX+ or DEP+/ANX+ men did not differ from asymptomatic men. DISCUSSION Depressed mood in older adults may be associated with accelerated age-related changes in sleep architecture. Longitudinal community-based studies using diagnostic measures are needed to further clarify relationships among common mental disorders, aging, and sleep.
Pain correlates with germline mutation in schwannomatosis

Abstract Schwannomatosis has been linked to germline mutations in the SMARCB1 and LZTR1 genes, and is frequently associated with pain. In a cohort study, we assessed the mutation status of 37 patients with clinically diagnosed schwannomatosis and compared to clinical data, whole body MRI (WBMRI), visual analog pain scale, and Short Form 36 (SF-36) bodily pain subscale. We identified a germline mutation in LZTR1 in 5 patients (13.5%) and SMARCB1 in 15 patients (40.5%), but found no germline mutation in 17 patients (45.9%). Peripheral schwannomas were detected in 3 LZTR1-mutant (60%) and 10 SMARCB1-mutant subjects (66.7%). Among those with peripheral tumors, the median tumor number was 4 in the LZTR1 group (median total body tumor volume 30 cc) and 10 in the SMARCB1 group (median volume 85cc), (P=.2915 for tumor number and P = .2289 for volume). mutation was associated with an increased prevalence of spinal schwannomas (100% vs 41%, P = .0197). The median pain score was 3.9/10 in the LZTR1 group and 0.5/10 in the SMARCB1 group (P = .0414), and SF-36 pain-associated quality of life was significantly worse in the LZTR1 group (P = .0106). Pain scores correlated with total body tumor volume (rho = 0.32471, P = .0499), but not with number of tumors (rho = 0.23065, P = .1696). We found no significant difference in quantitative tumor burden between mutational groups, but spinal schwannomas were more common in LZTR1-mutant patients. Pain was significantly higher in LZTR1-mutant than in SMARCB1-mutant patients, though spinal tumor location did not significantly correlate with pain. This suggests a possible genetic association with schwannomatosis-associated pain.
Carotenoid intake from natural sources and colorectal cancer: a systematic review and meta-analysis of epidemiological studies

Carotenoid intake from natural sources has been hypothesized to reduce the risk of colorectal cancer (CRC). The aim of this study was to systematically review the epidemiological evidence for the association between carotenoid intake from natural sources and CRC development. We carried out a systematic review and meta-analysis of epidemiological studies to investigate whether the intake of specific carotenoids from natural sources, as well as combined carotenoids, is associated with the risk of CRC overall and by anatomic subsite. A comprehensive literature search of MEDLINE and Scopus databases was performed. Twenty-two articles were identified from the literature search, of which 16 were case–control studies and 6 were cohort studies. In the random-effects meta-analysis of case–control and cohort studies, we found no association between the intake of individual and total carotenoids and the risk of CRC overall and by anatomic subsite. Overall, our findings do not support a significant association between intake of specific carotenoids from dietary sources, as well as combined carotenoids, and the risk of CRC overall and by anatomic subsite.
Cross-shelf benthic community structure on the Great Barrier Reef: relationships between macroalgal cover and herbivore biomass

The Great Barrier Reef (GBR) is one of the most extensively studied coral reef systems in the world, yet to date, there has been no comprehensive multi-spatial scale evaluation of its benthic community structure. Such descriptions provide a useful reference point for evaluating future community changes. Moreover, large-scale associations between macroalgae and herbivory on the GBR are yet to be investigated. Our aim, therefore, was to quantify all major substratum categories across multiple spatial scales and investigate cross-shelf relationships between macroalgal cover and herbivore biomass. Using point-intercept transects and timed underwater censuses, individual benthic components and roving herbivorous fish densities were quantified across 3 spatial scales: latitude, continental shelf position and within-reef habitat. Principal component analysis and analysis of similarities (ANOSIM) revealed a distinct separation of inner-shelf reef habitats from all mid- and outer-shelf habitats in both northern and central regions of the GBR. Macroalgal cover was generally high on inner-shelf reefs (36 to 66%) and decreased markedly on all mid- and outer-shelf habitats (0 to 15%). A significant negative correlation was found between macroalgal cover and total herbivorous fish biomass, but no relationship was found between macroalgal cover and macroalgal browser biomass. In contrast to macroalgae, the cover of crustose coralline algae and live scleractinian corals increased markedly across the shelf in both regions of the GBR. These patterns appear to be shaped by both physical and biological factors, including wave energy, sedimentation and grazing intensity.
VEGF and Ki-67 Overexpression in Predicting Poor Overall Survival in Adenoid Cystic Carcinoma

