Miracle-dz/UniFAR-FTUs huggingface dataset:
PUMA Sensitizes Lung Cancer Cells to Chemotherapeutic Agents and Irradiation

Purpose: Lung cancer, the leading cause of cancer mortality worldwide, is often diagnosed at late stages and responds poorly to conventional therapies, including chemotherapy and irradiation. A great majority of lung tumors are defective in the p53 pathway, which plays an important role in regulating apoptotic response to anticancer agents. PUMA was recently identified as an essential mediator of DNA damage–induced and p53-dependent apoptosis. In this study, we investigated whether the regulation of PUMA by anticancer agents is abrogated in lung cancer cells and whether PUMA expression suppresses growth of lung cancer cells and/or sensitizes lung cancer cells to chemotherapeutic agents and irradiation through induction of apoptosis. Experimental Designs: The expression of PUMA was examined in lung cancer cells with different p53 status treated with chemotherapeutic agents. An adenovirus expressing PUMA (Ad-PUMA), alone or in combination with chemotherapeutic agents or γ-irradiation, was used to treat lung cancer cells. The growth inhibitory and apoptotic effects of PUMA in vitro and in vivo were examined. The mechanisms of PUMA-mediated growth suppression and apoptosis were investigated through analysis of caspase activation and release of mitochondrial apoptogenic proteins. The cytotoxicities of PUMA on cancer and normal/nontransformed cells were compared. The efficacy of PUMA and p53 in suppressing the growth of lung cancer cells was also compared. Results: We showed that the induction of PUMA by chemotherapeutic agents is abolished in p53-deficient lung cancer cells. PUMA expression resulted in potent growth suppression of lung cancer cells and suppressed xenograft tumor growth in vivo through induction of apoptosis. Low dose of Ad-PUMA significantly sensitized lung cancer cells to chemotherapeutic agents and γ-irradiation through induction of apoptosis. The effects of PUMA are mediated by enhanced caspase activation and release of cytochrome c and apoptosis-inducing factor into the cytosol. Furthermore, PUMA seems to be selectively toxic to cancer cells and more efficient than p53 in suppressing lung cancer cell growth. Conclusions: Our findings indicate that PUMA is an important modulator of therapeutic responses of lung cancer cells and is potentially useful as a sensitizer in lung cancer therapy.
Analysis of Major Histocompatibility Complex-Bound HIV Peptides Identified from Various Cell Types Reveals Common Nested Peptides and Novel T Cell Responses

ABSTRACT Despite the critical role of epitope presentation for immune recognition, we still lack a comprehensive definition of HIV peptides presented by HIV-infected cells. Here we identified 107 major histocompatibility complex (MHC)-bound HIV peptides directly from the surface of live HIV-transfected 293T cells, HIV-infected B cells, and primary CD4 T cells expressing a variety of HLAs. The majority of peptides were 8 to 12 amino acids (aa) long and mostly derived from Gag and Pol. The analysis of the total MHC-peptidome and of HLA-A02-bound peptides identified new noncanonical HIV peptides of up to 16 aa that could not be predicted by HLA anchor scanning and revealed an heterogeneous surface peptidome. Nested sets of surface HIV peptides included optimal and extended HIV epitopes and peptides partly overlapping or distinct from known epitopes, revealing new immune responses in HIV-infected persons. Surprisingly, in all three cell types, a majority of Gag peptides derived from p15 rather than from the most immunogenic p24. The cytosolic degradation of peptide precursors in corresponding cells confirmed the generation of identified surface-nested peptides. Cytosolic degradation revealed peptides commonly produced in all cell types and displayed by various HLAs, peptides commonly produced in all cell types and selectively displayed by specific HLAs, and peptides produced in only one cell type. Importantly, we identified areas of proteins leading to common presentations of noncanonical peptides by several cell types with distinct HLAs. These peptides may benefit the design of immunogens, focusing T cell responses on relevant markers of HIV infection in the context of HLA diversity. IMPORTANCE The recognition of HIV-infected cells by immune T cells relies on the presentation of HIV-derived peptides by diverse HLA molecules at the surface of cells. The landscape of HIV peptides displayed by HIV-infected cells is not well defined. Considering the diversity of HLA molecules in the human population, it is critical for vaccine design to identify HIV peptides that may be displayed despite the HLA diversity. We identified 107 HIV peptides directly from the surface of three cell types infected with HIV. They corresponded to nested sets of HIV peptides of canonical and novel noncanonical lengths not predictable by the presence of HLA anchors. Importantly, we identified areas of HIV proteins leading to presentation of noncanonical peptides by several cell types with distinct HLAs. Including such peptides in vaccine immunogen may help to focus immune responses on common markers of HIV infection in the context of HLA diversity.
[Nutritional assessment and phytoestrogen exposure in a diet of students of the University of Costa Rica].

