Miracle-dz/UniFAR-FTUs huggingface dataset:
Tumor and Stem Cell Biology Homeoprotein Six 1 Increases TGF-b Type I Receptor and Converts TGF-b Signaling from Suppressive to Supportive for Tumor Growth

The Six1 homeodomain protein is a developmental transcription factor that has been implicated in tumor onset and progression. Our recent work shows that Six1 overexpression in human breast cancer cell lines is sufficient to induce epithelial-to-mesenchymal transition (EMT) andmetastasis. Importantly, Six1-induced EMT and metastasis are dependent on TGF-b signaling. The TGF-b pathway plays a dual role in cancer, acting as a tumor suppressor in early lesions but enhancing metastatic spread inmore advanced tumors. Our previous work indicated that Six1 may be a critical mediator of the switch in TGF-b signaling from tumor suppressive to tumor promotional. However, the mechanism by which Six1 impinges on the TGF-b pathway was, until now, unclear. In this work, we identify the TGF-b type I receptor (TbRI) as a target of Six1 and a critical effector of Six1-induced TGF-b signaling and EMT. We show that Six1-induced upregulation of TbRI is both necessary and sufficient to activate TGF-b signaling and induce properties of EMT. Interestingly, increased TbRI expression is not sufficient to induce experimental metastasis, providing in vivo evidence that Six1 overexpression is required to switch TGF-b signaling to the prometastatic phenotype and showing that induction of EMT is not sufficient to induce experimental metastasis. Together, these results show a novel mechanism for the activation of TGF-b signaling, identify TbRI as a new target of Six1, and implicate Six1 as a determinant of TGF-b function in breast cancer. Cancer Res; 70(24); 10371–80. 2010 AACR.
MRI assessment of human callosal surgery with neuropsychological correlates

MRI imaging using recovery and spin-echo techniques was carried out on three patients after surgical section of the corpus callosum to control intractable epilepsy. The scans revealed that the total callosotomy had been obtained in two patients, while partial sparing of splenial and rostra1 fibers was seen in the third.
Datasets for Aspect-Based Sentiment Analysis in French

Aspect Based Sentiment Analysis (ABSA) is the task of mining and summarizing opinions from text about specific entities and their aspects. This article describes two datasets for the development and testing of ABSA systems for French which comprise user reviews annotated with relevant entities, aspects and polarity values. The first dataset contains 457 restaurant reviews (2365 sentences) for training and testing ABSA systems, while the second contains 162 museum reviews (655 sentences) dedicated to out-of-domain evaluation. Both datasets were built as part of SemEval-2016 Task 5 “Aspect-Based Sentiment Analysis” where seven different languages were represented, and are publicly available for research purposes.
A robust, streamlined, and reproducible method for proteomic analysis of serum by delipidation, albumin and IgG depletion, and two‐dimensional gel electrophoresis

Serum is a readily available source for diagnostic assays, but the identification of disease‐specific serum biomarkers has been impeded by the dominance of human serum albumin and immunoglobulins (Igs) in the serum proteome. There is a need to reduce the technical variation in serum processing and analysis to allow for a reproducible analysis of large cohorts. To this end, we have developed a rapid and reproducible procedure for sample preparation and high‐resolution two‐dimensional gel electrophoresis to analyze human serum. Serum is centrifuged at high speed to remove lipids and aggregated proteins, incubated with protein G resin to remove IgG, precipitated with NaCl/ethanol to deplete albumin, and slowly resolubilized in a sodium dodecyl sulfate (SDS)/N‐(2‐hydroxyethyl)piperazine‐2’‐(2‐ethanesulfonic acid) (HEPES) buffer. The delipidated and IgG/albumin depleted serum proteins are focused on pH 4–7 linear large immobilized pH gradient strips, and then resolved by Bis‐Tris SDS‐polyacrylamide gel electrophoresis. The robustness and reproducibility of the optimized procedure was determined for three individual serum samples on three consecutive days. An image analysis of the nine silver‐stained gels demonstrated that the intensity and localization of protein spots are highly reproducible. Our IgG and albumin depletion procedure will aid in screening the patient sera for normal biological variation and disease‐specific biomarkers.
Monitoring autophagy in glioblastoma with antibody against isoform B of human microtubule-associated protein 1 light chain 3

