Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient Intracellular Delivery of Molecules with High Cell Viability Using Nanosecond-Pulsed Laser-Activated Carbon Nanoparticles

Conventional physical and chemical methods that efficiently deliver molecules into cells are often associated with low cell viability. In this study, we evaluated the cellular effects of carbon nanoparticles believed to emit photoacoustic waves due to nanosecond-pulse laser activation to test the hypothesis that this method could achieve efficient intracellular delivery while maintaining high cell viability. Suspensions of DU145 human prostate carcinoma cells, carbon black (CB) nanoparticles, and calcein were exposed to 5–9 ns long laser pulses of near-infrared (1064 nm wavelength) light and then analyzed by flow cytometry for intracellular uptake of calcein and cell viability by propidium iodide staining. We found that intracellular uptake increased and in some cases saturated at high levels with only small losses in cell viability as a result of increasing laser fluence, laser exposure time, and as a unifying parameter, the total laser energy. Changing interpulse spacing between 0.1 and 10 s intervals showed no significant change in bioeffects, suggesting that the effects of each pulse were independent when spaced by at least 0.1 s intervals. Pretreatment of CB nanoparticles to intense laser exposure followed by mixing with cells also had no significant effect on uptake or viability. Similar uptake and viability were seen when CB nanoparticles were substituted with India ink, when DU145 cells were substituted with H9c2 rat cardiomyoblast cells, and when calcein was substituted with FITC-dextran. The best laser exposure conditions tested led to 88% of cells with intracellular uptake and close to 100% viability, indicating that nanosecond-pulse laser-activated carbon nanoparticles can achieve efficient intracellular delivery while maintaining high cell viability.
Activation of Tumor-specific CD4+ T Lymphocytes by Major Histocompatibility Complex Class II Tumor Cell Vaccines

Mouse tumor cells transfected with syngeneic MHC class II and costimulatory molecule genes are therapeutic vaccines in mice, provided they do not coexpress the class II-associated invariant chain (Ii). We demonstrated previously that the vaccine cells present tumor peptides via the endogenous antigen presentation pathway to activate CD4+ and CD8+ T cells. Because of their efficacy in mice, we are translating this vaccine strategy for clinical use. To obtain MHC class II+CD80+Ii− human tumor cells, we developed retroviruses encoding HLA-DR and CD80. The HLA-DR virus encodes the DRα and DRβ0101 chains using an internal ribosomal entry site to coordinate expression. SUM159PT mammary carcinoma and Mel 202 ocular melanoma cells transduced with the retroviruses DRB1/CD80 express high levels of DRB0101 and CD80 on the cell surface in the absence of Ii. Irradiated SUM159PT/DR1/CD80 vaccines stimulate proliferation of non-HLA-DRB0101 peripheral blood mononuclear cells and present an exogenous DR1-restricted tetanus toxoid (TT) peptide, indicating that the transduced DRB0101 is functional. SUM159PT/DR1/CD80 vaccines were further transduced with a retrovirus encoding the TT fragment C gene, as a model tumor antigen. These cells stimulate IFN-γ release from TT-primed human DRB0101 peripheral blood mononuclear cells, demonstrating their ability to present “endogenous” tumor antigen. Depletion and antibody blocking experiments confirm that MHC class II-restricted, endogenously synthesized epitopes are presented to CD4+ T cells. Therefore, the MHC class II vaccines are efficient antigen-presenting cells that activate tumor-specific MHC class II-restricted, CD4+ T lymphocytes, and they are a novel and potential immunotherapeutic for metastatic cancers.
Motion as Shape: A Novel Method for the Recognition and Prediction of Biological Motion

We introduce a method for the recognition and prediction of motion, based on the idea that different motions trace out different shapes in some state space. In the recognition step we use a multidimensional generalization of the shape context [1] to find the closest prototype motion to the observed data. When tested against motion capture data, our model yields excellent (99%) recognition of gait and good (83%) recognition of identity. In addition to recognition, this process also allows us to find an aligning transform TDP that maps the observed data D onto the prototype P. Given this transform, and its inverse TPD, we use a Bayesian approach to make optimal predictions about the data in the prototype space and then map these predictions back into data space. This approach gives accurate predictions over several gait cycles despite the fact that there is often a significant difference between the observed data and the prototype manifold.
Influence of chloride on silver uptake by two green algae, Pseudokirchneriella subcapitata and Chlorella pyrenoidosa

