Miracle-dz/UniFAR-FTUs huggingface dataset:
SILAC-Based Proteomics of Human Primary Endothelial Cell Morphogenesis Unveils Tumor Angiogenic Markers*

Proteomics has been successfully used for cell culture on dishes, but more complex cellular systems have proven to be challenging and so far poorly approached with proteomics. Because of the complexity of the angiogenic program, we still do not have a complete understanding of the molecular mechanisms involved in this process, and there have been no in depth quantitative proteomic studies. Plating endothelial cells on matrigel recapitulates aspects of vessel growth, and here we investigate this mechanism by using a spike-in SILAC quantitative proteomic approach. By comparing proteomic changes in primary human endothelial cells morphogenesis on matrigel to general adhesion mechanisms in cells spreading on culture dish, we pinpoint pathways and proteins modulated by endothelial cells. The cell–extracellular matrix adhesion proteome depends on the adhesion substrate, and a detailed proteomic profile of the extracellular matrix secreted by endothelial cells identified CLEC14A as a matrix component, which binds to MMRN2. We verify deregulated levels of these proteins during tumor angiogenesis in models of multistage carcinogenesis. This is the most in depth quantitative proteomic study of endothelial cell morphogenesis, which shows the potential of applying high accuracy quantitative proteomics to in vitro models of vessel growth to shed new light on mechanisms that accompany pathological angiogenesis. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000359.
Collocational Analysis in Japanese Text Input

This paper proposes a new disambiguation method for Japanese text input. This method evaluates candidate sentences by measuring the number of Word Co-occurrence Patterns (WCP) included in the candidate sentences. An automatic WCP extraction method is also developed. An extraction experiment using the example sentences from dictionaries confirms that WCP can be collected automatically with an accuracy of 98.7% using syntactic analysis and some heuristic rules to eliminate erroneous extraction. Using this method, about 305,000 sets of WCP are collected. A co-occurrence pattern matrix with semantic categories is built based on these WCP, Using this matrix, the mean number of candidate sentences in Kana-to-Kanji translation is reduced to about 1/10 of those from existing morphological methods.
ELiRF-UPV at IberEval 2017: Classification Of Spanish Election Tweets (COSET)

This paper describes the participation of ELiRF-UPV team at Classification Of Spanish Election Tweets (COSET) task. We tested several approaches based on different classifiers and features representations. Our main approach is based on neural networks, concretely, Multilayer Perceptrons (MLP) with bag-of-words representation of the tweets. Our system achieved the best score on the test set of the COSET task with 64.82 of macro-F1.
Genetic variants in the IL1A gene region contribute to intestinal‐type gastric carcinoma susceptibility in European populations

The most studied genetic susceptibility factors involved in gastric carcinoma (GC) risk are polymorphisms in the inflammation‐linked genes interleukin 1 (IL1) B and IL1RN. Despite the evidence pointing to the IL1 region, definite functional variants reproducible across populations of different genetic background have not been discovered so far. A high density linkage disequilibrium (LD) map of the IL1 gene cluster was established using HapMap to identify haplotype tagSNPs. Eighty‐seven SNPs were genotyped in a Portuguese case‐control study (358 cases, 1,485 controls) for the discovery analysis. A replication study, including a subset of those tagSNPs (43), was performed in an independent analysis (EPIC‐EurGast) containing individuals from 10 European countries (365 cases, 1284 controls). Single SNP and haplotype block associations were determined for GC overall and anatomopathological subtypes. The most robust association was observed for SNP rs17042407, 16Kb upstream of the IL1A gene. Although several other SNP associations were observed, only the inverse association of rs17042407 allele C with GC of the intestinal type was observed in both studies, retaining significance after multiple testing correction (p = 0.0042) in the combined analysis. The haplotype analysis of the IL1A LD block in the combined dataset revealed the association between a common haplotype carrying the rs17042407 variant and GC, particularly of the intestinal type (p = 3.1 × 10−5) and non cardia localisation (p = 4.6 × 10−3). These results confirm the association of IL1 gene variants with GC and reveal a novel SNP and haplotypes in the IL1A region associated with intestinal type GC in European populations.
Variations in the Earth's Orbit: Pacemaker of the Ice Ages