Autophagy, an evolutionarily conserved response to stress, has recently been implicated in cancer initiation and progression, but the detailed mechanisms and functions have not yet been fully elucidated. One major obstacle to our understanding is lack of an efficient and robust method to specifically monitor autophagic cells in cancer specimens. To identify molecular events associated with autophagy, we performed cDNA microarray analysis of autophagic glioblastoma cell lines. Based on the analysis, we raised a polyclonal antibody against isoform B of human microtubule-associated protein 1 light chain 3 (LC3B). Application of the anti-LC3B antibody revealed the presence of autophagic cells in both in vitro and in vivo settings. Of the 65 glioblastoma tissues, 31 had highly positive cytoplasmic staining of LC3B. The statistical interaction between cytoplasmic staining of LC3B and Karnofsky Performance Scale score was significant. High expression of LC3B was associated with an improved outcome for patients with poorer performance, whereas, for patients with normal performance, survival was better for patients with low staining than with high staining of LC3B. Anti-LC3B antibody provides a useful tool for monitoring the induction of autophagy in cancer cells and tissues.
VAST 2007 Contest - Blue Iguanodon

Visual analytics experts realize that one effective way to push the field forward and to develop metrics for measuring the performance of various visual analytics components is to hold an annual competition. The second visual analytics science and technology (VAST) contest was held in conjunction with the 2007 IEEE VAST symposium. In this contest participants were to use visual analytic tools to explore a large heterogeneous data collection to construct a scenario and find evidence buried in the data of illegal and terrorist activities that were occurring. A synthetic data set was made available as well as tasks. In this paper we describe some of the advances we have made from the first competition held in 2006.
Effects of ecogeographic variables on genetic variation in montane mammals: implications for conservation in a global warming scenario

Aim Evolutionary theory predicts that levels of genetic variation in island populations will be positively correlated with island area and negatively correlated with island isolation. These patterns have been empirically established for oceanic islands, but little is known about the determinants of variation on habitat islands. The goals of this study were twofold. Our first aim was to test whether published patterns of genetic variation in mammals occurring on montane habitat islands in the American Southwest conformed to expectations based on evolutionary theory. The second aim of this research was to develop simple heuristic models to predict changes in genetic variation that may occur in these populations as a result of reductions in available mountaintop habitat in response to global warming.
Optimization of DNA extraction for quantitative marine bacterioplankton community analysis

The coupling between the presence of predominant bacterial species and particular biogeochemical processes is of primary interest in current microbial ecology. Molecular methods such as microarrays and real‐time polymerase chain reaction (PCR) may be used to estimate presence or expression of different genes (e.g., 16S rDNA and nifH) in environmental samples; however, to be quantitative, these methods require a reproducible and efficient DNA extraction protocol. Using picogreen DNA quantification, real‐time PCR, and an internal DNA standard, we step‐wise examined and optimized a protocol for DNA extraction from centrifuged or filtered seawater samples (vol. 2 to 300 mL). Sample volume had a pronounced effect on DNA extraction efficiency showing that comparison of samples with different volumes is problematic. The duration of enzyme treatment (lysozyme and proteinase K) significantly influenced the DNA extraction efficiency. Dissolved DNA contributed significantly to total DNA when extracted from small filtering volumes (<10 mL). Addition of a coprecipitant (yeast tRNA) improved the precipitation of low‐concentration DNA from 13% to 89%. When tested on various seawater samples, as well as on isolates, the optimized extraction protocol was found to be highly reproducible with an average extraction efficiency for seawater samples of 92% and for isolates of 96%. The quantitative outcome and the high extraction efficiency of the presented extraction protocol will be of value to future studies based on DNA extracted from seawater samples.
Molecular Cloning and Sequence Analysis of a gene encoding WD repeat-containing protein 13 from Ginkgo biloba