Purpose The purpose of this study was to evaluate potential prognostic factors in patients with adenoid cystic carcinoma (ACC). Materials and Methods A total of 68 patients who underwent curative surgery and had available tissue were enrolled in this study. Their medical records and pathologic slides were reviewed and immunohistochemistry for basic fibroblast growth factor, fibroblast growth factor receptor (FGFR) 2, FGFR3, c-kit, Myb proto-oncogene protein, platelet-derived growth factor receptor beta, vascular endothelial growth factor (VEGF), and Ki-67 was performed. Univariate and multivariate analysis was performed for determination of disease-free survival (DFS) and overall survival (OS). Results In univariate analyses, primary site of nasal cavity and paranasal sinus (p=0.022) and Ki-67 expression of more than 7% (p=0.001) were statistically significant factors for poor DFS. Regarding OS, perineural invasion (p=0.032), high expression of VEGF (p=0.033), and high expression of Ki-67 (p=0.007) were poor prognostic factors. In multivariate analyses, primary site of nasal cavity and paranasal sinus (p=0.028) and high expression of Ki-67 (p=0.004) were independent risk factors for poor DFS, and high expression of VEGF (p=0.011) and Ki-67 (p=0.011) showed independent association with poor OS. Conclusion High expression of VEGF and Ki-67 were independent poor prognostic factors for OS in ACC.
PM2.5, Population Exposure and Economic Effects in Urban Agglomerations of China Using Ground-Based Monitoring Data

This paper adopts the PM2.5 concentration data obtained from 1497 station-based monitoring sites, population and gross domestic product (GDP) census data, revealing population exposure and economic effects of PM2.5 in four typical urban agglomerations of China, i.e., Beijing-Tianjin-Hebei (BTH), the Yangtze River delta (YRD), the Pearl River delta (PRD), and Chengdu-Chongqing (CC). The Cokriging interpolation method was used to estimate the PM2.5 concentration from station-level to grid-level. Next, an evaluation was conducted mainly at the grid-level with a cell size of 1 × 1 km, assisted by the urban agglomeration scale. Criteria including the population-weighted mean, the cumulative percent distribution and the correlation coefficient were applied in our evaluation. The results showed that the spatial pattern of population exposure in BTH was consistent with that of PM2.5 concentration, as well as changes in elevation. The topography was also an important factor in the accumulation of PM2.5 in CC. Moreover, the most polluted urban agglomeration based on the population-weighted mean was BTH, while the least was PRD. In terms of the cumulative percent distribution, only 0.51% of the population who lived in the four urban agglomerations, and 2.33% of the GDP that was produced in the four urban agglomerations, were associated with an annual PM2.5 concentration smaller than the Chinese National Ambient Air Quality Standard of 35 µg/m3. This indicates that the majority of people live in the high air polluted areas, and economic development contributes to air pollution. Our results are supported by the high correlation between population exposure and the corresponding GDP in each urban agglomeration.
Modeling auditory processing of amplitude modulation. I. Detection and masking with narrow-band carriers.

This paper presents a quantitative model for describing data from modulation-detection and modulation-masking experiments, which extends the model of the "effective" signal processing of the auditory system described in Dau et al. [J. Acoust. Soc. Am. 99, 3615-3622 (1996)]. The new element in the present model is a modulation filterbank, which exhibits two domains with different scaling. In the range 0-10 Hz, the modulation filters have a constant bandwidth of 5 Hz. Between 10 Hz and 1000 Hz a logarithmic scaling with a constant Q value of 2 was assumed. To preclude spectral effects in temporal processing, measurements and corresponding simulations were performed with stochastic narrow-band noise carriers at a high center frequency (5 kHz). For conditions in which the modulation rate (fmod) was smaller than half the bandwidth of the carrier (delta f), the model accounts for the low-pass characteristic in the threshold functions [e.g., Viemeister, J. Acoust. Soc. Am. 66, 1364-1380 (1979)]. In conditions with fmod > delta f/2, the model can account for the high-pass characteristic in the threshold function. In a further experiment, a classical masking paradigm for investigating frequency selectivity was adopted and translated to the modulation-frequency domain. Masked thresholds for sinusoidal test modulation in the presence of a competing modulation masker were measured and simulated as a function of the test modulation rate. In all cases, the model describes the experimental data to within a few dB. It is proposed that the typical low-pass characteristic of the temporal modulation transfer function observed with wide-band noise carriers is not due to "sluggishness" in the auditory system, but can instead be understood in terms of the interaction between modulation filters and the inherent fluctuations in the carrier.
Permanent and Transitory Components in Macroeconomic Fluctuations

Fluctuations in real GNP have traditionally been viewed as transitory deviations from a deterministic time trend. The purpose of this paper is to review some of the recent developments that have led to a new view of output fluctuations and then to provide some additional evidence. Using post-war quarterly data, it is hard to reject the view that real GNP is as persistent as a random walk with drift. We also consider the hypothesis that the recent finding of persistence are due to the failure to distinguish the business cycle from other fluctuations in real GNP. We use the measured unemployment rate to decompose output fluctuations. We find no evidence for the view that business cycle fluctuations are more quickly trend-reverting.
The psychosocial impact of contralateral risk reducing mastectomy (CRRM) on women: A rapid review

For women who have been diagnosed with unilateral breast cancer, there is an increasing trend for them to request removal of the contralateral healthy breast, the so‐called contralateral risk reducing mastectomy (CRRM). The current literature is only just beginning to identify patient‐reported reasons for undergoing CRRM and associated patient‐reported outcomes. It is also unclear whether women at moderate/high risk of developing a subsequent primary contralateral breast cancer report similar outcomes to those considered to be at low/average risk. This lack of knowledge provides the rationale for this review.