Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential expression of neurogenes among breast cancer subtypes identifies high risk patients

The nervous system is now recognized to be a relevant component of the tumor microenvironment. Receptors for neuropeptides and neurotransmitters have been identified in breast cancer. However, very little is known about the role of neurogenes in regulating breast cancer progression. Our purpose was to identify neurogenes associated with breast cancer tumorigenesis with a potential to be used as biomarker and/or targets for treatment. We used three databases of human genes: GeneGo, GeneCards and Eugenes to generate a list of 1266 relevant neurogenes. Then we used bioinformatics tools to interrogate two published breast cancer databases SAGE and MicMa (n=96) and generated a list of 7 neurogenes that are differentially express among breast cancer subtypes. The clinical potential was further investigated using the GOBO database (n=1881). We identified 6 neurogenes that are differentially expressed among breast cancer subtypes and whose expression correlates with prognosis. Histamine receptor1 (HRH1), neuropilin2 (NRP2), ephrin-B1 (EFNB1), neural growth factor receptor (NGFR) and amyloid precursor protein (APP) were differentially overexpressed in basal and HER2-enriched tumor samples and syntaxin 1A (STX1A) was overexpressed in HER2-enriched and luminal B tumors. Analysis of HRH1, NRP2, and STX1A expression using the GOBO database showed that their expression significantly correlated with a shorter overall survival (p < 0.0001) and distant metastasis-free survival (p < 0.0001). In contrast, elevated co-expression of NGFR, EFNB1 and APP was associated with longer overall (p < 0.0001) and metastasis-free survival (p < 0.0001). We propose that HRH1, NRP2, and STX1A can be used as prognostic biomarkers and therapeutic targets for basal and HER2-enriched breast cancer subtypes.
Neutralising antibodies for Mayaro virus in Pantanal, Brazil

The Pantanal hosts diverse wildlife species and therefore is a hotspot for arbovirus studies in South America. A serosurvey for Mayaro virus (MAYV), eastern (EEEV), western (WEEV) and Venezuelan (VEEV) equine encephalitis viruses was conducted with 237 sheep, 87 free-ranging caimans and 748 equids, including 37 collected from a ranch where a neurologic disorder outbreak had been recently reported. Sera were tested for specific viral antibodies using plaque-reduction neutralisation test. From a total of 748 equids, of which 264 were immunised with vaccine composed of EEEV and WEEV and 484 had no history of immunisation, 10 (1.3%) were seropositive for MAYV and two (0.3%) for VEEV using criteria of a ≥ 4-fold antibody titre difference. Among the 484 equids without history of immunisation, 48 (9.9%) were seropositive for EEEV and four (0.8%) for WEEV using the same criteria. Among the sheep, five were sero- positive for equine encephalitis alphaviruses, with one (0.4%) for EEEV, one (0.4%) for WEEV and three (1.3%) for VEEV. Regarding free-ranging caimans, one (1.1%) and three (3.4%), respectively, had low titres for neutralising antibodies to VEEV and undetermined alphaviruses. The neurological disorder outbreak could not be linked to the alphaviruses tested. Our findings represent strong evidence that MAYV and all equine encephalitis alphaviruses circulated in the Pantanal.
Hausdorff dimension of the harmonic measure on trees

For a large class of Markov operators on trees we prove the formula ${\bf HD}\,\nu=h/l$ connecting the Hausdorff dimension of the harmonic measure $\nu$ on the tree boundary, the rate of escape $l$ and the asymptotic entropy $h$. Applications of this formula include random walks on free groups, conditional random walks, random walks in random environment and random walks on treed equivalence relations.
Comparing Edge Detection Methods Based on Stochastic Entropies and Distances for PolSAR Imagery