The WD-repeat proteins are found in eukaryotes and play an important role in the regulation of a wide variety of cellular functions including signal transduction, pre-mRNA processing and cytoskeleton assembly. In this study, a cDNA encoding a WD repeat-containing protein 13 (GbWDR13) was cloned by PCR from Ginkgo biloba. The length of GbWDR13 gene is 1500 bp, encoding 496 amino acids. The predicted amino acid sequence of GbWDR13 containing a WD40 domain display extensive homology to WD-repeat amino acids from other plants including Vitis vinifera, Solanum lycopersicum, Phoenix dactylifera and Cicer arietinum. Phylogenetic analysis showed that the GbWDR13 has a closer relationship with WDR13 from Gymnosperms than from other plants, suggesting it may be from the same ancestor as WD-repeat proteins from other gymnosperms. The isolation and sequence analysis of GbWDR13 gene provided a foundation for further studying the function of WD-repeat proteins in
Fault tolerant robust flight control using surface actuator hinge moments

A robust, flight control law is investigated to provide fault tolerance for air vehicles experiencing inertial state measurement sensor degradation. The method is particularly useful on low cost, precision weapons pursuing dynamic targets. Observation techniques are facilitated by representing the surface actuator aerodynamic induced hinge moment by a function that is Lipschitz within the actuator sweep angle. A stable output feedback flight control law, requiring only actuator angular position and current measurements, is designed to handle the hinge moment effects and track a predetermined angle-of-attack reference trajectory. Benefits include improved effectiveness, improved reliability without additional hardware, and a cost and weight savings. Simulations are conducted on a tactical missile interceptor to evaluate the controller at various operating conditions in the flight envelope.
Factors Related to Adaptation to Cystectomy With Urinary Diversion: An Integrative Review

Patients with bladder (urothelial) cancer undergoing urinary diversion (UD) experience physical changes that require important adjustments in their daily lives. This integrative review aims to identify factors that influence adult adaptation to life after cystectomy with the creation of a UD. A review of primary research articles published between 1990 and 2014 was conducted using the PubMed and CINAHL Plus electronic databases. Results of the studies were summarized into 5 categories: (1) individual and family factors, (2) technical aspects related to the individual's ability to care for his or her UD, (3) perioperative nursing care, (4) educational needs, and (5) symptom experience. Bladder cancer patients treated with a cystectomy with a UD have a complex set of needs during postoperative adaptation to their reconstructed urinary system. This integrative review summarizes existing knowledge of factors that affect adaptation to a UD in patients with bladder cancer and may guide future studies. Research on this is limited and more studies are needed.
The Effects of Simulated Inertia and Force Prediction on Delayed Telepresence

This paper presents two methods aimed at alleviating the negative effects of network delays on teleoperation. The problem of telepresence across delayed networks is well known. A delay in feedback information such as visual and haptic data can make the task at hand very unintuitive and difficult for the operator. The first presented method investigates the hypothesis that simulated inertia in the haptic input device can be a supporting factor during teleoperation across delayed networks. An experiment involving 36 human subjects was carried out under varying network and inertia conditions. Psychophysical experiments were conducted to determine suitable values of inertia. However, simulated inertia was found to be neither a supporting factor nor a detrimental factor to operator performance and immersion in the presence of both delayed and non-delayed networks. The second presented method is a force prediction approach, which extends the teleoperation system with a local force model. This is a learned force model situated locally at the operator-side. Instead of relying on the delayed force signals from the teleoperator-side, haptic information can be extracted from this local force model. An experiment has been created to demonstrate the benefits of this approach in compensating for the instabilities due to time delay.
Special Issue on Robust Methods in Analysis of Natural Language Data