1) Three indices of global climate have been monitored in the record of the past 450,000 years in Southern Hemisphere ocean-floor sediments. 2) Over the frequency range 10–4 to 10–5 cycle per year, climatic variance of these records is concentrated in three discrete spectral peaks at periods of 23,000, 42,000, and approximately 100,000 years. These peaks correspond to the dominant periods of the earth's solar orbit, and contain respectively about 10, 25, and 50 percent of the climatic variance. 3) The 42,000-year climatic component has the same period as variations in the obliquity of the earth's axis and retains a constant phase relationship with it. 4) The 23,000-year portion of the variance displays the same periods (about 23,000 and 19,000 years) as the quasi-periodic precession index. 5) The dominant, 100,000-year climatic [See table in the PDF file] component has an average period close to, and is in phase with, orbital eccentricity. Unlike the correlations between climate and the higher-frequency orbital variations (which can be explained on the assumption that the climate system responds linearly to orbital forcing), an explanation of the correlation between climate and eccentricity probably requires an assumption of nonlinearity. 6) It is concluded that changes in the earth's orbital geometry are the fundamental cause of the succession of Quaternary ice ages. 7) A model of future climate based on the observed orbital-climate relationships, but ignoring anthropogenic effects, predicts that the long-term trend over the next sevem thousand years is toward extensive Northern Hemisphere glaciation.
Method Input Parameters and Performance of EJB Applications

We investigated the impact of method input parameters on component performance, which is usually neglected during an application design stage. We evaluated a set of Commercial Off-The-Shelf (COTS) components which use Enterprise Java Beans (EJB) technology. These components were deployed on WebSphere Application Server and tested using a custom-built remote client. The client keeps track of execution times, while the server has JProbe Profiler embedded in the EJB container to monitor the interactions. For test purposes we used only stateless session beans, allowing us to concentrate on the possible dependency of server performance on input parameter variations. Test results show that significant performance impacts can be caused by a relatively small number of input parameter dependencies.
Audio source separation with time-frequency velocities

Separating complex audio sources from a single measurement channel, with no training data, is highly challenging. We introduce a new approach, which relies on the time dynamics of rigid audio models, based on harmonic templates. The velocity vectors of such models are defined and computed in a time-frequency scalogram calculated with a wavelet transform. Similarly to rigid object segmentation in videos, multiple audio sources are discriminated by approximating their velocity vectors with low-dimensional models. The different audio sources are segmented by optimizing a harmonic template selection, which provides piecewise constant velocity approximations. Numerical experiments give examples of blind source separation from single channel audio signals.
Cardioprotective Effect of &bgr;-Adrenoceptor Blockade in Patients With Breast Cancer Undergoing Chemotherapy: Follow-Up Study of Heart Failure

Background—Chemotherapy with trastuzumab and anthracycline is associated with incident heart failure (HF) in patients with breast cancer. We hypothesized that continuous incidental use of &bgr;-blocker agents (BB) was protective against HF in patients without established structural heart disease who were receiving trastuzumab and anthracycline. Methods and Results—We identified 920 consecutive patients with breast cancer (age 52.3±11.0 years) with normal ejection fraction before receiving trastuzumab and anthracycline therapy at our institution between 2005 and 2010. Using a propensity score and a greedy 5 to 1 digit-matching algorithm, 106 of these patients on continuous BB during cancer treatment were matched with 212 patients from the same pool with similar characteristics but not on continuous BB. During a median follow-up of 3.2±2.0 years, 32 incident HF admissions were identified in these 318 patients with breast cancer, whereas 28 cancer-related (noncardiac) deaths occurred before any incident HF. Cumulative incidence regression models and cause-specific hazards of new HF events were estimated from competing risk Cox models of time-dependent covariates. Although trastuzumab therapy showed significant association with incident HF, independent of anthracycline-related cardiotoxicity (hazard ratio, 9.0; 95% confidence interval, 3.0–27.0; P<0.0001), continuous use of BB was associated with lower risk of new HF events (hazard ratio, 0.2; 95% confidence interval, 0.1–0.5; P=0.003). Conclusions—Coincidental, continuous use of BB is associated with lower incidence of HF in patients with breast cancer and normal baseline ejection fraction in a competing risk framework, and after matching for demographics, clinical, and cancer-related treatment characteristics. Prospective randomized clinical trials to validate these findings are warranted.
A Supervised Learning Algorithm for Information Extraction from Textual Data

