Miracle-dz/UniFAR-FTUs huggingface dataset:
Recurrent copy number alterations in young women with breast cancer

Breast cancer diagnosis in young women has emerged as an independent prognostic factor with higher recurrence risk and death than their older counterparts. We aim to find recurrent somatic copy number alteration (CNA) regions identified from breast cancer microarray data and associate the CNA status of the genes harbored in the regions to the survival of young women with breast cancer. By using the interval graph-based algorithm we developed, and the CNA data consisting of a Discovery set with 130 young women and a Validation set with 125 young women, we identified 38 validated recurrent CNAs containing 39 protein encoding genes. CNA gain regions encompassing genes CAPN2, CDC73 and ASB13 are the top 3 with the highest occurring frequencies in both the Discovery and Validation dataset, while gene SGCZ ranked top for the recurrent CNA loss regions. The mutation status of 9 of the 39 genes shows significant associations with breast cancer specific survival. Interestingly, the expression level of 2 of the 9 genes, ASB13 and SGCZ, shows significant association with survival outcome. Patients with CNA mutations in both of these genes had a worse survival outcome when compared to patients without the gene mutations. The mutated CNA status in gene ASB13 was associated with a higher gene expression, which predicted patient survival outcome. Together, identification of the CNA events with prognostic significance in young women with breast cancer may be used in genomic-guided treatment.
Ecological niche modelling tool for aquatic life population distribution using maximum entropy model

The declining trend of the population of certain marine organisms may be due to lack of management where juveniles are being caught and grown out. In the Philippines, among the marine species affected by this practice is the Plectropomus leopardus, locally known as Lapu-Lapu. Identifying the factors that contribute to the persistence of Lapu-Lapu would be a great help in the thrust of protecting threatened species in the Philippines. Niche Modeling has been widely used in determining the distributions of species and its suitable habitat based on the environmental conditions in which species populations could be maintained. Thus, modeling techniques that require presence-only data such as Maximum Entropy Models (Maxent) have been widely used to predict habitat distributions. This system aims to predict the current and future potential population distribution of the Lapu-Lapu species, using Maxent modelling. PiLNiMo is an application designed to predict the population distribution of Plectropomus leopardus based on the mean sea level pressure, mean temperature, and thunderstorm occurrence.
High expression of DJ‐1 promotes growth and invasion via the PTEN‐AKT pathway and predicts a poor prognosis in colorectal cancer

Cancer cell invasion and unlimited proliferation are key factors in patients with colorectal cancer (CRC). Increased protein deglycase DJ‐1 in cancer cells is known to promote tumor growth; however, its role in CRC progression is not well defined. In this study, we investigated 100 CRC patients with disease stages I–IV to determine whether DJ‐1 could serve as a prognostic biomarker in CRC. These results showed that DJ‐1 expression in CRC tissues was higher than that in normal colon tissues and was associated with the (Tumor Node Metastasis) TNM stage. CRC patients with low DJ‐1 expression had a longer overall survival than those with high expression, and multivariate and univariate analyses indicated that DJ‐1 expression was an independent prognostic factor for overall survival in CRC. Furthermore, DJ‐1 overexpression in two colon cancer cell lines, HCT116 and SW480, activated protein kinase AKT and downregulated tumor suppressor PTEN, whereas DJ‐1 knockdown upregulated PTEN expression and effectively suppressed CRC cell invasion and proliferation both in vitro and in vivo, revealing a mechanism underlying DJ‐1 pro‐oncogenic activity in CRC. Treatment of MK2206, the specific AKT inhibitor, significantly decreased DJ‐1‐mediated cell proliferation and mobility in vitro. Taken together, these results suggest that DJ‐1 may be a novel prognostic biomarker and potential therapeutic target in human CRC.
Anorectal melanoma: experience from a tertiary cancer care centre in South India

INTRODUCTION Mucosal malignant melanoma of the anorectum is a rare and aggressive disease, in which early diagnosis is difficult. The prognosis remains extremely poor, irrespective of the treatment. We share our experience in treating this malignancy at our centre in South India. METHODS This study describes a retrospective analysis of 31 cases of anorectal melanoma presented to our centre between January 2001 and December 2013. RESULTS Twenty‐two patients (71%) presented with metastasis and had a median overall survival of nine months. None of the 22 patients survived for two years. Nine patients (29%) had curative surgery, in the form of abdominoperineal resection (six patients), abdominoperineal resection with bilateral inguinal node dissection (one patient), abdominoperineal resection with liver resection (one patient) and posterior exenteration (one patient). In patients who underwent curative surgery, the median overall survival was 15 months and disease‐free survival was nine months, with a two‐year overall survival of 22%. CONCLUSIONS Anorectal melanoma is an aggressive disease with a poor prognosis. The majority of patients present with distant metastases. Prognosis depends on stage at presentation. Early diagnosis and surgical resection may improve the overall outcome. Newer modalities such as immunotherapy and targeted therapies such as anti‐CTLA4 monoclonal antibody and anti‐programmed cell death protein 1 monoclonal antibodies have radically changed the management of mucosal melanoma and may, in the future, improve the overall prognosis of anorectal melanoma.
Analysis of body imbalance in various writing sitting postures using sitting pressure measurement

