Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of LRP5 Polymorphisms on Normal Variation in BMD

Genetic studies based on cohorts with rare and extreme bone phenotypes have shown that the LRP5 gene is an important genetic modulator of BMD. Using family‐based and case‐control approaches, this study examines the role of the LRP5 gene in determining normal population variation of BMD and describes significant association and suggestive linkage between LRP5 gene polymorphisms and BMD in >900 individuals with a broad range of BMD.
Complete inhibition of rhabdomyosarcoma xenograft growth and neovascularization requires blockade of both tumor and host vascular endothelial growth factor.

Growth of the human rhabdomyosarcoma A673 cell line in nude mice is substantially reduced but not completely suppressed after systemic administration of the antihuman vascular endothelial growth factor (VEGF) monoclonal antibody (Mab) A.4. 6.1. Potentially, such escape might be attributable to incomplete local penetration of the antibody because of a diffusion barrier associated with tumor growth. Alternatively, it might reflect a compensatory up-regulation of murine VEGF, produced by the stroma of the host, or of other angiogenic factor genes. To test these potential mechanisms, systemic administration of Mab A.4. 6.1, was performed in conjunction with intratumoral administration of an irrelevant antibody, an antihuman VEGF Fab or mFlt(1-3)-IgG that neutralizes both human and murine VEGF. Tumor growth in the systemic-plus-intratumoral anti-VEGF group was not different from that in the systemic anti-VEGF-plus-intratumoral-control antibody group, arguing against the possibility that bioavailability is the factor that limits the antitumor efficacy of Mab A.4. 6.1. However, intratumoral mFlt(l-3)-IgG administration dramatically enhanced the activity of systemic anti-VEGF Mab and resulted in complete suppression of tumor growth, which indicated that host VEGF significantly contributes to tumor growth. Systemic administration of mFlt(1-3)-IgG alone replicated these findings. Histological analysis of residual tumor tissues revealed an almost complete absence of host-derived vasculature and massive tumor-cell necrosis in the mFlt(1-3)-IgG groups. Such extensive necrotic areas were not present in the other groups. Real-time reverse transcription-PCR analysis of total RNA derived from tumor tissues indicated strong up-regulation of both human and murine VEGF as well as other genes regulated by hypoxia. Our findings emphasize the need to completely block VEGF for maximal inhibition of tumor growth.
Rhetorical structure and argumentation structure in monologue text

On the basis of a new corpus of short “microtexts” with parallel manual annotations, we study the mapping from discourse structure (in terms of Rhetorical Structure Theory, RST) to argumentation structure. We ﬁrst perform a qualitative analysis and discuss our ﬁndings on correspondence patterns. Then we report on experiments with deriving argumentation structure from the (gold) RST trees, where we compare a tree transformation model, an aligner based on subgraph matching, and a more complex “evidence graph” model.
Cost-Effectiveness of Five Commonly Used Prosthesis Brands for Total Knee Replacement in the UK: A Study Using the NJR Dataset

Background There is a lack of evidence on the effectiveness or cost-effectiveness of alternative brands of prosthesis for total knee replacement (TKR). We compared patient-reported outcomes, revision rates, and costs, and estimated the relative cost-effectiveness of five frequently used cemented brands of unconstrained prostheses with fixed bearings (PFC Sigma, AGC Biomet, Nexgen, Genesis 2, and Triathlon). Methods We used data from three national databases for patients who had a TKR between 2003 and 2012, to estimate the effect of prosthesis brand on post-operative quality of life (QOL) (EQ-5D-3L) in 53 126 patients at six months. We compared TKR revision rates by brand over 10 years for 239 945 patients. We used a fully probabilistic Markov model to estimate lifetime costs and quality-adjusted life years (QALYs), incremental cost effectiveness ratios (ICERs), and the probability that each prosthesis brand is the most cost effective at alternative thresholds of willingness-to-pay for a QALY gain. Findings Revision rates were lowest with the Nexgen and PFC Sigma (2.5% after 10 years in 70-year-old women). Average lifetime costs were lowest with the AGC Biomet (£9 538); mean post-operative QOL was highest with the Nexgen, which was the most cost-effective brand across all patient subgroups. For example, for 70-year-old men and women, the ICERs for the Nexgen compared to the AGC Biomet were £2 300 per QALY. At realistic cost per QALY thresholds (£10 000 to £30 000), the probabilities that the Nexgen is the most cost-effective brand are about 98%. These results were robust to alternative modelling assumptions. Conclusions AGC Biomet prostheses are the least costly cemented unconstrained fixed brand for TKR but Nexgen prostheses lead to improved patient outcomes, at low additional cost. These results suggest that Nexgen should be considered as a first choice prosthesis for patients with osteoarthritis who require a TKR.
Antiproliferative Effects of Homogenates Derived from Five Strains of Candidate Probiotic Bacteria