Polarimetric synthetic aperture radar (PolSAR) has achieved a prominent position as a remote imaging method. However, PolSAR images are contaminated by speckle noise due to the coherent illumination employed during the data acquisition. This noise provides a granular aspect to the image, making its processing and analysis (such as in edge detection) hard tasks. This paper discusses seven methods for edge detection in multilook PolSAR images. In all methods, the basic idea consists in detecting transition points in the finest possible strip of data which spans two regions. The edge is contoured using the transitions points and a B-spline curve. Four stochastic distances, two differences of entropies, and the maximum likelihood criterion were used under the scaled complex Wishart distribution; the first six stem from the h-φ class of measures. The performance of the discussed detection methods was quantified and analyzed by the computational time and probability of correct edge detection, with respect to the number of looks, the backscatter matrix as a whole, the SPAN, the covariance an the spatial resolution. The detection procedures were applied to three real PolSAR images. Results provide evidence that the methods based on the Bhattacharyya distance and the difference of Shannon entropies outperform the other techniques.
Multi-annual droughts in the English Lowlands: a review of their characteristics and climate drivers in the winter half-year

The English Lowlands is a relatively dry, densely populated region in the south-east of the UK in which water is used intensively. Consequently, parts of the region are water-stressed and face growing water resource pressures. The region is heavily dependent on groundwater and particularly vulnerable to long, multi-annual droughts primarily associated with dry winters. Despite this vulnerability, the atmospheric drivers of multi-annual droughts in the region are poorly understood, an obstacle to developing appropriate drought management strategies, including monitoring and early warning systems. To advance our understanding, we assess known key climate drivers in the winter half-year (October–March) and their likely relationships with multi-annual droughts in the region. We characterise historic multi-annual drought episodes back to 1910 for the English Lowlands using various meteorological and hydrological data sets. Multi-annual droughts are identified using a gridded precipitation series for the entire region, and refined using the Standardized Precipitation Index (SPI), Standardized Streamflow Index (SSI) and Standardized Groundwater level Index (SGI) applied to regional-scale river flow and groundwater time series. We explore linkages between a range of potential climatic driving factors and precipitation, river flow and groundwater level indicators in the English Lowlands for the winter half-year. The drivers or forcings include El Nino–Southern Oscillation (ENSO), the North Atlantic tripole sea surface temperature (SST) pattern, the Quasi-Biennial Oscillation (QBO), solar and volcanic forcing and the Atlantic Multi-decadal Oscillation (AMO). As expected, no single driver convincingly explains the occurrence of any multi-annual drought in the historical record. However, we demonstrate, for the first time, an association between La Nina episodes and winter rainfall deficits in some major multi-annual drought episodes in the English Lowlands. We also show significant (albeit relatively weak) links between ENSO and drought indicators applied to river flow and groundwater levels. We also show that some of the other drivers listed above are likely to influence English Lowlands rainfall. We conclude by signposting a direction for this future research effort.
Parameter Estimation Techniques , Optimization Frequency , and Equity Portfolio Return Enhancement

Various ex ante portfolio parameter estimation techniques and optimization/holding period frequency intervals are tested for their ability to enhance managed portfolio returns relative to a benchmark. The potential for return enhancement is accomplished by optimizing over highly correlated size-based constituent portfolios of the benchmark. Overall, the results suggest that it is possible to consistently achieve enhanced returns at much the same level of return per unit of risk as the benchmark portfolio.
Ventilatory assistance in patients with Duchenne muscular dystrophy

Duchenne muscular dystrophy (DMD) leads to progressive muscle weakness, causing respiratory failure 1, 2. Untreated patients die at <25 yrs of age, and the mean age of death in the 1960s was 15 yrs. The introduction of mechanical ventilation has improved survival compared with historical controls 1–3. This finding has led to general agreement that noninvasive ventilation prolongs life in patients with DMD, although no controlled studies have been performed to confirm this hypothesis 4. Noninvasive mechanical ventilation is initially offered at night to treat sleep-related breathing disorders and hypoventilation, which are common in patients with DMD 5, 6. Breathing during sleep should be evaluated by polysomnography with continuous CO2 monitoring 7, or by continuous CO2 monitoring alone if polysomnography is not available. Overnight pulse oximetry combined with an early-morning arterial blood gas measurement (to detect a base excess) may also be used to monitor nocturnal ventilation. As the disease progresses, hypoventilation starts to occur during the daytime, and additional daytime ventilation is offered 4. When noninvasive mechanical ventilation is inadequately effective, poorly tolerated or not feasible owing to …
Regional Prevalence, Patterns and Correlates of Sexual Coercion Among Women in Sub-Saharan Africa: A Multi-Country Population-Based Study

