Miracle-dz/UniFAR-FTUs huggingface dataset:
The Retinoblastoma Tumor Suppressor Modulates DNA Repair and Radioresponsiveness

Purpose: Perturbations in the retinoblastoma pathway are over-represented in advanced prostate cancer; retinoblastoma loss promotes bypass of first-line hormone therapy. Conversely, preliminary studies suggested that retinoblastoma-deficient tumors may become sensitized to a subset of DNA-damaging agents. Here, the molecular and in vivo consequence of retinoblastoma status was analyzed in models of clinical relevance. Experimental Design: Experimental work was performed with multiple isogenic prostate cancer cell lines (hormone sensitive: LNCaP and LAPC4 cells and hormone resistant C42, 22Rv1 cells; stable knockdown of retinoblastoma using shRNA). Multiple mechanisms were interrogated including cell cycle, apoptosis, and DNA damage repair. Transcriptome analysis was performed, validated, and mechanisms discerned. Cell survival was measured using clonogenic cell survival assay and in vivo analysis was performed in nude mice with human derived tumor xenografts. Results: Loss of retinoblastoma enhanced the radioresponsiveness of both hormone-sensitive and castrate-resistant prostate cancer. Hypersensitivity to ionizing radiation was not mediated by cell cycle or p53. Retinoblastoma loss led to alteration in DNA damage repair and activation of the NF-κB pathway and subsequent cellular apoptosis through PLK3. In vivo xenografts of retinoblastoma-deficient tumors exhibited diminished tumor mass, lower PSA kinetics, and decreased tumor growth after treatment with ionizing radiation (P < 0.05). Conclusions: Loss of retinoblastoma confers increased radiosensitivity in prostate cancer. This hypersensitization was mediated by alterations in apoptotic signaling. Combined, these not only provide insight into the molecular consequence of retinoblastoma loss, but also credential retinoblastoma status as a putative biomarker for predicting response to radiotherapy. Clin Cancer Res; 20(21); 5468–82. ©2014 AACR.
Aspect Based Sentiment Analysis of Spanish Tweets

on de aspectos Abstract: This article presents the participation of the Intelligent Systems Group (GSI) at Universidad Polit ecnica de Madrid (UPM) in the Sentiment Analysis work- shop focused in Spanish tweets, TASS2015. This year two challenges have been proposed, which we have addressed with the design and development of a modu- lar system that is adaptable to dierent contexts. This system employs Natural Language Processing (NLP) and machine-learning technologies, relying also in pre- viously developed technologies in our research group. In particular, we have used a wide number of features and polarity lexicons for sentiment detection. With regards to aspect detection, we have relied on a graph-based algorithm. Once the challenge has come to an end, the experimental results are promising.
Understanding pain in depression

A dysfunction of the serotonergic and noradrenergic pathways is commonly accepted as playing a major role in the aetiology of depression. Serotonergic cell bodies, located in the raphe nucleus, send projections to various parts of the brain where they are involved in the control of mood, movement, emotions such as anxiety and regulate behaviours such as eating, sexual activity and the feeling of pleasure. Similarly, the noradrenergic neurons, located in the locus coeruleus, project to the same regions where they regulate, in addition, attention and cognition. A further projection tothe cerebellum regulates motor control. A dysfunction at the level of the monoamine neurons thus results in the classical symptoms of depression. Inaddition to these ascending pathways, however, the neurons in the raphe nucleus and the locus ceruleus also project to the spinal cord. These descending pathways serve to inhibit input from the intestines, the skeletal muscles and other sensory inputs. Under normal conditions, these inhibitory effects are modest, but in times of stress, in the interests of the survival of the individual, they can completely inhibit the input from painful stimuli. A dysfunction at the level of the serotonergic and noradrenergic neurons can thus affect both the ascending and descending pathways resulting in the psychological and somatic symptoms of depression but also in physical painful symptoms. Copyright © 2004 John Wiley & Sons, Ltd.
Transient Disruption of Autocrine TGF-β Signaling Leads to Enhanced Survival and Proliferation Potential in Single Primitive Human Hemopoietic Progenitor Cells1