Silver bioavailability in the presence of chloride was estimated from short‐term (≤60 min) uptake experiments with two green algae, Pseudokirchneriella subcapitata and Chlorella pyrenoidosa. In the first experiment, silver uptake was monitored under two concentration regimes in which total dissolved silver ([Ag]tot) and [Cl] were manipulated to maintain [Ag+] at a constant value (10 nM). Comparable uptake rates were measured for both treatments despite the dramatic changes in [Cl] and [Ag]tot. In the second experiment, ambient [Ag]tot was held constant (10 or 115 nM), but [Cl] was varied (0.005‐50 mM) to explore the whole range of silver chloro‐complexes. Intracellular silver varied markedly along the [Cl] gradient and exhibited a clear, positive correlation with ambient [Ag+] for both algae. We conclude that the biotic ligand model reliably describes silver bioavailability in the presence of chloride for the two test algae and that its applicability depends on the relative magnitudes of silver fluxes through the unstirred diffusion layer and across the cell membrane, with the latter being affected by the presence or absence of a Cu(I) transporter. In the presence of chloride, no evidence was found for the internalization of silver via anion transport or passive diffusion of the neutral mono‐chloro‐complex, AgCl0.
The Effects of Associative, Phonological, Semantic, and Linguistic Properties of Words Upon Recall: An Experiment on Verbal Memory

To test what associative, semantic, linguistic, and habitual factors affected verbal recall in long term memory, 37 participants (11 male, 26 female) performed a three part experiment on verbal memory. The first part involved memorising as many words as possible from a list of 59 words presented on-screen. This was followed by an interfering text to read that was either partially relevant or irrelevant to certain words on the recall list. Participants were then presented with a recognition task to test their recollection of the 59 words alongside 60 other distracter words. Reading habits were also briefly evaluated. The text's relevance had no noticeable effect on recall (t(35) = . 29, p = . 59, d = . 18). Self reported reading habits were related to increased recall numerically, but not statistically (r = .2, p = .23). A word's phonological length and concreteness facilitated higher rates of recall, albeit statistically insignificant in interpreting variance in recall (p = .09, p = .11). The single most predictive factor of a word's likelihood of being recalled was it's rarity in the language (β = .56, p < .001). This alongside other results are discussed with relevance to interference theories of memory and forgetting, and relating to the novelty effect with regard to rarity predicting recall. In conclusion measuring a word's frequency of occurrence in a language may be an important measure to include in studies of verbal memory for the aforementioned reasons.
A Resource-Sharing Platform for Trading Biomedical Intellectual Property

In this paper, a Web-based platform, BiolPMall, consolidates research results from different universities to create a nationwide resource for biotech development. Its unique sharing mechanism for trading and analyzing intellectual property disseminates viable research results to promote IP commercialization. BioIPMall is based on taxonomy system to efficiently classify and categorize biotechnology, and thus facilitate resource and knowledge sharing. The e-commerce-type platform's search capabilities help it match the needs and requirements of IP providers and buyers, facilitating the transfer of biotechnologies from academia into industrial applications.
BBX21, an Arabidopsis B-box protein, directly activates HY5 and is targeted by COP1 for 26S proteasome-mediated degradation