Abstract Objective: This study investigates the prevalence, perpetrators, and factors associated with forced sexual acts. Methods: Pooled secondary data from the most recent Demographic and Health Survey (DHS) in 22 sub-Saharan African countries was used in this study. The individual woman components of the questionnaire involving 148,720 women of reproductive age (15-49 years) were analyzed. Percentages and graphs were used to present distribution of study variables. Multivariable logistic regression was used to examine factors associated with sexual coercion. Results: Forced sexual acts were prominent in Rwanda (15.7%), Gabon (12.3%) and Democratic Republic of Congo (10.9%). The lowest mean age at first forced sexual acts was recorded in Gabon (14.1 years), Comoros and Mali (14.9 years each), whereas the maximum was recorded in Namibia (25.9 years). Results from adjusted logistic regression models identified that factors such as high women decision making power, large spousal age difference, rural residence, Islamic religious beliefs and listening to radio were significantly associated with reduction in the odds of forced sexual acts. Conversely, high-risk partner’s behavior, older age at start of first marriage, early age at sexual debut, most disadvantaged community, education, and the use of newspapers were significantly associated with higher odds of forced sexual acts. Conclusion: Based on the findings of this study, policies should be reinforced to handle perpetrators of sexual violence especially non-intimate partners. Population-based preventive measures of sexual coercion are essential to complement justice system responses. Our findings also showed the importance of building gender equity as part of sexual violence prevention approach.
The role of cytology in the evaluation of pericardial effusions.

Pericardial effusions from 47 patients were examined for cancer cells. Fluids from 13 of the 15 patients with neoplasm involving the pericardium were decisively “positive. ” There were no false positive reports. Three patients had malignancy localized to the chest, but not metastatic to the pericardium. Effusions from these three patients contained no tumor cells. The accumulation of fluid in a patient with a known or suspected malignancy does not necessarily mean metastatic disease. Cytologic evaluation of these fluids is helpful in establishing a prognosis and mode of therapy.
End stage renal disease patients on haemodialysis profiled epidemiologically at medical college of sub-Himalayan region of India

Background: Mostly, end organ damage becomes the reason for morbidity and mortality among patients with non-communicable diseases (NCDs) due their chronicity. Derangement of renal function along with brain and heart damage are considered to be a significant problem of NCDs. The objectives of this study were on this background of end stage renal disease (ESRD) as a common complication for common NCDs, present study was planned to study the distribution of responsible NCDs.Methods: Over three-year period, all the cases reported GFR <15ml/min/1.73m2 were studied.Results: Total 100 patients (male:65) were studied with mean age of 51.0±13.0 years. Diabetes mellitus (38.0%), hypertension (28.0%), and glomerulonephritis (16.0%) were three leading cause for ESRD. Idiopathic cause was observed among 12.0% patients. Fifteen percent patients could not survive.Conclusions: NCDs mainly diabetes mellitus and hypertension observed to be most common cause for ESRD.
Cigarette smoking and DNA methylation

DNA methylation is the most studied epigenetic modification, capable of controlling gene expression in the contexts of normal traits or diseases. It is highly dynamic during early embryogenesis and remains relatively stable throughout life, and such patterns are intricately related to human development. DNA methylation is a quantitative trait determined by a complex interplay of genetic and environmental factors. Genetic variants at a specific locus can influence both regional and distant DNA methylation. The environment can have varying effects on DNA methylation depending on when the exposure occurs, such as during prenatal life or during adulthood. In particular, cigarette smoking in the context of both current smoking and prenatal exposure is a strong modifier of DNA methylation. Epigenome-wide association studies have uncovered candidate genes associated with cigarette smoking that have biologically relevant functions in the etiology of smoking-related diseases. As such, DNA methylation is a potential mechanistic link between current smoking and cancer, as well as prenatal cigarette-smoke exposure and the development of adult chronic diseases.
Can mind-wandering be timeless? Atemporal focus and aging in mind-wandering paradigms