Hemopoietic stem cells (HSCs) are maintained at relative quiescence by the balance between the positive and negative regulatory factors that stimulate or inhibit their proliferation. Blocking the action of negative regulatory factors may provide a new approach for inducing HSCs into proliferation. A variety of studies have suggested that TGF-β negatively regulates cell cycle progression of HSCs. In this study, a dominant negatively acting mutant of TGF-β type II receptor (TβRIIDN) was transiently expressed in HSCs by using adenoviral vector-mediated gene delivery, such that the effects of disrupting the autocrine TGF-β signaling in HSCs can be directly examined at a single cell level. Adenoviral vectors allowing the expression of TβRIIDN and green fluorescence protein in the same CD34+CD38−Lin− cells were constructed. Overexpression of TβRIIDN specifically disrupted TGF-β-mediated signaling. Autocrine TGF-β signaling in CD34+CD38−Lin− cells was studied in single cell assays under serum-free conditions. Transient blockage of autocrine TGF-β signaling in CD34+CD38−Lin− cells enhanced their survival. Furthermore, the overall proliferation potential and proliferation kinetics in these cells were significantly enhanced compared with the CD34+CD38−Lin− cells expressing green fluorescence protein alone. Therefore, we have successfully blocked the autocrine TGF-β-negative regulatory loop of primitive hemopoietic progenitor cells.
Localization of NMDA receptor subunits and mapping NMDA drive within the mammalian retina

Glutamate is a major neurotransmitter in the retina and other parts of the central nervous system, exerting its influence through ionotropic and metabotropic receptors. One ionotropic receptor, the N-methyl-D-aspartate (NMDA) receptor, is central to neural shaping, but also plays a major role during neuronal development and in disease processes. We studied the distribution pattern of different subunits of the NMDA receptor within the rat retina including quantifying the pattern of labelling for all the NR1 splice variants, the NR2A and NR2B subunits. The labelling pattern for the subunits was confined predominantly in the outer two-thirds of the inner plexiform layer. We also wanted to probe NMDA receptor function using an organic cation, agmatine (AGB); a marker for cation channel activity. Although there was an NMDA concentration-dependent increase in AGB labelling of amacrine cells and ganglion cells, we found no evidence of functional NMDA receptors on horizontal cells in the peripheral rabbit retina, nor in the visual streak where the type A horizontal cell was identified by GABA labelling. Basal AGB labelling within depolarizing bipolar cells was also noted. This basal bipolar cell AGB labelling was not modulated by NMDA and was completely abolished by the use of L-2-amino-4-phosphono-butyric acid, which is known to hyperpolarize retinal depolarizing bipolar cells. AGB is therefore not only useful as a probe of ligand-gated drive, but can also identify neurons that have constitutively open cationic channels. In combination, the NMDA receptor subunit distribution pattern and the AGB gating experiments strongly suggests that this ionotropic glutamate receptor is functional in the cone-driven pathway of the inner retina.
DeepDiary: Automatic Caption Generation for Lifelogging Image Streams

Lifelogging cameras capture everyday life from a first-person perspective, but generate so much data that it is hard for users to browse and organize their image collections effectively. In this paper, we propose to use automatic image captioning algorithms to generate textual representations of these collections. We develop and explore novel techniques based on deep learning to generate captions for both individual images and image streams, using temporal consistency constraints to create summaries that are both more compact and less noisy. We evaluate our techniques with quantitative and qualitative results, and apply captioning to an image retrieval application for finding potentially private images. Our results suggest that our automatic captioning algorithms, while imperfect, may work well enough to help users manage lifelogging photo collections.
Recent outbreaks of highly pathogenic avian influenza viruses in South Korea

Outbreaks of H5 highly pathogenic avian influenza viruses (HPAIVs) have caused economic loss for the poultry industry and posed a threat to public health. In South Korea, novel reassortants of HPAIVs such as H5N6 and H5N8 had been circulating in poultry. Here, we will discuss the identity of recent novel reassortants of Korean H5 HPAIVs and the recent advances in vaccine development, which will be useful for controlling HPAIV transmission in poultry and for effectively preventing future epidemics and pandemics.
QUKU: A Coarse Grained Paradigm for FPGAs

To fill the gap between increasing demand for reconfigurability and performance efficiency, coarse grain reconfigurable architectures are seen to be an emerging platform. The advantage lies in quick dynamic reconfiguration and power efficiency. Despite having these advantages they have failed to show their mark. This paper describes the QUKU architecture, which uses a coarse- grained dynamically reconfigurable PE array overlaid on an FPGA. The low- speed reconfigurability of the FPGA is used to optimize the CGRA for different applications, whilst the high-speed CGRA reconfiguration is used within an ap- plication for operator re-use.
Digital creativity in dementia care support

This paper reports the application of digital creativity to the care for people with dementia. A digital app was developed for use by staff in residential homes caring for people with dementia. The app invokes a set of computational services to undertake creative work, the results of which are presented to encourage and support cognitive creativity by care staff. The services undertake computational work such as retrieving resolutions to care problems encountered previously, matching care situations to situations in analogical domains such as parenting, teaching and prison life, and automatically generating customised creativity prompts. The app was designed so that care staff can generate contributions to resident care plans that are novel and hence individualised to the resident as part of a shift towards more person-centred care.
COXZN1-XFE2O4 SYNTHESIZED BY METALLO-ORGANIC DECOMPOSITION TECHNIQUE