The automated analysis of natural language data has become a central issue in the design of Intelligent Information Systems. The term natural language is intended to cover all the possible modalities of human communication and it is not restricted to written or spoken language. Processing unrestricted natural language is still considered as an AI-hard task. However various analysis techniques have been proposed in order to address specific aspects of natural language. In particular, recent interest has been on providing approximate analysis techniques, assuming that perfect analysis is not possible, but that partial results are still very useful.
Combinatorics of γ-Structures

In this article we study canonical γ-structures, a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A γ-structure is composed of specific building blocks that have topological genus less than or equal to γ, where composition means concatenation and nesting of such blocks. Our main result is the derivation of the generating function of γ-structures via symbolic enumeration using so called irreducible shadows. We furthermore recursively compute the generating polynomials of irreducible shadows of genus ≤ γ. The γ-structures are constructed via γ-matchings. For 1 ≤ γ ≤ 10, we compute Puiseux expansions at the unique, dominant singularities, allowing us to derive simple asymptotic formulas for the number of γ-structures.
CONTRACEPTIVE PRACTICES OF WOMEN IN NORTHERN TSHWANE, GAUTENG PROVINCE

Despite the availability of free contraceptives in the Republic of South Africa (RSA), unwanted and unintended pregnancies continue to pose challenges to reproductive health services. Opsomming Alhoewel voorbehoedmiddels vrylik beskikbaar is in die Republiek van Suid-Afrika (RSA), bied ongewenste en onbeplande swangerskappe steeds uitdagings aan voortplantingsgesondheidsdienste. *Please note: This is a reduced version of the abstract. Please refer to PDF for full text.
The current state of evolution of content addressable memory architecture and aspects of its usage in the PDCS “Buran”

The article provides an overview of the main directions of the development of architectures of content addressable memory and associative processors. The main problems that are facing the developers of these devices are identified. The description of the content addressable memory of keys in the matching processor, which is the main computation process control device in the parallel dataflow computing system (PDCS) “Buran”, is given. Existing methods to increase the speed and reduce power consumption for various types of content addressable memory (CAM, TCAM, etc.) are considered. Various TCAM architectures implemented on the nonvolatile memory technology, as well as associative processors are described.
Insurance coverage, medical conditions, and visits to alternative medicine providers: results of a national survey.

BACKGROUND In 1997, patients made an estimated 629 million visits to complementary and alternative medicine (CAM) providers; however, little is known about factors associated with visits to CAM providers. OBJECTIVE To examine the effect of insurance coverage on frequency of use of CAM providers. METHODS We conducted a nationally representative, random household telephone survey of 2055 adults. MAIN OUTCOME MEASURE The number of visits made to CAM providers. RESULTS An estimated 44% of the US population used at least 1 CAM therapy in 1997. Of those using CAM, 52% had seen at least 1 CAM provider in the last year. Among those who used a CAM therapy, factors independently associated with seeing a provider were having been in the upper quartile of visits to conventional providers in the last year (adjusted odds ratio [AOR], 2.00; 95% confidence interval [CI], 1.33-3.01), female sex (AOR, 1.67; 95% CI, 1.17-2.38), and having used the therapy to treat diabetes (AOR, 5.20; 95% CI, 1.40-19.40), cancer (AOR, 2.99; 95% CI, 1.04-8.62), or back or neck problems (AOR, 1.51; 95% CI, 1.02-2.23). Factors independently associated with frequent use (. or = 8 visits per year) of a CAM provider were full insurance coverage of the CAM provider (AOR, 5.06; 95% CI, 2.45-10.47), partial insurance coverage (AOR, 3.26; 95% CI, 1.72-6.19), having used the therapy for wellness (AOR, 2.85; 95% CI, 1.63-4.98), and having seen the provider for back or neck problems (AOR, 2.26; 95% CI, 1.29-3.94). Conservative extrapolation to national estimates suggests that 8.9% of the population (17.5 million adults) accounted for more than 75% of the 629 million visits made to CAM providers in 1997. CONCLUSIONS A small minority of persons accounted for more than 75% of visits to CAM providers. Extent of insurance coverage for CAM providers and use for wellness are strong correlates of frequent use of CAM providers.
Barley phenolic compounds impedes oxidative stress in lead acetate intoxicated rabbits