Recent research has examined how often mind-wandering occurs about past vs. future events. However, mind-wandering may also be atemporal, although previous investigations of this possibility have not yielded consistent results. Indeed, it is unclear what proportion of mind-wandering is atemporal, and also how an atemporal response option would affect the future-oriented bias often reported during low-demand tasks used to measure mind-wandering. The present study examined self-reported (Experiment 1) and probe-caught (Experiment 2) mind-wandering using the low-demand Sustained Attention to Response Task (SART) in younger (18–30) and older (50–73) adults in an experimental paradigm developed to measure mind-wandering using Amazon's Mechanical Turk (Mturk). Across self-reported and probe-caught mind-wandering, the atemporal response option was used at least as frequently as past or future mind-wandering options. Although older adults reported far fewer mind-wandering events, they showed a very similar temporal pattern to younger adults. Most importantly, inclusion of the atemporal report option affected performance on the SART and selectively eliminated the prospective bias in self-reported mind-wandering, but not in probe-caught mind-wandering. These results suggest that both young and older participants are often not thinking of past or future events when mind-wandering, but are thinking of events that cannot easily be categorized as either.
Impact of directional transmission in large-scale multi-hop wireless ad hoc networks

In multi-hop wireless networks, per-hop forwarding strategies that optimize local transmissions can have a subtle impact on network performance. Motivated by a number of scenarios for improving signal strength or mitigating interference, we study a fundamental problem that arises in a wireless ad hoc network with directional transmission (e.g., using directional antennas), where nodes are randomly placed with their transmission footprints (each as a sector) aligned toward the destinations. Only the nodes located in the transmission footprint of a transmitter act as forwarders. Our study addresses connectivity of this setting. We first examine through simulation the percolation probability and the number of cross-area paths available to directional transmission, at different spread angles of transmission footprints. We observe that there is a critical spread angle, above which there is little impact on these properties. Analytically, we derive upper and lower bounds for the critical spread angle. Moreover, we show that with high probability there exist at least Ω(n/ log n) number of disjoint paths across a strip area of n × Θ(n), when the critical spread angle lies above the threshold. Our results provide insights on optimizing directional transmission in wireless ad hoc networks.
Diagnostic urinary proteome profile for immunoglobulin a nephropathy.

INTRODUCTION Immunoglobulin A (IgA) nephropathy, the most common type of glomerulonephritis, is only diagnosed by invasive kidney biopsy. Urine proteome panel might help in noninvasive diagnosis and also better understanding of pathogenesis of IgA nephropathy. MATERIALS AND METHODS Second mid-stream urine samples of 13 patients with biopsy-proven IgA nephropathy and 8 healthy controls were investigated by means of nanoscale liquid chromatography tandem mass spectrometry. Multivariate analysis of quantified label-free proteins was performed by the principal component analysis and partial least squares models. RESULTS A total number of 493 unique proteins were quantified by nanoscale liquid chromatography tandem mass spectrometry, of which 46 proteins were considered as putative biomarkers of IgA nephropathy, after multivariate analysis and additional filter criterion and comparing the patients and the controls. Some of the significant differentially expressed proteins were CD44, glycoprotein 2, vasorin, epidermal growth factor, CLM9, protocadherin, utreoglobin, dipeptidyl peptidase IV, NHL repeat-containing protein 3, and SLAM family member 5. These proteins were related to various involved pathogenic pathways of inflammatory response and complement system. CONCLUSIONS This proteome profile could be utilized in the diagnosis of IgA nephropathy. In addition, providing a noninvasive diagnostic tool, it may shed light on the pathogenesis of IgA nephropathy.
Effect of preload on left atrial function: evaluated by tissue Doppler and strain imaging.