ABSTRACT Unheated and heat-treated homogenates were separately prepared from candidate probiotic bacteria, including Lactobacillus rhamnosus GG, Bifidobacterium lactis,Lactobacillus acidophilus, Lactobacillus delbrueckii subsp. bulgaricus, andStreptococcus thermophilus. We compared the phytohemagglutinin-induced proliferation of mononuclear cells in the presence of homogenates and in the presence of a control containing no homogenate by assessing thymidine incorporation in cell cultures. All homogenates suppressed proliferation, whether the enzymatic activity was inactivated or not inactivated by heating. When the proliferation assays were repeated with cytoplasmic and cell wall extracts derived from the homogenate of L. rhamnosus GG, the cytoplasmic extract but not the cell wall extract was suppressive. These findings indicate that candidate probiotic bacteria possess a heat-stable antiproliferative component(s). These bacteria may be used to generate microbiologically nonviable yet immunologically active probiotic food products that are easier to store and have a longer shelf life.
How flickr helps us make sense of the world: context and content in community-contributed media collections

The advent of media-sharing sites like Flickr and YouTube has drastically increased the volume of community-contributed multimedia resources available on the web. These collections have a previously unimagined depth and breadth, and have generated new opportunities - and new challenges - to multimedia research. How do we analyze, understand and extract patterns from these new collections? How can we use these unstructured, unrestricted community contributions of media (and annotation) to generate "knowledge". As a test case, we study Flickr - a popular photo sharing website. Flickr supports photo, time and location metadata, as well as a light-weight annotation model. We extract information from this dataset using two different approaches. First, we employ a location-driven approach to generate aggregate knowledge in the form of "representative tags" for arbitrary areas in the world. Second, we use a tag-driven approach to automatically extract place and event semantics for Flickr tags, based on each tag's metadata patterns. With the patterns we extract from tags and metadata, vision algorithms can be employed with greater precision. In particular, we demonstrate a location-tag-vision-based approach to retrieving images of geography-related landmarks and features from the Flickr dataset. The results suggest that community-contributed media and annotation can enhance and improve our access to multimedia resources - and our understanding of the world.
Domain Adaptation for Opinion Mining: A Study of Multipolarity Words

Expression of opinion depends on the domain. For instance, some words, called here multi-polarity words, have dierent polarities across domain. Therefore, a classifier trained on one domain and tested on another one will not perform well without adaptation. This article presents a study of the influence of these multi-polarity words on domain adaptation for automatic opinion classification. We also suggest an exploratory method for detecting them without using any label in the target domain. We show as well how these multi-polarity words can improve opinion classification in an open-domain corpus.
Tubular breast cancer. A retrospective study.