In this article we present a supervised learning algorithm for the discovery of finite state automata in the form of regular expressions in textual data. The automata generate languages that consist of various representations of features useful in information extraction. We have successfully applied this learning technique in the extraction of textual features from police incident reports [2]. In this article we present the result of the application of our algorithm in extraction of the ‘problem solved’ in patents. The ‘problem solved’ in a patent identifies the particular solution to an insufficiency in prior art that the patent addresses.
Intertemporal Choice Behavior in Emerging Adults and Adults: Effects of Age Interact with Alcohol Use and Family History Status

Adults with alcohol use disorders (AUDs) show marked immediate reward selection (or “Now”) bias in intertemporal choice tasks. This Now bias persists long into abstinence, suggesting an irreversible consequence of chronic alcohol abuse or a pre-existing AUD intermediate phenotype. However, some data show substantial Now bias among emerging adults (18–25), regardless of drinking behavior, suggesting age-dependent effects on Now bias. The objectives of the present study were to determine (1) whether Now bias is greater among emerging adults relative to adults, (2) whether any such age effect on Now bias is diminished in sub-clinical heavy alcohol users, and (3) whether having a problem drinking first degree relative is independently associated with elevated Now bias. To achieve these objectives, we used an intertemporal choice task to quantify Now bias in n = 237 healthy participants (ages 18–40; 50% female), and a wide range of non-zero alcohol use, based on the Alcohol Use Disorders Identification Test (AUDIT). We found that among non-heavy drinkers, Now bias inversely correlated with age; this relationship was not present among heavy drinkers. We found no significant relationship between AUDIT score and Now bias among emerging adults, but AUDIT scores and Now bias were positively correlated among 26–40 year olds. Additionally, non-heavy drinking adults who reported a problem drinking first degree relative showed greater Now bias compared to those not reporting familial problem drinking. While not definitive, these findings lend support for elevated Now bias in adulthood as an intermediate phenotype for AUDs. Moreover, non-additive effects of age and heavy drinking on Now bias suggest perturbations in largely common neural circuits in both groups.
Using a Paradigm Shift to Teach Neurobiology and the Nature of Science—a C.R.E.A.T.E.-based Approach

Decades ago, classic experiments established the phenomenon of “neural induction” (Spemann and Mangold, 1924; Holtfreter, 1933). It appeared clear that amphibian ectoderm was pre-programmed to form epidermis, and that the neural phenotype was induced by a chemical signal from mesoderm. The “ectoderm makes skin, unless induced to make nervous system” model appeared in many textbooks. This interpretation, however, was not simply incorrect but 180 degrees out of alignment with the actual situation. As subsequently demonstrated, the default state of amphibian ectoderm is neuronal, and the expression of the epidermal phenotype requires cell signaling (Hemmati-Brivanlou and Melton, 1992; 1994; 1997). In this activity, students are presented with key experiments in a stepwise fashion. At several points, they work in groups to devise models that explain particular experimental results. The stepwise presentation of results mirrors the history of discoveries in this experimental system. Eventually, faced with seemingly contradictory data, students must revise their models substantially and in doing so, experience the paradigm shift. The lesson also examines the history of this paradigm shift. Data inconsistent with the “epidermal default” model were published years before the “neural default” model was proposed, but the significance of the surprising new data was underemphasized by the scientists who made the discovery. Discussing this situation provides insight into how science works and highlights the possibility that working scientists may become entrenched in prevailing paradigms. Such “nature of science” discussions emphasize research as a human activity, and help to dispel student misconceptions about science and scientists.
Optimized sectionalizing switch placement strategy in distribution systems