AIMS Both strain and strain rate (SR) measure the regional myocardial deformation and can assess phasic left atrial (LA) function. However, there is still a lack of evidence for their volume independency. In this study, strain and SR determined by tissue Doppler imaging were used to evaluate the effect of preload reduction in end-stage renal disease patients who were undergoing regular haemodialysis (HD). METHODS AND RESULTS Forty-one subjects who underwent transthoracic echocardiography just before and after HD were enrolled. LA strain was measured during late systole, and LA peak tissue velocity and SR were measured during systole and during early and late diastolic periods. The values of tissue velocity, strain, and SR were obtained in the basal septal, lateral, inferior, and anterior walls of the LA. The mean strain value was 23.89 ± 7.29% at baseline and decreased to 21.88 ± 5.85% after HD (P = 0.019). SR during systole (before HD 1.55 ± 0.40; after HD 1.38 ± 0.35, P = 0.001) and early diastole (before HD -1.41 ± 0.54; after HD -1.16 ± 0.45, P = 0.001) also changed. However, the acute preload change caused by HD did not affect the peak tissue velocity (before HD -6.34 ± 1.58 cm/s; after HD -6.46 ± 1.54 cm/s, P = 0.436) and the SR (before HD -1.36 ± 0.45/s; after HD -1.34 ± 0.29/s, P = 0.621) measured during late diastole. CONCLUSION Both tissue velocity and SR during late diastole, representing the contractile function of the LA, are relatively preload-independent parameters and are available for the evaluation of the LA function.
Development of Guidelines for Permitted Left-Turn Phasing Using Flashing Yellow Arrows

The objective of this project was to develop guidelines for time-of-day use of permitted left-turn phasing, which can then be implemented using flashing yellow arrows (FYA). This required determining how the risk for left-turn crashes varied as traffic-flow conditions varied during the course of a representative day. This was accomplished by developing statistical models, which expressed the risk of occurrence of a left-turn crash during a given hour as a function of the left-turn demand, the opposing traffic volume, and a classification of the approach with respect to the opposing traffic speed limit, the type of left-turn protection, and whether or not opposing left-turn traffic could obstruct sight distance. The models were embedded in a spreadsheet tool which will allow operations personnel to enter, for a candidate intersection approach, existing turning movement counts, and a classification of the approach with respect to speed limit, turn protection, and sight distance issues and receive a prediction of how the risk of left-turn crash occurrence varies throughout the day, relative to a user-specified reference condition.
Brain Areas Involved in Perception of Biological Motion

Abstract These experiments use functional magnetic resonance imaging (fMRI) to reveal neural activity uniquely associated with perception of biological motion. We isolated brain areas activated during the viewing of point-light figures, then compared those areas to regions known to be involved in coherent-motion perception and kinetic-boundary perception. Coherent motion activated a region matching previous reports of human MT/MST complex located on the temporo-parieto-occipital junction. Kinetic boundaries activated a region posterior and adjacent to human MT previously identified as the kinetic-occipital (KO) region or the lateral-occipital (LO) complex. The pattern of activation during viewing of biological motion was located within a small region on the ventral bank of the occipital extent of the superior-temporal sulcus (STS). This region is located lateral and anterior to human MT/MST, and anterior to KO. Among our observers, we localized this region more frequently in the right hemisphere than in the left. This was true regardless of whether the point-light figures were presented in the right or left hemifield. A small region in the medial cerebellum was also active when observers viewed biological-motion sequences. Consistent with earlier neuroimaging and single-unit studies, this pattern of results points to the existence of neural mechanisms specialized for analysis of the kinematics defining biological motion.
Advantages and disadvantages of Computer-based Testing: A case study of service learning

The Computer-based Testing (CBT) has developed successfully with its adoption by educators. The authors of this paper point out the advantages and disadvantages of CBT by taking the case study to probe into the scoring algorithm in CBT. The case is the experimental graduates of service learning, who take some pre- tests and post-tests by CBT.