Cobalt doped Zinc ferrites, CoxZn1-xFe2O4, (x = 0, 0.2, 0.4, and 0.6) were prepared by chemical solution method using metallo-organic precursors. The crystalline structure, microstructure, magnetic and dielectric properties of the samples were investigated by X-ray diffraction (XRD), scanning electron microscopy (SEM), vibrating sample magnetometer (VSM) and impedance analyser respectively. All samples show cubic spinel structure with minor Fe2O3 phase and lattice parameter decreases from 8. 419Å to 8. 308Å with increasing cobalt content from 0 to 60%. Magnetic measurement shows that CoxZn1-xFe2O4 samples exhibit ferromagnetic behavior at room temperature. The saturation magnetization initially increases from 2.17 to 71.2emu/g on increasing Co content to 40% and then decreases to value 55.9emu/g at Co concentration of 60%. The coercivity also increases to Hc ~ 330Oe for the sample with Co=20% and then decreases to minimum value of Hc ~ 32Oe for sample having 40% Co content. The coercivity value is then increases and is measured as Hc ~ 154Oe for sample with 60% Co content. The magnetic properties are explained in terms of cation distribution and grain size effect. The dielectric properties of the samples were studied with varying temperature and frequencies. The dielectric properties are influenced by electron hopping mechanism between Fe and Fe ions.
Coupling CARS with multiphoton fluorescence and high harmonic generation imaging modalities using a femtosecond laser source

Multimodal nonlinear optical imaging has opened new opportunities and becomes a powerful tool for imaging complex tissue samples with inherent 3D spatial resolution. We present a robust and easy-to-operate approach to add the coherent anti-stokes Raman scattering (CARS) imaging modality to a widely used multiphoton microscope. The laser source composed of a Mai Tai femtosecond laser and an optical parametric oscillator (OPO) offers one-beam, two-beam and three-beam modalities. The Mai Tai output at 790 nm is split into two beams, with 80% of the power being used to pump the OPO. The idler output at 2036 nm from OPO is doubled using a periodically poled lithium niobate (PPLN) crystal. This frequency-doubled idler beam at 1018 nm is sent through a delay line and collinearly combined with the other Mai Tai beam for CARS imaging on a laser-scanning microscope. This Mai Tai beam is also used for multiphoton fluorescence and second harmonic generation (SHG) imaging. The signal output at 1290 nm from OPO is used for SHG and third-harmonic generation (THG) imaging. External detectors are installed for both forward and backward detection, whereas two internal lamda-scan detectors are employed for microspectroscopy analysis. This new system allows vibrationally resonant CARS imaging of lipid bodies, SHG imaging of collagen fibers, and multiphoton fluorescence analysis in fresh tissues. As a preliminary application, the effect of diacylglycerol acyltransferase 1 (DGAT1) deficiency on liver lipid metabolism in mice was investigated.
Magnetic Dispersion at Microwave Frequencies

A method is described which has been developed for the measurement of initial permeabilities of ferromagnetic wires in the microwave region and successfully applied over the range from 3 to 13 cm. wavelength to a variety of materials. The measurements are carried out by comparing the attenuations of coaxial transmission lines with the ferromagnetic specimen and with a non-ferromagnetic reference material as inner conductors. The attenuation constants are derived from observations on the input impedance of the line for different terminations as embodied in a circle diagram of impedance. The results are interpreted in the light of modern theories of magnetic dispersion and an estimate of domain sizes is made. The limitations of the theoretical treatments are indicated.
Fast visualization by shear warp using spline models for data reconstruction

This work concerns oneself with the rendering of huge three-dimensional data sets. The target thereby is the development of fast algorithms by also applying recent and accurate volume reconstruction models to obtain at most artifact-free data visualizations. In part I a comprehensive overview on the state of the art in volume rendering is given. Part II is devoted to the recently developed trivariate (linear,) quadratic and cubic spline models defined on symmetric tetrahedral partitions directly obtained by slicing volumetric partitions of a three-dimensional domain. This spline models define piecewise polynomials of total degree (one,) two and three with respect to a tetrahedron, i.e. the local splines have the lowest possible total degree and are adequate for efficient and accurate volume visualization. The following part III depicts in a step by step manner a fast software-based rendering algorithm, called shear-warp. This algorithm is prominent for its ability to generate projections of volume data at real time. It attains the high rendering speed by using elaborate data structures and extensive pre-computation, but at the expense of data redundancy and visual quality of the finally obtained rendering results. However, to circumvent these disadvantages a further development is specified, where new techniques and sophisticated data structures allow combining the fast shear-warp with the accurate ray-casting approach. This strategy and the new data structures not only grant a unification of the benefits of both methods, they even easily admit for adjustments to trade-off between rendering speed and precision. With this further development also the 3-fold data redundancy known from the original shear-warp approach is removed, allowing the rendering of even larger three-dimensional data sets more quickly. Additionally, real trivariate data reconstruction models, as discussed in part II, are applied together with the new ideas to onward the precision of the new volume rendering method, which also lead to a one order of magnitude faster algorithm compared to traditional approaches using similar reconstruction models. In part IV, a hierarchy-based rendering method is developed which utilizes a wavelet decomposition of the volume data, an octree structure to represent the sparse data set, the splines from part II and a new shear-warp visualization algorithm similar to that presented in part III. This thesis is concluded by the results centralized in part V.
Research on the development path of China's solar photovoltaic industry based on technology roadmapping and bibliometric