Introducción: este estudio presenta resultados respecto a dieta y un análisis más en profundidad de la exposición a estrógenos naturales (fitoestrógenos) en la ingesta, y como este tipo de compuestos influye y se relaciona con otros aspectos importantes que pueden modular funciones biológicas relacionadas con la salud en estudiantes universitarios. Objetivos: valorar hábitos nutricionales y estimar la ingesta de fitoestrógenos de la población en estudio. Material y métodos: población costarricense universitaria femenina (n: 211, edades 18,83 ± 2,06 años) y masculina (n: 199, edades 19,64 ± 3,05 años) de la Universidad de Costa Rica y se han aplicado pruebas antropométricas mediante el DEXA y cuestionarios de Frecuencia de Consumo de Alimentos (FFQ) y Recuerdos de 24 Horas (R-24). Resultados: los errores nutricionales más graves fueron: la elevada ingesta de sodio, lípidos y proteínas de origen animal en hombres y mujeres, y el déficit importante de fibra y ácido fólico en las mujeres. La ingesta total de fitoestrógenos referidos a la daizdeína fue de 0.23 ± 0.40 mg/día y 7,01 ± 11,94 mg/mes en mujeres y de 0,17 ± 0,13 mg/día y de 5,14 ± 3,96 mg/mes en varones; principalmente consumida en forma de lignanos 0,24 ± 0,12 mg/día (mujeres) y 0,23 ± 0,14 mg/día (hombres), mientras la ingesta de isoflavonas fue de 0,09 ± 0,38 mg/día (mujeres) y de 0,04 ± 0,08 mg/día (hombres). Conclusiones: la población de estudio presentó porcentajes de grasa elevados nutricionalmente hablando, aunque el consumo de vegetales, cereales, granos enteros y frutas tiende un poco a la dieta mediterránea, su patrón alimentario se acerca mucho más a la dieta occidental.
Financial Networks and Contagion

We study cascades of failures in a network of interdependent financial organizations: how discontinuous changes in asset values (e.g., defaults and shutdowns) trigger further failures, and how this depends on network structure. Integration (greater dependence on counterparties) and diversification (more counterparties per organization) have different, nonmonotonic effects on the extent of cascades. Diversification connects the network initially, permitting cascades to travel; but as it increases further, organizations are better insured against one another's failures. Integration also faces trade-offs: increased dependence on other organizations versus less sensitivity to own investments. Finally, we illustrate the model with data on European debt cross-holdings.
Near-duplicate video retrieval by using pattern-based Prefix tree and temporal relation forest

With the explosive growth of the social multimedia sharing, copyright protection and search result refinement are always the critical issues for the service operators. To resolve the problems, content-based near-duplicate video retrieval is developed in recent years. In this paper, we construct a condensed Pattern-based Prefix tree (PP-tree) to index the patterns of reference videos for fast retrieval. To calculate how likely a query video and a reference video are near-duplicates, a novel algorithm for discovering the temporal relations among patterns is proposed. Comprehensive experiments on public datasets are conducted to verify the effectiveness and efficiency of the proposed method. Experimental results show that the proposed near-duplicate video retrieval approach outperforms the state-of-the-art approaches in terms of precision, recall, and execution time.
Gastrointestinal injury from NSAID therapy