Significance CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and ELONGATED HYPOCOTYL 5 (HY5) are two central regulators of photomorphogenesis. COP1 destabilizes HY5 to repress photomorphogenesis in darkness. On light illumination, accumulated HY5 regulates the expression of a large number of genes to optimize photomorphogenesis. Thus, COP1-HY5 defines a regulatory hub for light control of seedling development. In this work, our data indicate that BBX21 is a key component involved in the COP1-HY5 regulatory hub. BBX21 is controlled by COP1 via its E3 ubiquitin ligase activity in darkness. In the light, BBX21 promotes photomorphogenesis by binding to the promoter of HY5 and activating HY5 expression. BBX21 (also known as SALT TOLERANCE HOMOLOG 2), a B-box (BBX)-containing protein, has been previously identified as a positive regulator of light signaling; however, the precise role of BBX21 in regulating seedling photomorphogenesis remains largely unclear. In this study, we report that CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) interacts with BBX21 in vivo and is able to ubiquitinate BBX21 in vitro. Thus, BBX21 is targeted for 26S proteasome-mediated degradation in dark-grown Arabidopsis seedlings in a COP1-dependent manner. Moreover, we show that BBX21 binds to the T/G-box in the ELONGATED HYPOCOTYL 5 (HY5) promoter and directly activates HY5 expression in the light. Transgenic seedlings overexpressing BBX21 exhibit dramatically shortened hypocotyls in the light, and this phenotype is dependent on a functional HY5. Taken together, our data suggest a molecular base underlying BBX21-mediated seedling photomorphogenesis, indicating that BBX21 is a pivotal component involved in the COP1-HY5 regulatory hub.
Custom topology generation for network-on-chip

This paper compares simulated annealing and tabu search for generating custom topologies for applications with periodic behaviour executing on a network-on-chip. The approach differs from previous work by starting from a fixed mapping of IP-cores to routers and performing design space exploration around an initial topology. The tabu search has been modified from its normally encountered form to allow easier escaping from local minima. A number of synthetic benchmarks are used for tuning the parameters of both heuristics and for testing the quality of the solutions each heuristic produces. An analytical model is used to determine communication latencies in the network-on-chip.
Actin Can Reorganize into Podosomes in Aortic Endothelial Cells, a Process Controlled by Cdc42 and RhoA

ABSTRACT Members of the Rho GTPase family play a central role in the orchestration of cytoskeletal rearrangements, which are of prime importance in endothelial cell physiology. To explore their role in this specialized cell type, we used the bacterial toxin cytotoxic necrotizing factor 1 (CNF1) as a Rho GTPase activator. Punctate filamentous actin structures appeared along the ventral plasma membrane of endothelial cells and were identified as the core of podosomes by the distinctive vinculin ring around the F-actin. Rho, Rac, and Cdc42 were all identified as targets of CNF1, but only a constitutively active mutant of Cdc42 could substitute for CNF1 in podosome induction. Accordingly, organization of F-actin in these structures was highly dependent on the main Cdc42 cytoskeletal effector N-Wiskott-Aldrich syndrome protein. Other components of the actin machinery such as Arp2/3 and for the first time WIP also colocalized at these sites. Like CNF1 treatment, sustained Cdc42 activity induced a time-dependent F-actin-vinculin reorganization, prevented cytokinesis, and downregulated Rho activity. Finally, podosomes were also detected on endothelial cells explanted from patients undergoing cardiac surgery. These data provide the first description of podosomes in endothelial cells. The identification of such specialized structures opens up a new field of investigation in terms of endothelium pathophysiology.
Error bounds based stochastic approximations and simulations of hybrid dynamical systems

This paper introduces, develops and discusses an integration-inspired methodology for the simulation and analysis of deterministic hybrid dynamical systems. When simulating hybrid systems, and thus unavoidably introducing some numerical error, a progressive tracking of this error can be exploited to discern the properties of the system, i.e., it can be used to introduce a stochastic approximation of the original hybrid system, the simulation of which would give a more complete representation of the possible trajectories of the system. Moreover, the error can be controlled to check and even guarantee (in certain special cases) the robustness of simulated hybrid trajectories
The politics of landing: Urban agriculture, socioecological imaginaries and the production of space in the San Francisco Bay region