[Purpose] This study set out to substantiate the importance of the right sitting posture by measuring the sitting pressure. It also described the influence of an imbalanced sitting posture on the body. [Subjects and Methods] The subjects included 30 healthy adults. A pressure mapping system was used to measure the sitting pressure in the right, one side prone, chin propped, and slumped sitting positions. [Results] The WDI (XAP) showed a statistically significant difference between the 3 incorrect postures (one side prone, chin propped, and slumped sitting) and the right sitting posture. With regard to the WDI (XLR), there was a statistically significant difference between the right sitting posture and the one side prone sitting posture only. [Conclusion] One side prone sitting was found to affect the body balance most adversely. This imbalanced posture may have an indirect effect on chronic diseases. The results prove that it is important to assume a proper posture to maintain body balance.
Layout metrics for Euler diagrams

We present an aesthetics based method for drawing Euler diagrams. Aesthetic layout metrics have been found to be useful in graph drawing algorithms, which use metrics motivated by aesthetic principles that aid user understanding of diagrams. We have taken a similar approach to Euler diagram drawing, and have defined a set of suitable metrics to be used within a hill climbing multicriteria optimiser to produce "good" drawings. There are added difficulties when drawing Euler diagrams as they are made up of contours whose structural properties of intersection and containment must be preserved under any layout improvements. We describe our Java implementation of a pair of hill climbing variants to find good drawings, a set of metrics that measure aesthetics for good diagram layout, and issues concerning the choice of weightings for a useful combination of the metrics.
Using Automatic Refactoring to Improve Energy Efficiency of Android Apps

The ever-growing popularity of mobile phones has brought additional challenges to the software development lifecycle. Mobile applications (apps, for short) ought to provide the same set of features as conventional software, with limited resources: such as, limited processing capabilities, storage, screen and, not less important, power source. Although energy efficiency is a valuable requirement, developers often lack knowledge of best practices. In this paper, we study whether or not automatic refactoring can aid developers ship energy efficient apps. We leverage a tool, Leafactor, with five energy code smells that tend to go unnoticed. We use Leafactor to analyze code smells in 140 free and open source apps. As a result, we detected and fixed code smells in 45 apps, from which 40% have successfully merged our changes into the official repository.
Clinical Manifestations of Pediatric Psoriasis: Results of a Multicenter Study in the United States

The clinical features of pediatric psoriasis warrant further attention. A national study was conducted to determine the prevalence of scalp and nail involvement and a history of guttate psoriasis at onset according to age, sex, and disease severity. One hundred eighty‐one children ages 5 to 17 years with plaque psoriasis were enrolled in a multicenter, cross‐sectional study. Subjects and guardians were asked about a history of scalp and nail involvement and whether the initial presentation was guttate. Peak psoriasis severity was assessed and defined historically as mild psoriasis (MP) or severe psoriasis (SP) according to the Physician's Global Assessment and body surface area measures. One hundred forty‐three (79.0%) subjects reported a history of scalp involvement, and 71 (39.2%) described a history of nail involvement. Boys were less likely than girls to report a history of scalp involvement (odds ratio [OR] = 0.40, 95% confidence interval [CI] = 0.19–0.84) but more likely to have had nail involvement (OR = 3.01, 95% CI = 1.62–5.60). Scalp and nail involvement was not related to psoriasis severity. In contrast, subjects with SP (35.9%) more often reported a history of guttate lesions than did those with MP (21.8%) (p = .02). Antecedent streptococcal infection was more common in children with guttate than those with plaque psoriasis at onset (p = .02) but did not correlate with severity. Sex‐related differences in scalp and nail involvement suggest koebnerization. Preceding streptococcal infection predicts guttate morphology but not severity, and initial guttate morphology is associated with eventual greater severity of disease. More aggressive monitoring and management should be considered for guttate psoriasis, given its later association with more severe disease.
Local Antibody Responses in Periodontal Diseases.