BACKGROUND The well-characterized tubular-type of breast tumors is classified as low-risk breast cancer. PATIENTS AND METHODS We report on the results of a retrospective analysis on clinical and biological features of 248 tubular breast tumors including follow-up and treatment data from two German series of 21,065 breast cancer cases. The majority of tumors were stage I or stage II, ER- and PR-positive and c-erbB2-negative with a 5-year survival-rate of 96.3%. 51.3% of patients received hormonal treatment, 75.5% had post-operative radiotherapy and 11.8% were treated with a chemotherapeutical regimen. CONCLUSION Our retrospective analysis showed no treatment benefit for either anti-hormonal or chemotherapeutical regimens. Post-operative radiotherapy, however, improved the survival rate of patients with tubular carcinoma (log-rank=5, p=0.025). Our data suggest that post-operative radiotherapy is an important treatment to prolong survival for patients suffering from tubular breast cancer.
Evolving software product lines with aspects

Software product lines (SPLs) enable modular, large-scale reuse through a software architecture addressing multiple core and varying features. To reap the benefits of SPLs, their designs need to be stable. Design stability encompasses the sustenance of the product line's modularity properties in the presence of changes to both the core and varying features. It is usually assumed that aspect-oriented programming promotes better modularity and changeability of product lines than conventional variability mechanisms, such as conditional compilation. However, there is no empirical evidence on its efficacy to prolong design stability of SPLs through realistic development scenarios. This paper reports a quantitative study that evolves two SPLs to assess various design stability facets of their aspect-oriented implementations. Our investigation focused upon a multi-perspective analysis of the evolving product lines in terms of modularity, change propagation, and feature dependency. We have identified a number of scenarios which positively or negatively affect the architecture stability of aspectual SPLs.
Optogenetic inhibition of cocaine seeking in rats

Inhibitory optogenetics was used to examine the roles of the prelimbic cortex (PL), the nucleus accumbens core (NAcore) and the PL projections to the NAcore in the reinstatement of cocaine seeking. Rats were microinjected into the PL or NAcore with an adeno‐associated virus containing halorhodopsin or archaerhodopsin. After 12 days of cocaine self‐administration, followed by extinction training, animals underwent reinstatement testing along with the presence/absence of optically induced inhibition via laser light. Bilateral optical inhibition of the PL, NAcore or the PL fibers in the NAcore inhibited the reinstatement of cocaine seeking.
Integrated Epigenome Profiling of Repressive Histone Modifications, DNA Methylation and Gene Expression in Normal and Malignant Urothelial Cells

Epigenetic regulation of gene expression is commonly altered in human cancer. We have observed alterations of DNA methylation and microRNA expression that reflect the biology of bladder cancer. This common disease arises by distinct pathways with low and high-grade differentiation. We hypothesized that epigenetic gene regulation reflects an interaction between histone and DNA modifications, and differences between normal and malignant urothelial cells represent carcinogenic events within bladder cancer. To test this we profiled two repressive histone modifications (H3K9m3 and H3K27m3) using ChIP-Seq, cytosine methylation using MeDIP and mRNA expression in normal and malignant urothelial cell lines. In genes with low expression we identified H3K27m3 and DNA methylation each in 20–30% of genes and both marks in 5% of genes. H3K9m3 was detected in 5–10% of genes but was not associated with overall expression. DNA methylation was more closely related to gene expression in malignant than normal cells. H3K27m3 was the epigenetic mark most specifically correlated to gene silencing. Our data suggest that urothelial carcinogenesis is accompanied by a loss of control of both DNA methylation and H3k27 methylation. From our observations we identified a panel of genes with cancer specific-epigenetic mediated aberrant expression including those with reported carcinogenic functions and members potentially mediating a positive epigenetic feedback loop. Pathway enrichment analysis revealed genes marked by H3K9m3 were involved with cell homeostasis, those marked by H3K27m3 mediated pro-carcinogenic processes and those marked with cytosine methylation were mixed in function. In 150 normal and malignant urothelial samples, our gene panel correctly estimated expression in 65% of its members. Hierarchical clustering revealed that this gene panel stratified samples according to the presence and phenotype of bladder cancer.
Comparative study of signal decomposition methods for enhancement of the accuracy of T-wave end localisation