This study was conducted to explore the effects of lead acetate and barley phenolic compounds, alone or in combination, on lipid peroxidation marker and some antioxidant enzymes using a rabbit model. Rabbits were provided with drinking water containing lead acetate (500 ppm) and/or gastro-gavaged with barley phenolic compounds (250 mg/kg/day) for 30 days. Following overnight fasting, the animals were sacrificed, and the levels of glutathione and malondialdehyde and the activities of glutathione S-transferase and glutathione peroxidase in brain, liver and kidney tissues were measured spectrophotometrically. Treatment with lead acetate significantly decreased the activities of glutathione S-transferase, glutathione peroxidase and the level of reduced glutathione, and it significantly increased the level of lipid peroxidation marker. Conversely, treatment with barley phenolic compounds, whether alone or in combination with lead acetate, significantly increased the activity of antioxidant enzymes and the level of reduced glutathione, and significantly decreased the level of lipid peroxidation marker. The use of barley phenolic compounds were successive to ameliorate the toxic effects of lead acetate, as reflected in the decreased levels of lipid peroxidation marker and the increased antioxidant activity.
Electric generation using electric organs of electric rays by chemical stimulation

An electric ray is a kind of electric fish generating strong pulse currency using electric organs which are serially integrated electrocytes converting chemical energy (ATP) into electric energy using ion pumps and ion channels on the cells. We here present a power generation method using this electric organ by chemical stimuli and injecting systems. Firstly, we have confirmed pulse generation by physical stimuli to an electric ray itself. Secondly, we investigated the electrical response of electric organs against chemical injection, and demonstrated power generation by this method. Finally, we have constructed a power generation device based on this result using fluidic control systems, and achieved about 400 mV voltage generation. This is extremely higher than single cell level generation of neurons or muscle cells against chemical stimuli (about μV order). This is because of the use of natural multi-layered organ for generation. The most important advantage of this system is just using biological energy and easy to be controlled.
Vagal nerve stimulator infection: a lead-salvage protocol.

OBJECT Vagal nerve stimulator (VNS) hardware infections are fraught with difficult management decisions. As with most implanted medical device-related infections, standard practice traditionally involves complete hardware removal, systemic antibiotic therapy, and subsequent reimplantation of the device. To avoid the potential morbidity of 2 repeat left carotid sheath surgical dissections, the authors have implemented a clinical protocol for managing VNS infections that involves generator removal and antibiotic therapy without lead removal. METHODS A prospective, single-surgeon database was compared with hospital billing records to identify patients who underwent primary implantation or reimplantation of a VNS lead, generator, or both, from January 2001 to May 2010, at Oregon Health & Science University. From these records, the authors identified patients with VNS hardware infections and characterized their management, using a lead salvage protocol. RESULTS In their review, the authors found a matching cohort of 206 children (age 3 months-17 years) who met the inclusion criteria. These children underwent 258 operations (including, in some children, multiple operations for generator end of life and/or lead malfunction). Six children experienced a single postimplantation infection (2.3% of the 258 operative cases), and no child experienced repeated infection. A lead-salvage protocol was used in 4 of 6 infected patients and was successful in 3 (75%), with clinical follow-up ranging from 10 months to 7.5 years. The fourth patient subsequently underwent lead removal and later reimplantation in standard fashion, with no adverse sequelae. CONCLUSIONS Vagal nerve stimulator lead salvage is a safe and potentially advantageous strategy in the management of VNS-related infection. Further study is necessary to validate appropriate patient selection, success rates, and risks of this approach.