Summary form only given. Automation is acknowledged by distribution utilities as a successful investment strategy to enhance reliability and operation efficiency. However, practical approaches that can handle the complex decision making process faced by decision makers, to justify the long-term financial effects of distribution automation, have remained scarce. Automated and remote controlled sectionalizing switch play a fundamental role in an automated distribution network. This paper introduces a new optimization approach for distribution automation in terms of automated and remotely controlled sectionalizing switch placement. Mixed-integer linear programming (MILP) is utilized to model the problem. The proposed model can be solved with large-scale commercial solvers in a computationally efficient manner. The proposed sectionalizing switch placement problem considers customer outage costs in conjunction with sectionalizing switch capital investment, installation and annual operation and maintenance costs. The effectiveness of the proposed approach is tested on a reliability test system and a typical real size system. The results presented indicate the accuracy and efficiency of the proposed method.
The validation of electronic health records in accurately identifying patients eligible for colorectal cancer screening in safety net clinics.

BACKGROUND While electronic health records (EHRs) play a key role in increasing colorectal cancer (CRC) screening by identifying individuals who are overdue, important shortfalls remain. OBJECTIVES As part of the Strategies and Opportunities to STOP Colon Cancer (STOP CRC) study, we assessed the accuracy of EHR codes in identifying patients eligible for CRC screening. METHODS We selected a stratified random sample of 800 study participants from 26 participating clinics, in the Pacific Northwest region of the USA. We compared data obtained through codes in the EHR to conduct a manual chart audit. A trained chart abstractor completed the abstraction of eligible and ineligible patients. RESULTS Of 520 individuals in need of CRC screening, identified via the EHR, 459 were confirmed through chart review (positive predictive value = 88%). Of 280 individuals flagged as up-to-date in their screening per EHR data, 269 were confirmed through chart review (negative predictive value = 96%). Among the 61 patients incorrectly classified as eligible, 83.6% of disagreements were due to evidence of a prior colonoscopy or referral that was not captured in recognizable fields in the EHR. CONCLUSIONS Our findings highlight importance of better capture of past screening events in the EHR. While the need for better population-based data is not unique to CRC screening, it provides an important example of the use of population-based data not only for tracking care, but also for delivering interventions.
Addressing model complexity in automotive system development: Selection of system model elements for allocation of requirements

Modern automotive embedded systems are developed by Original Equipment Manufacturers (OEM) together with multiple suppliers. A key problem for a supplier is to allocate an OEM's requirements specification to their own subsystem design. This is a difficult manual task especially on complex systems and it requires expert knowledge about the system design. To address this problem, this paper presents a design science research to develop and evaluate a Requirements Allocation Assistant tool (RAA). The tool provides functionality to search through and filter requirements and system models to enable efficient requirements allocation even in the presence of complexity. RAA is built on top of the EATOP/Eclipse framework using EAST-ADL as system modelling language. The tool was evaluated and validated during a qualitative usability study with 17 engineers active in the Swedish automotive industry. Key findings are that searching is used to learn about a system, whereas filtering is used to narrow down a set of candidate elements of the system design. Engineers request further support in narrowing down a set of candidate elements and in checking that an allocation is correct.
Model Intercomparison of Atmospheric 137Cs From the Fukushima Daiichi Nuclear Power Plant Accident: Simulations Based on Identical Input Data