The goal of this study was to compare several ECG signal decomposition methods in order to enhance the accuracy of T wave end localisation. PTB Diagnostic ECG Database comprising 549 recordings was used. The idea was to combine the 8 independent leads (I, II, V1,., V6) of the standard 12-leads ECG into a single lead.The signal decomposition methods were applied to reconstruct the combined T wave in such a way as to obtain maximal accuracy of the automatic T-end localisation. Four signal decomposition methods were used: Dominant T-wave (DTW), Principal Component analysis (PCA), and two Spatial Vectors (SVI & SV2) synthesized from the orthogonal x, y, and z vectors. The T-ends were localized using the same previously published software program. The results were compared to a published 'gold standard' dataset of manually determined T ends. Mean and standard deviation of the difference between the automatic and manual T-end locations were calculated in [ms]: DTW=8.72+14.19; PCA=10.30+12.69; SVI= -8.14+14.53; SV2=8. 59+17.93. The best results (i.e. smallest standard deviation) were obtained by PCA followed by DTW. Compared to manual measurement, all signal decomposition methods except SVI moved the mean Tend location slightly to the right.
Comparative Analysis of Lycorine in Wild Plant and Callus Culture Samples of Hymenocallis littoralis by HPLC-UV Method

The Hymenocallis littoralis, an ornamental and medicinal plant, had been traditionally used for wound healing. In the present study, an analytical method using HPLC with ultraviolet detection was developed for the quantification of lycorine in the extracts of different parts of wild plant and tissue culture samples of H. littoralis. The separation was achieved using a reversed-phase column. The method was found to be accurate, repeatable, and sensitive for the quantification of minute amount of lycorine present in the samples. The highest lycorine content was found in the bulb extract (2.54 ± 0.02 μg/mg) whereas the least was in the root extract (0.71 ± 0.02 μg/mg) of the wild plants. Few callus culture samples had high content of lycorine, comparable to that of wild plants. The results showed that plant growth regulators, 2,4-dichlorophenoxyacetic acid (2,4-D) alone at 4.5 μM (2.58 ± 0.38 μg/mg) or a combination of 2,4-D at 9.00 μM with 4.5 μM of 6-benzylaminopurine (BAP), were the optimum concentrations for the production of high lycorine (2.45 ± 0.15 μg/mg) content in callus culture. The present analytical method could be of value for routine quantification of lycorine in the tissue culture production and standardization of the raw material or extracts of H. littoralis.
The Current Status of Research in Residential Treatment

Recent studies conducted in residential or hospital settings were reviewed. Although major obstacles continue to impede the research endeavor in residential ueatmenl, several areas of notable progress are evident. Developmental psychopathology research conducted in residential treatment settings is confirming or modifying conclusions based on research with non-referred samples of young people. Outcome studies of single samples have demonstrated increasing reliance upon standardized measures and have clarified he components of, and confirmed the importance of, the post-discharge environment. Comparative outcome studies have served to emphasize the importance of defining the treatment program in residential care.
A new approach in designing electrically controlled capacitance multipliers

A new solution for capacitance multiplier based on current injection from a reference capacitor in a circuit loop which contains gate to source voltages is proposed. The loop can be unbalanced thanks to a dc voltage, thereby causing that drain current in one of the transistors to have a multiplied value of the current from reference capacitor. Multiplied current is translated to the circuit input, causing its capacitive behavior.
Self-Reported Truck Traffic on the Street of Residence and Symptoms of Asthma and Allergic Disease: A Global Relationship in ISAAC Phase 3