The relationship between local and systemic host antibody responses, colonization of subgingival plaque by periodontal disease-associated microorganisms and the progression of periodontal disease was assessed in 61 patients. Serum antibody levels to a battery of oral microorganisms were determined by an enzyme-linked immunosorbent assay (ELISA), and an organism to which each patient exhibited a significantly elevated IgG response was chosen for further study. To detect the presence of the specific microorganism, plaque samples were obtained and examined using a seroELISA. Static crevicular fluid (SCF) samples were also obtained from all teeth and analyzed for IgG antibody to the homologous organism. A modification of the standard ELISA using biotin and avidin allowed a 5- to 10-fold increase in sensitivity for detection of IgG antibody in serum and SCF. Comparison of the distribution of elevated SCF antibody and the presence of the corresponding microorganism in each patient showed that the proportion of agreement was 54 to 78% in the samples. Schematic representation of the temporal relationship between the organism, the host response and disease activity were prepared to explain the results obtained in investigations of these parameters and to provide a testable hypothetical framework for future studies.
Epistasis-Induced Evolutionary Plateaus in Selection Responses

Understanding and predicting evolution is a central challenge in both population and quantitative genetics. The amount of genetic variance for quantitative traits available in a population conditions the particular way in which this population will (or will not) evolve under natural or artificial selection. Here, we explore the potential of gene-gene interactions (epistasis) to induce evolutionary plateaus at which evolutionary change virtually collapses for a number of generations, followed by the release of previously cryptic genetic variation. First, we demonstrate theoretically that a wide range of epistatic interactions has the potential to generate temporary decelerations in the course of response to selection. Second, we perform simulations to show that such microevolutionary plateaus may occur in selection responses under empirically based assumptions. Finally, we show that such events can be traced in artificial selection experiments, thus providing further empirical evidence for this phenomenon.
Improving search results in life science by recommendations based on semantic information

The management and handling of big data is a major challenge in the area of life science. Beside the data storage, information retrieval methods have to be adapted to huge data amounts as well. Therefore we present an approach to improve search results in life science by recommendations based on semantic information. In detail we determine relationships between documents by searching for shared database IDs as well as ontology identifiers. We have established a pipeline based on Hadoop allowing a distributed computation of large amounts of textual data. A comparison with the widely used cosine similarity has been performed. Its results are presented in this work as well.
Bayesian information criterion for multidimensional sinusoidal order selection

Detecting the sinusoidal order is a prerequisite step for parametric multidimensional sinusoidal frequency estimation methods, whose applications range from radar and wireless communications to nuclear magnetic resonance spectroscopy. Although the Bayesian information criterion (BIC) has been commonly applied for model order selection, its application to sinusoidal order estimation is recent. By means of estimation of Fisher information matrix, we extend the 1-D BIC to multidimensional case for multidimensional sinusoidal order selection. The multidimensional BIC is shown in simulations to outperform the state-of-the-art algorithms in terms of probability of correct detection.
Robust LPV control applied to a personal pendulum vehicle

Linear-Parameter-Varying theory has making a revolution during the last two decades to the study of nonlinear control and robust control, because they were taking into consideration the non-stationeries in the model and their uncertainties. In this article we suggest to exploit the LPV theory to design a robust gain-scheduled H» controller applied to an Inverted Pendulum, specifically named Personal Pendulum Vehicle, which is a nonlinear system. The representation of both of the plant and the controller is a Linear-Fractional-Transformation (LFT) based LPV systems. The synthesis of the controller is achieved by scaling small-gain theorem and their tests are applied to the nonlinear model itself.
Linear Modelling and Identification of a Mobile Robot With Differential Drive

This paper presents a modelling and identification method for a wheeled mobile robot, including the actuator dynamics. Instead of the classic modelling approach, where the robot position coordinates (x, y) are utilized as state variables (resulting in a non linear model), the proposed discrete model is based on the travelled distance increment ∆l. Thus, the resulting model is linear and time invariant and it can be identified through classical methods such as Recursive Least Mean Squares. This approach has a problem: ∆l can not directly measured. In this paper, this problem is solved using an estimate f ∆l based on a second order curve approximation. Experimental data were colected and the proposed method was used to identify the model of a real robot.
New Caledonian crows attend to multiple functional properties of complex tools

The ability to attend to the functional properties of foraging tools should affect energy-intake rates, fitness components and ultimately the evolutionary dynamics of tool-related behaviour. New Caledonian crows Corvus moneduloides use three distinct tool types for extractive foraging: non-hooked stick tools, hooked stick tools and tools cut from the barbed edges of Pandanus spp. leaves. The latter two types exhibit clear functional polarity, because of (respectively) a single terminal, crow-manufactured hook and natural barbs running along one edge of the leaf strip; in each case, the ‘hooks’ can only aid prey capture if the tool is oriented correctly by the crow during deployment. A previous experimental study of New Caledonian crows found that subjects paid little attention to the barbs of supplied (wide) pandanus tools, resulting in non-functional tool orientation during foraging. This result is puzzling, given the presumed fitness benefits of consistently orienting tools functionally in the wild. We investigated whether the lack of discrimination with respect to (wide) pandanus tool orientation also applies to hooked stick tools. We experimentally provided subjects with naturalistic replica tools in a range of orientations and found that all subjects used these tools correctly, regardless of how they had been presented. In a companion experiment, we explored the extent to which normally co-occurring tool features (terminal hook, curvature of the tool shaft and stripped bark at the hooked end) inform tool-orientation decisions, by forcing birds to deploy ‘unnatural’ tools, which exhibited these traits at opposite ends. Our subjects attended to at least two of the three tool features, although, as expected, the location of the hook was of paramount importance. We discuss these results in the context of earlier research and propose avenues for future work.
Batch Fabrication of Shape Memory Actuated Polymer Microvalves by Transfer Bonding Techniques