China's solar photovoltaic (PV) industry has experienced a rapid progress in the last 10 year. To achieve the sustainable development of the solar PV industry in China, it is necessary to review the emergence path of the industry, and analyze the future development of the industry. This paper firstly reviews the emergence path of China's solar PV industry based on technology roadmapping from R&D, technology, production, market and policy to understand the characteristics of the industry, and identifies the problems impeding China's solar PV industry development. Then, in order to analyze the future development path of China's solar PV industry, the bibliometric method is applied to analyze the development status of China's dye-sensitized solar cells technology. Finally, combined with the analysis results of the emergence path of China's solar PV industry and the bibliometric method, the policy recommendations for the future development of China's solar PV industry are presented. These results can be a useful reference for the development of solar PV industry in China, and other developing countries around the world can benefit from this study to develop their own solar PV industry or others emerging industry.
Roles for wbtC, wbtI, and kdtA Genes in Lipopolysaccharide Biosynthesis, Protein Glycosylation, Virulence, and Immunogenicity in Francisella tularensis Strain SCHU S4

Using a strategy of gene deletion mutagenesis, we have examined the roles of genes putatively involved in lipopolysaccharide biosynthesis in the virulent facultative intracellular bacterial pathogen, Francisella tularensis subspecies tularensis, strain SCHU S4 in LPS biosynthesis, protein glycosylation, virulence and immunogenicity. One mutant, ∆wbtI, did not elaborate a long chain O-polysaccharide (OPS), was completely avirulent for mice, and failed to induce a protective immune response against challenge with wild type bacteria. Another mutant, ∆wbtC, produced a long chain OPS with altered chemical and electrophoretic characteristics. This mutant showed markedly reduced glycosylation of several known glycoproteins. Additionally this mutant was highly attenuated, and elicited a protective immune response against systemic, but not respiratory challenge with wild type SCHU S4. A third mutant, ∆kdtA, produced an unconjugated long chain OPS, lacking a detectable core structure, and which was not obviously expressed at the surface. It was avirulent and elicited partial protection against systemic challenge only.
Development and Characterization of Probe-Based Real Time Quantitative RT-PCR Assays for Detection and Serotyping of Foot-And-Mouth Disease Viruses Circulating in West Eurasia

Rapid and accurate diagnosis of foot-and-mouth disease (FMD) and virus serotyping are of paramount importance for control of this disease in endemic areas where vaccination is practiced. Ideally this virus characterization should be achieved without the need for virus amplification in cell culture. Due to the heterogeneity of FMD viruses (FMDVs) in different parts of the world, region specific diagnostic tests are required. In this study, hydrolysable probe-based real time reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays were developed for specific detection and serotyping of the FMDVs currently circulating in West Eurasia. These assays were evaluated, in parallel with pan-FMDV diagnostic assays and earlier serotype-specific assays, using field samples originating from Pakistan and Afghanistan containing FMD viruses belonging to different sublineages of O-PanAsia, A-Iran05 and Asia-1 (Group-II and Group-VII (Sindh-08)). In addition, field samples from Iran and Bulgaria, containing FMDVs belonging to the O-PanAsiaANT-10 sublineage were also tested. Each of the three primer/probe sets was designed to be specific for just one of the serotypes O, A and Asia-1 of FMDV and detected the RNA from the target viruses with cycle threshold (CT) values comparable with those obtained with the serotype-independent pan-FMDV diagnostic assays. No cross-reactivity was observed in these assays between the heterotypic viruses circulating in the region. The assays reported here have higher diagnostic sensitivity (100% each for serotypes O and Asia-1, and 92% [95% CI = 81.4–100%] for serotype A positive samples) and specificity (100% each for serotypes O, A and Asia-1 positive samples) for the viruses currently circulating in West Eurasia compared to the serotyping assays reported earlier. Comparisons of the sequences of the primers and probes used in these assays and the corresponding regions of the circulating viruses provided explanations for the poor recognition of some of the viruses by the earlier assays. These new assays should help in the early detection and typing of serotype O, A and Asia-1 FMDVs circulating in West Eurasia to enable improved disease control.