Background Associations between traffic pollution on the street of residence and a range of respiratory and allergic outcomes in children have been reported in developed countries, but little is known about such associations in developing countries. Methods The third phase of the International Study of Asthma and Allergies in Childhood (ISAAC) was carried out in 13- to 14-year-old and 6- to 7-year-old children across the world. A question about frequency of truck traffic on the street of residence was included in an additional questionnaire. We investigated the association between self-reported truck traffic on the street of residence and symptoms of asthma, rhinoconjunctivitis, and eczema with logistic regression. Adjustments were made for sex, region of the world, language, gross national income, and 10 other subject-specific covariates. Results Frequency of truck traffic on the street of residence was positively associated with the prevalence of symptoms of asthma, rhinoconjunctivitis, and eczema with an exposure–response relationship. Odds ratios (95% confidence intervals) for “current wheeze” and “almost the whole day” versus “never” truck traffic were 1.35 (1.23–1.49) for 13- to 14-year-olds and 1.35 (1.22–1.48) for 6- to 7-year-olds. Conclusions Higher exposure to self-reported truck traffic on the street of residence is associated with increased reports of symptoms of asthma, rhinitis, and eczema in many locations in the world. These findings require further investigation in view of increasing exposure of the world’s children to traffic.
Adaptive Radio-Frequency Resource Management for MIMO MC-CDMA on Antenna Selection

The performance of a MIMO system could be significantly improved by employing a large number of transmission and /or reception antennas. The necessary need of multiple radio-frequency chain for each antenna increases the complexity of hardware. In this paper, we present a novel adaptive transmission technique for MIMO MC-CDMA systems, with the aim to flexibly manage RF resource based on antenna selection. Instead of choosing transmission antennas together, we simply select them one by one from entire set of possible transmission antennas. The simulation results, depending on both numbers of users and signal to noise ratio (SNR) value, show significant gains compared to fixed systems for a predefined target bit error rate (BER).
Generating 1-DOF limit cycle walking at target walking speed by feedforward limit cycle control

This paper proposes the feedforward control systems for generating the limit cycle walking at a target walking speed by an active combined rimless wheel (CRW) model. We propose the feedforward control systems which can design the control input at the beginning of each step based on the mathematical analysis of the initial and target walking states. As a result, the limit cycle walking at the target walking speeds are generated by numerical simulations. In addition, for controlling the walking stability, we extend the feedforward to the two-period stepwise control systems. The limit cycle walking at target walking speed are also generated and the walking stability are controlled by the settling time parameter.
Mass spectrometry and next‐generation sequencing reveal an abundant and rapidly evolving abalone sperm protein

Abalone, a broadcast spawning marine mollusk, is an important model for molecular interactions and positive selection in fertilization, but the focus has previously been on only two sperm proteins, lysin and sp18. We used genomic and proteomic techniques to bring new insights to this model by characterizing the testis transcriptome and sperm proteome of the Red abalone Haliotis rufescens. One pair of homologous, testis‐specific proteins contains a secretion signal and is small, abundant, and associated with the acrosome. Comparative analysis revealed that homologs are extremely divergent between species, and show strong evidence for positive selection. The acrosomal localization and rapid evolution of these proteins indicates that they play an important role in fertilization, and could be involved in the species‐specificity of sperm‐egg interactions in abalone. Our genomic and proteomic characterization of abalone fertilization resulted in the identification of interesting, novel peptides that have eluded detection in this important model system for 20 years. Mol. Reprod. Dev. 80: 460–465, 2013. © 2013 Wiley Periodicals, Inc.
Learning Nonparametric Forest Graphical Models with Prior Information

We present a framework for incorporating prior information into nonparametric estimation of graphical models. To avoid distributional assumptions, we restrict the graph to be a forest and build on the work of forest density estimation (FDE). We reformulate the FDE approach from a Bayesian perspective, and introduce prior distributions on the graphs. As two concrete examples, we apply this framework to estimating scale-free graphs and learning multiple graphs with similar structures. The resulting algorithms are equivalent to finding a maximum spanning tree of a weighted graph with a penalty term on the connectivity pattern of the graph. We solve the optimization problem via a minorize-maximization procedure with Kruskal's algorithm. Simulations show that the proposed methods outperform competing parametric methods, and are robust to the true data distribution. They also lead to improvement in predictive power and interpretability in two real data sets.