PREVIEW Use of nonsteroidal anti-inflammatory drugs (NSAIDs) and low-dose aspirin is accompanied by risk of upper and lower gastrointestinal (GI) complications, some of which can be serious or even fatal. Management strategies to reduce this risk include gastroprotective pharmacotherapy, use of safer NSAIDs, and eradication of Helicobacter pylori infection. In this article, Dr Lanas summarizes the GI risks associated with NSAID and low-dose aspirin therapy and weighs the efficacy of current risk management strategies.
Evaluating the Potential of Portulaca oleracea L. for Parkinson's Disease Treatment Using a Drosophila Model with dUCH-Knockdown

Parkinson's disease (PD), which is characterized by the decreased motor function and the loss of dopaminergic neurons, is a common neurodegenerative disorder in elders. There have been numerous in vitro and in vivo models developed to study mechanisms of PD and screen potential drug. Recently, dUCH-knockdown Drosophila model has been established and showed potential for screening antioxidants for PD treatment. The dUCH-knockdown Drosophila model of PD mimics most of main PD pathologies such as dopaminergic neurons degeneration, locomotor dysfunction, and shortage of dopamine in the brain. Common purslane (Portulaca oleracea L.) is a nutritious vegetable containing a variety of antioxidants, levodopa, and dopamine, a neurotransmitter closely related to PD. Purslane has been reported to exert neuroprotective effects against several neurotoxins including rotenone and 6-OHDA in PD models. However, the recent data have not provided sufficient evidence for using purslane to treat PD or decelerate disease progression. Therefore, in this study, we utilized dUCH-knockdown fly to evaluate the capacity of purslane extracts for PD treatment. The results showed that purslane extracts improved locomotor ability in the larval stage and decelerated disease progression in the adult stage. Additionally, purslane extracts also reduced dopaminergic neuron degeneration. Taken together, our data strongly demonstrated that purslane extracts effectively rescued PD-like phenotypes in the fly model. This result contributed a foundation for further study on the application of purslane in PD treatment.
Generalized Dantzig Selector for Low-tubal-rank Tensor Recovery

Due to the superiority in exploiting the ubiquitous "spatial-shifting" property in modern multi-way data, the recently proposed low-tubal-rank model has been successfully applied for tensor recovery in signal processing and computer vision. In this paper, we define the generalized tensor Dantzig selector to recover a low-tubal-rank tensor from noisy linear measurements. Algorithmically, we develop an efficient algorithm based on the ADMM framework. Statistically, we establish non-asymptotic upper bounds on the estimation error for the problems of tensor completion and compressive sensing. Numerical experiments illustrate that our bounds can predict the scaling behavior of the estimation error. Experiments on realword datasets show the effectiveness of the proposed model.
Fatal Pasteurella sepsis and hairy‐cell leukemia

Letters and correspondence submitted for possible publication must be identified as such. Text length must not exceed 500 words and five bibliographic references. A single concise figure or table may be included if it is essential to support the communication. Letters not typed double-spaced will not be considered for publication. Letters not meeting these specifications will not be returned to authors. Letters to the Editor are utilized to communicate a single novel observation or finding. Correspondence is to be used to supplement or constructively comment on the contents of a publication in the journal and cannot exceed the restrictions for Letters to the Editor. The Editor reserves the right to shorten text, delete objectional comments, and make other changes to comply with the style of the journal. Permission for publication must be appended as a postscript. Submissions must be sent to Paul Chervenick, M.D., Editor of Brief Reports/Letters to Editors, American Journal of Hematology, H. Lee Moffitt Cancer Center, University of South Florida, 12902 Magnolia Drive, Tampa, FL 33612 to permit rapid consideration for publication.
Defining a Conceptual Topography of Word Concreteness: Clustering Properties of Emotion, Sensation, and Magnitude among 750 English Words