Polymer based microvalves offer outstanding properties for biomedical and life science applications. They can be produced cost efficiently by batch fabrication methods. Further, by adapting the polymer material, custom-tailored properties of the valve are possible. For mechanically active microvalves, actuation with smart materials like shape memory alloys is highly attractive due to their high work output per volume and favorable scaling behavior. For the integration of such smart materials, fabrication process incompatibilities between the actuator material and the polymer target system need to be avoided. This can be achieved by novel transfer bonding technologies being optimized for batch fabrication. These technologies are demonstrated for polymer microvalves actuated by a shape memory alloy but they can also be applied to other functional materials and structures.
Hypothesis – buttressed rings assemble, clamp, and release SNAREpins for synaptic transmission

Neural networks are optimized to detect temporal coincidence on the millisecond timescale. Here, we offer a synthetic hypothesis based on recent structural insights into SNAREs and the C2 domain proteins to explain how synaptic transmission can keep this pace. We suggest that an outer ring of up to six curved Munc13 ‘MUN’ domains transiently anchored to the plasma membrane via its flanking domains surrounds a stable inner ring comprised of synaptotagmin C2 domains to serve as a work‐bench on which SNAREpins are templated. This ‘buttressed‐ring hypothesis’ affords straightforward answers to many principal and long‐standing questions concerning how SNAREpins can be assembled, clamped, and then released synchronously with an action potential.
Use of genetic markers to quantify bumblebee foraging range and nest density

Bumblebees (Hymenoptera: Apidae) are important pollinators of crops and wildflowers, but many species have suffered dramatic declines in recent decades. Strategies for their conservation require knowledge of their foraging range and nesting density, both of which are poorly understood. Previous studies have mainly focussed on the cosmopolitan bumblebee species Bombus terrestris, and implicitly assume this to be representative of other species. Here we use a landscape-scale microsatellite study to estimate the foraging range and nesting density of two ecologically dissimilar species, B. terrestris and B. pascuorum. Workers were sampled along a 10 km linear transect and 8-9 polymorphic microsatellite markers used to identify putative sisters. We provide the first published estimates of the number of colonies using a circle of radius 50 m in an agricultural landscape: 20.4 for B. terrestris and 54.7 for B. pascuorum. Estimates of nest density differed significantly between the two species: 13 km-2 for B. terrestris and 193 km-2 for B. pascuorum. Foraging ranges also differed substantially, with B. pascuorum foraging over distances less than 312 m and B. terrestris less than 625 m. Clearly bumblebee species differ greatly in fundamental aspects of their ecology. This has significant implications for the development of conservation strategies for rare bumblebees and isolated plant populations, for the management of bumblebees as pollinators, and for predicting patterns of gene flow from genetically modified plants.
Dynamical Asymmetry of Upper-Limb Movements During Swimming

Purpose. This study aimed at introducing a method towards determining the dynamical asymmetry of the upper extremities during swimming and to find its relationship with lower-limb movements in children when swimming the breaststroke. Methods. Twenty boys participated in the research, where seven boys were found to perform incorrect lower-limb movements when swimming. Therefore, the subjects were divided into two groups, those who maintained correct lower-limb movements when swimming and those who did not. The subjects swam for short distances using either only their upper limbs or both upper and lower limbs. The water pressure that was exerted on the right and left hand of the subject was recorded for both tests. On the basis of the compiled data, the upper-limb movements’ asymmetry index was calculated. Results. Incorrect lower extremity movements when performing the breaststroke resulted in increased upper-limb dynamical asymmetry. Conclusion. The method applied in this study enables one to diagnosis the dynamical asymmetry of upper-limb movements when swimming. Altogether, it was found in the examined group that incorrect lower-limb movements in the breaststroke did not decrease swimming efficiency. However, an increase of the upper extremities’ dynamical asymmetry might have decreased the efficiency of the shoulder-girdle muscles’ symmetrization. In the case of individuals performing incorrect lower-limb movements in the breaststroke, it is recommended to improve their performance or to swim with the upper limbs only.