This dissertation illustrates how alternative food initiatives are entangled in the broader political economy of the production of space. Through a regional analysis of the land politics articulations of organized urban gardening projects in the San Francisco Bay Area, I ask what are the landscapes of possibility or closure resulting from these entanglements. Historically urban gardening has been used as a temporary land use to ameliorate various social problems until the land owner, either public or private, chose to put the land to different use, most frequently the use that gained the highest market value. In the Bay Area, where land markets are highly competitive, land access is a central concern for gardeners. Urban agriculture has been theorized and embraced by social movement activists as a means to resist the allocation of land based on market valuation and the realization of the authority of property ownership. Yet, through research based on semi-structured interviews with gardeners and city officials, documents analysis, and participant observation, this dissertation describes a more complex terrain of activist engagements in the practices of land access and enactments of property. Two dominant imaginaries of land politics emerge from these engagements. One emphasizes the need for flexible, even portable gardens, in order to cultivate more resilient cities and movements. This imaginary is ultimately facilitative of development priorities, supporting neoliberal urban regimes, and reaffirming of contemporary property relations. The second imaginary identifies the importance of long-term tenure, community-management of land resources, and developing movement coalitions concerned with land access. This imaginary connects with the international work of food sovereignty, a framework that gardeners and US food movement activists are increasingly adopting, and which works to resist neoliberal capitalism, colonial legacies, and top-down governance. I suggest that the everyday utopian projects of gardeners is a key site to understanding the US left questioning if reforming contemporary social democratic institutions, like the provision of public space, are sufficient strategies. This analysis contributes to the developing field of urban political ecology by describing socio-ecological space in the Bay Region as socially produced through a history of practices, representations, and experiences of gardeners.
GSNP: A DNA Single-Nucleotide Polymorphism Detection System with GPU Acceleration

We have developed GSNP, a software package with GPU acceleration, for single-nucleotide polymorphism detection on DNA sequences generated from second-generation sequencing equipment. Compared with SOAPsnp, a popular, high-performance CPU-based SNP detection tool, GSNP has several distinguishing features: First, we design a sparse data representation format to reduce memory access as well as branch divergence. Second, we develop a multipass sorting network to efficiently sort a large number of small arrays on the GPU. Third, we compute a table of frequently used scores once to avoid repeated, expensive computation and to reduce random memory access. Fourth, we apply customized compression schemes to the output data to improve the I/O performance. As a result, on a server equipped with an Intel Xeon E5630 2.53 GHZ CPU and an NVIDIA Tesla M2050 GPU, it took GSNP about two hours to analyze a whole human genome dataset whereas the CPU-based, single-threaded SOAPsnp took three days for the same task on the same machine.
Determination of Structural Femoral Head Allograft Viability and Integrity with a Novel Diagnostic Tool: SPECT/CT. A Preliminary Study

Objective To evaluate the viability and integrity of fresh frozen bulk femoral head allografts obtained from the institutional bone bank that were used to reconstruct severe acetabular defects and to validate the SPECT/CT method which gives both anatomical and functional data for this purpose. Methods We retrospectively reviewed 9 patients (6 female, 3 male; mean age 63.6 years). Preoperative and postoperative leg lengths, existence of the Trendelenburg sign, range of motion of the hip, visual analogue score (VAS), Harris Hip Score (HHS) and any complication were assesed at each follow-up. Radiographically, position of the cup, signs of loosening or migration, and union of the graft were all determined. At the latest follow-up, patients were evaluated with hybrid SPECT/CT. Results The average duration of follow-up was 38.1 months (24-50 months). The overall mean HHS and VAS scores were significantly improved (p<0.05). When hybrid SPECT/CT results were evaluated, the vascular phase of scintigraphy showed hyperaemia of the graft and the bone phase of scintigraphy showed normal or increased radiotracer uptake in the graft site in 7 patients. SPECT/CT images were used to determine the exact localisation of osteoblastic activity. 1 patient with minor resorption of the graft without clinical symptoms revealed mild osteoblastic activity. The patient who had no activity in the graft site was rerevised because of infection. Conclusions Institutional bank allografts are still excellent options for treating large acetabular defects in revision total hip arthroplasty where trabecular metals are not available or in common use. The Hybrid SPECT/CT method is a reliable, noninvasive method for evaluating both the integrity and viability of a bulk graft in 3-D.
In Vivo and In Vitro Evidence for Impaired Arginine Transport in Human Heart Failure