Cognitive science has a longstanding interest in the ways that people acquire and use abstract vs. concrete words (e.g., truth vs. piano). One dominant theory holds that abstract and concrete words are subserved by two parallel semantic systems. We recently proposed an alternative account of abstract-concrete word representation premised upon a unitary, high dimensional semantic space wherein word meaning is nested. We hypothesize that a range of cognitive and perceptual dimensions (e.g., emotion, time, space, color, size, visual form) bound this space, forming a conceptual topography. Here we report a normative study where we examined the clustering properties of a sample of English words (N = 750) spanning a spectrum of concreteness in a continuous manner from highly abstract to highly concrete. Participants (N = 328) rated each target word on a range of 14 cognitive dimensions (e.g., color, emotion, valence, polarity, motion, space). The dimensions reduced to three factors: Endogenous factor, Exogenous factor, and Magnitude factor. Concepts were plotted in a unified, multimodal space with concrete and abstract concepts along a continuous continuum. We discuss theoretical implications and practical applications of this dataset. These word norms are freely available for download and use at http://www.reilly-coglab.com/data/.
Ion velocities in direct current arc plasma generated from compound cathodes

Arc plasma from Ti-C, Ti-Al, and Ti-Si cathodes was characterized with respect to charge-state-resolved ion energy. The evaluated peak velocities of different ion species in plasma generated from a compound cathode were found to be equal and independent on ion mass. Therefore, measured difference in kinetic energies can be inferred from the difference in ion mass, with no dependence on ion charge state. The latter is consistent with previous work. These findings can be explained by plasma quasineutrality, ion acceleration by pressure gradients, and electron-ion coupling. Increasing the C concentration in Ti-C cathodes resulted in increasing average and peak ion energies for all ion species. This effect can be explained by the “cohesive energy rule,” where material and phases of higher cohesive energy generally result in increasing energies (velocities). This is also consistent with the here obtained peak velocities around 1.37, 1.42, and 1.55 (104 m/s) for ions from Ti0.84Al0. 16, Ti0.90Si0. 10, and Ti0.90C.
Treatment of Pituitary Adenomas with a Transsphenoidal Approach

OBJECTIVE:To evaluate the overall therapeutic effectiveness of transsphenoidal microsurgery for pituitary adenomas and explore the surgical technique, application of new technology, and postoperative follow-up. METHODS:The clinical presentation, imaging features, endocrine examination, pathological types, conditions of operation, postoperative complications, and follow-up of 4050 patients with pituitary adenomas who had undergone transsphenoidal microsurgery from December 1981 to January 2004 were analyzed retrospectively. RESULTS:During the past 6 years, total tumor resection (under microscope) has been achieved in 97.3% of the patients with Hardy Grade I adenomas, 95.2% of Hardy Grade II, 90.4% of Hardy Grade III, and 47.4% of Hardy Grade IV. The percentages of total and subtotal resection achieved extended from 87.6% before 1987 to 96.9% in 2003. CONCLUSION:With the improvement of microsurgical technique and application of novel technology, the indications for transsphenoidal microsurgery for pituitary adenomas were increasingly extended. We believe that more than 90% of pituitary adenomas could be treated by the transsphenoidal approach and totally removed through the microscope. The transnasal perpendicular plate-sphenoid sinus approach will be the dominant mode. Routine postoperative radiotherapy is not required for patients with total resection.
Optimization of the Degree of Polarization for Enhanced Ship Detection Using Polarimetric RADARSAT-2

The scattered wave is represented in terms of two independent and rotation invariant parameters: the degree of polarization (DoP) and the total scattered intensity R0. The scattered wave polarization signature is introduced as a convenient graphical representation of the variations of the two scattered wave observable parameters as a function of the transmitting antenna polarization. It is shown that the signature of the DoP and the total scattered intensity (R0) provide information on ocean and ship scattering that is complementary to that provided by the conventional received wave intensity polarization signature. While R0 polarization signature of the ocean's Bragg scattering is sensitive to wind speed and synthetic aperture radar illumination angle, the DoP polarization signature appears to depend mainly on ocean surface roughness. The large dynamic range and low pedestal height of ship DoP polarization signature, in comparison with that of the ocean, favors the use of DoP for ship detection in comparison with R0. Optimization of the scattered wave parameters appears to be a convenient tool for efficient ship detection. The scattered wave optimization technique introduced by R. Touzi et al. in the nineties, is reconsidered and applied for enhanced ship detection. It is shown that the excursion of DoP, Δp, and the minimum DoP, pmin, permits a significant improvement in ship-sea contrast in comparison with conventional (i.e., scalar) single channel polarizations (HH, VV, and HV). The additional information provided by the maximum DoP, pmax solves for ship ambiguities with land targets. Quantification of the ship-ocean contrast is reconsidered in the context of nonstationary ship signal. The ship peak signal quantification appears to be the most suitable method for accurate measurement of ship-ocean contrast in the presence of a nonstationary ship signal. The local pmin performs better than the peak of Δp and single polarizations (HH, VV, and HV). The added value of polarimetric RS2 information for ship detection is demonstrated using wide swath (50 km) polarimetric RADARSAT-2 data collected at 29° and 40° incidence angle over vessels (validated with Automatic Identification System data) in the Strait of Georgia, near Vancouver, Canada.
Use of fascia lata autograft for repair of urinary bladder defect in rabbits