A model intercomparison of the atmospheric dispersion of cesium‐137 (137Cs) emitted after the Fukushima Daiichi Nuclear Power Plant accident in Japan was conducted to understand the behavior of atmospheric 137Cs in greater detail. The same meteorological data with a fine spatiotemporal resolution and an emission inventory were applied to all models to exclude the differences among the models originating from differences in meteorological and emission data. The meteorological data were used for initial, boundary, and nudging data or offline meteorological field. Furthermore, a horizontal grid with the same resolution as that of the meteorological data was adopted for all models. This setup enabled us to focus on model variability originating from the processes included in each model, for example, physical processes. The multimodel ensemble captured 40% of the atmospheric 137Cs events observed by measurements, and the figure of merit in space for the total deposition of 137Cs exceeded 80. The lower score of the atmospheric 137Cs than that of the deposition originated from the difference in timing between observed and simulated atmospheric 137Cs. Our analyses indicated that meteorological data were most critical for reproducing the atmospheric 137Cs events. The results further revealed that differences in 137Cs concentrations among the models originated from deposition and diffusion processes when the meteorological field was simulated reasonably well. The models with small deposition fluxes produced higher scores for atmospheric 137Cs, and those with strong diffusion succeeded in capturing the high 137Cs concentrations observed; however, they also tended to overestimate the concentrations.
Top-Down Discovery of Cross-Level Web Browsing Sequences on Taxonomy

Web mining has been studied extensively in recent years due to the fact that the discovered information can be used to improve web site design and services, among 2 others. In particular, many techniques for mining user browsing patterns have been proposed in recent years. However, most of these works focus on mining browsing patterns of web pages directly. In this work, we consider the problem of mining generalized browsing patterns on both multiple-level and cross-level of taxonomy comprised of web pages. We propose here an algorithm to discover these generalized browsing patterns based on top-down level-wise searching approach. Example demonstrating the proposed approach is given. Comparisons with the Generalized Sequential Patterns (GSP) approach [16] and Apriori-Level approach [19] show that the proposed top-down approach generates fewer candidate sequences. This indicates that the proposed algorithm is more efficient in discovering cross-level web browsing sequences.
Spine-based coordinate system

Traditional techniques for analyzing tortuous anatomical structures (e.g. arteries, colon, spine) in the coordinate system of the 3D image generally do not provide sufficient or qualitative enough diagnostic information, because planar cross-sections do not follow curved paths along the structures. To overcome this shortcoming, images in the coordinate system of the structure must be created. We propose a transformation from standard image-based to a novel spine-based coordinate system. The origin and axes of the proposed spine-based coordinate system are determined on the curve that represents the vertebral column, and the rotation of the vertebrae around the spine curve, both of which are described by polynomial models. The optimal polynomial parameters are obtained in an image analysis based optimization framework. The method has been evaluated on five CT spine images
Microarray-Based Comparisons of Ion Channel Expression Patterns: Human Keratinocytes to Reprogrammed hiPSCs to Differentiated Neuronal and Cardiac Progeny

Ion channels are involved in a large variety of cellular processes including stem cell differentiation. Numerous families of ion channels are present in the organism which can be distinguished by means of, for example, ion selectivity, gating mechanism, composition, or cell biological function. To characterize the distinct expression of this group of ion channels we have compared the mRNA expression levels of ion channel genes between human keratinocyte-derived induced pluripotent stem cells (hiPSCs) and their somatic cell source, keratinocytes from plucked human hair. This comparison revealed that 26% of the analyzed probes showed an upregulation of ion channels in hiPSCs while just 6% were downregulated. Additionally, iPSCs express a much higher number of ion channels compared to keratinocytes. Further, to narrow down specificity of ion channel expression in iPS cells we compared their expression patterns with differentiated progeny, namely, neurons and cardiomyocytes derived from iPS cells. To conclude, hiPSCs exhibit a very considerable and diverse ion channel expression pattern. Their detailed analysis could give an insight into their contribution to many cellular processes and even disease mechanisms.