BackgroundThe clinical features of congestive heart failure (CHF) result from a complex interaction between reduced ventricular function, neurohormonal activation, and impaired endothelial function. Although endothelial dysfunction has been well documented, the mechanisms that contribute to this abnormality remain unknown. Recent studies, however, indicate a potential therapeutic role for supplemental l-arginine, suggesting the presence of an underlying disorder of l-arginine metabolism. Methods and ResultsWe used 2 complementary approaches to assess l-arginine transport in control subjects and patients with CHF. During a steady-state intra-arterial infusion of [3H]l-arginine (100 nCi/min), forearm clearance of [3H]l-arginine was significantly reduced in CHF patients compared with forearm kinetics in control subjects (64±2 versus 133±14 mL/min, P =0.002). In conjunction with this, [3H]l-arginine uptake by peripheral blood mononuclear cells (PBMCs) was also substantially reduced in heart failure patients compared with controls (Vmax 10.1±1.3 versus 49.8±7.1 pmol/105 cells per 5 minutes, P <0.001). In association with this finding, we observed a 76% (P <0.01) reduction in mRNA expression for the cationic amino acid transporter CAT-1, as assessed by ribonuclease protection assay. ConclusionsThese data document both in vivo and in vitro evidence for a marked depression of l-arginine transport in human CHF and therefore provide an explanation for the restorative actions of supplemental l-arginine on vascular function in CHF.
Avaliação da expressão do gene BDNF em doenças neurodegenerativas

RESUMO O Factor Neurotrófico Derivado do Cérebro (BDNF) está associado a processos de crescimento, diferenciação e sobrevivência das células neuronais. A expressão diferencial do BDNF, particularmente no hipocampo, está relacionada com a manifestação clínica de algumas doenças do foro psiquiátrico e cognitivo como a doença de Huntington, Alzheimer, depressão e esquizofrenia. Este trabalho pretende dar conhecimento das técnicas utilizadas para avaliar a expressão do gene BDNF. As técnicas de ELISA, IHC e Western blot, por permitirem a avaliação precisa da expressão de BDNF, são úteis para uma melhor compreensão, diagnóstico e tratamento de algumas doenças neurodegenerativas. The Brain-Derived Neurotrophic Factor (BDNF) is associated with processes of growth, differentiation and survival of neuronal cells. The differential expression of BDNF, particularly in the hippocampus, is related to the clinical manifestation of some psychiatric and cognitive diseases like Huntington's disease, Alzheimer's, depression and schizophrenia. This work aims to give knowledge of techniques used to evaluate the expression of the BDNF gene. The techniques of ELISA, IHC and Western blot, by allowing precise evaluation of the expression of BDNF, are useful for improved understanding, diagnosis and treatment of some neurodegenerative diseases.
Inference by Genetic Programming of an analytical expression for the Optimal Exercise Threshold of an asset that follows a Mean Reversion Process

The American option evaluation is a relatively complex and expensive process due to commonly used methodologies as Finite Differences, Dynamic Programming, Monte Carlo Simulation, etc. needs high computational performance. Besides that, the complexity needed to calculate the option value and the optimal threshold increases when the price of underlying asset follows the Mean Reversion Stochastic Process. By this way, is interesting to achieve an analytical approximation in order to make easier to obtain the optimal threshold and the option value. There are many analytical approximations mentioned in bibliography respecting to American Options about asset prices following a Geometric Brownian Motion [1] [2], but none about it follows Mean Reversion Processes. This work proposes a model based on Symbolic Regression by Genetic Programming to obtain an analytical approximation for the optimal threshold respecting to an American option which its asset follows a Mean Reversion Process. The Optimal Threshold that separates during the option life-cycle the decision to exercise the option, is later employed to evaluate the option. The result achieved by the proposed model (Threshold Analytical Function) seemed to be satisfactory.