The aim of this study was to investigate the compatibility of a fascia lata autograft for urinary bladder tissue defect, to evaluate the biomechanical, radiographical, macroscopical, biochemical, and histopathological test findings, and early and late complications of the surgical processes in rabbits. Thirty two adult healthy New Zealand rabbits were randomly allocated to 4 different groups of 8 animals. A 2 × 2 cm urinary bladder defect was repaired by the same size of fascia lata in experimental groups (Group 1, 2, 3). Rabbits in Group 1, 2 and 3 were euthanized at the end of the 4th, 8thand 12thweek after surgeries, respectively. No surgical procedure was carried out for the urinary bladder of the rabbits in the control group, but their urinary bladders were used for biomechanical tests and the values compared with those of Group 1, 2 and 3. Histopathological examination of the grafted area was performed. The grafted area was consistent with that of the tissue of urinary bladder. No significant difference was found between the urinary bladder and the grafted area. No differences in biomechanical tests were recorded between grafted and ungrafted urinary bladders. Histopathologically, fascia lata turned into a normal urinary bladder tissue. Therefore, a fascia lata autograft can be succesfully used in urinary bladder defects. Fascia lata grafts can be used successfully in pathological conditions of the urinary bladder that require a new tissue.
Perceptual Consequences of Tinnitus: Effects of Sensory Deficits and Top-Down Attention

Author(s): Richardson, Matthew Lyle | Advisor(s): Zeng, Fan-Gang | Abstract: Tinnitus is the phantom perception of sound without an external acoustic source. Although tinnitus affects 10-15% of adults, with symptoms from mildly bothersome to debilitating, current treatments are limited by an inadequate understanding of its underlying pathophysiology. Improved understanding must address perception at all levels, from a peripheral deficit (e.g. hearing loss), to central auditory plasticity generating the internal signal, to higher-order brain networks governing its conscious awareness. The first study examined top-down mechanisms of attention in modulating tinnitus and potentially its loudness, pitch, or distress. Subjects with and without chronic tinnitus monitored one of two tonal steams, one with similar frequency as tinnitus and the other well-outside this region. Cortical evoked-potentials showed enhanced attentional gain when tinnitus subjects focused to the tinnitus frequency, which related to increased tinnitus loudness. A later enhancement to the non-tinnitus frequency suggested tinnitus also impacts selective processing of other sounds. A discrimination analysis indicated that attention-derived variables could serve as a biomarker to detect tinnitus from control subjects with similar age and hearing. The second study employed psychophysical methods to uncover sensory deficits in tinnitus and improve its diagnosis. Tinnitus subjects showed normal temporal acuity for detecting silent gaps in pure-tones, including those matching the tinnitus pitch. Although gap detection is widely used to assess tinnitus in animal research, assuming tinnitus “fills-in” the gap, the procedure appears ill-suited for clinical diagnosis in humans. Tinnitus subjects also showed normal frequency discrimination. However, slightly improved intensity discrimination of low-level sounds indicated a mechanism of increased auditory gain in the central pathways. Together, these results suggest that “bottom-up” sensory deficits in tinnitus have subtle impacts on basic auditory processing, while top-down attention plays a central role in gating tinnitus perception and may be developed as an objective clinical biomarker.