Miracle-dz/UniFAR-FTUs huggingface dataset:
A Dual-Color Fluorescence-Based Platform to Identify Selective Inhibitors of Akt Signaling

Background Inhibition of Akt signaling is considered one of the most promising therapeutic strategies for many cancers. However, rational target-orientated approaches to cell based drug screens for anti-cancer agents have historically been compromised by the notorious absence of suitable control cells. Methodology/Principal Findings In order to address this fundamental problem, we have developed BaFiso, a live-cell screening platform to identify specific inhibitors of this pathway. BaFiso relies on the co-culture of isogenic cell lines that have been engineered to sustain interleukin-3 independent survival of the parental Ba/F3 cells, and that are individually tagged with different fluorescent proteins. Whilst in the first of these two lines cell survival in the absence of IL-3 is dependent on the expression of activated Akt, the cells expressing constitutively-activated Stat5 signaling display IL-3 independent growth and survival in an Akt-independent manner. Small molecules can then be screened in these lines to identify inhibitors that rescue IL-3 dependence. Conclusions/Significance BaFiso measures differential cell survival using multiparametric live cell imaging and permits selective inhibitors of Akt signaling to be identified. BaFiso is a platform technology suitable for the identification of small molecule inhibitors of IL-3 mediated survival signaling.
Photovoice: Engaging Children with Autism and their Teachers

Imagine Mark. a kindergarten student with autism. He doesn't communicate verbally, hut he uses one or two pictures to make requests. He runs from one classroom location to another, tapping objects on his desk and walls and moving his eyes laterally away from learning materials, Mark rarely Initiates interactions with peers or adults in even the most structured learning situations. Now, imagine another child of similar age. He sits in a chair looking appropriately at his learning materials with no adult support. When approached by apeer, he looks at a set of photographs, engaging In a joint attention activity for several minutes. He points to the photograph, looks to an adult sitting at the table, and looks back at the pictures. The two students sound very different. The first child sounds socially isolated; the second child is beginning to engage in interactions with peers. Yet, both scenarios describe the same child. How could the child Seem so distracted and disengaged in one description and interacting with a peer in the next? A process known all photovotce facilitated such changes for students with autism and their teachers. This article describes how a visual teaching method known as photovolce led to Improved engagement with peers and learning materials for two young boys with autism. The article
Design and modeling of a silicone-based bendable tip for colonoscopy

In this paper, the authors describe the design of a bendable robotic tip for semi-autonomous colonoscopy called COLOBOT. It is a flexible robotic manipulator made of silicone rubber in view of the compact size and safety compatibility in the medical context. The outer diameter of the tip is 17 mm which is lesser than the average diameter of colon (20mm). Three servo-valves are used to control the pressure of each chamber of this tip to obtain the flexible movement of this tip. The promising results of this new prototype show that it can bend until 120 degrees under the pressure of 2 Bar. Based on the geometric deformation, a direct kinematic model analogous to the forward kinematics of a conventional industrial robot kinematics chain has been put forward. A polynomial approximation is used to characterize the behavior of each chamber actuator. This kinematic model is then validated experimentally and can be used to optimize the structure and the actuator. KeywordsMicro-robot, colonoscopy, modeling, medical robot Kinematics, silicone rubber, continuum robot, actuator
6 Neuronal Correlates of Decision Making

Decision making involves selection from sets of options based on current evidence about the state of the world and estimates of the value or utility of different outcomes. The neural correlates of evidence assessment that guide simple perceptual judgments are now well understood, and we argue that this process can serve as a simple model for organizing behavioral and neural correlates of decision making in more complex contexts, including those that involve economic transactions, social interaction, emotional stimulation, and conscious awareness. Bridging the methodological and theoretical gaps between simple and more complicated decision problems remains a fundamental, but in our view soluble, challenge for understanding the neurobiology of decision making.
On the way to understand biological complexity in plants: S-nutrition as a case study for systems biology

The establishment of technologies for high-throughput DNA sequencing (genomics), gene expression (transcriptomics), metabolite and ion analysis (metabolomics/ionomics) and protein analysis (proteomics) carries with it the challenge of processing and interpreting the accumulating data sets. Publicly accessible databases and newly development and adapted bioinformatic tools are employed to mine this data in order to filter relevant correlations and create models describing physiological states. These data allow the reconstruction of networks of interactions of the various cellular components as enzyme activities and complexes, gene expression, metabolite pools or pathway flux modes. Especially when merging information from transcriptomics, metabolomics and proteomics into consistent models, it will be possible to describe and predict the behaviour of biological systems, for example with respect to endogenous or environmental changes. However, to capture the interactions of network elements requires measurements under a variety of conditions to generate or refine existing models. The ultimate goal of systems biology is to understand the molecular principles governing plant responses and consistently explain plant physiology.
Transport of vesicular stomatitis virus G protein to the cell surface is signal mediated in polarized and nonpolarized cells

Current model propose that in nonpolarized cells, transport of plasma membrane proteins to the surface occurs by default. In contrast, compelling evidence indicates that in polarized epithelial cells, plasma membrane proteins are sorted in the TGN into at least two vectorial routes to apical and basolateral surface domains. Since both apical and basolateral proteins are also normally expressed by both polarized and nonpolarized cells, we explored here whether recently described basolateral sorting signals in the cytoplasmic domain of basolateral proteins are recognized and used for post TGN transport by nonpolarized cells. To this end, we compared the inhibitory effect of basolateral signal peptides on the cytosol-stimulated release of two basolateral and one apical marker in semi-intact fibroblasts (3T3), pituitary (GH3), and epithelial (MDCK) cells. A basolateral signal peptide (VSVGp) corresponding to the 29-amino acid cytoplasmic tail of vesicular stomatitis virus G protein (VSVG) inhibited with identical potency the vesicular release of VSVG from the TGN of all three cell lines. On the other hand, the VSVG peptide did not inhibit the vesicular release of HA in MDCK cells not of two polypeptide hormones (growth hormone and prolactin) in GH3 cells, whereas in 3T3 cells (influenza) hemagglutinin was inhibited, albeit with a 3x lower potency than VSVG. The results support the existence of a basolateral-like, signal-mediated constitutive pathway from TGN to plasma membrane in all three cell types, and suggest that an apical-like pathway may be present in fibroblast. The data support cargo protein involvement, not bulk flow, in the formation of post-TGN vesicles and predict the involvement of distinct cytosolic factors in the assembly of apical and basolateral transport vesicles.
Mimicking the Kidney: A Key Role in Organ-on-Chip Development

Pharmaceutical drug screening and research into diseases call for significant improvement in the effectiveness of current in vitro models. Better models would reduce the likelihood of costly failures at later drug development stages, while limiting or possibly even avoiding the use of animal models. In this regard, promising advances have recently been made by the so-called “organ-on-chip” (OOC) technology. By combining cell culture with microfluidics, biomedical researchers have started to develop microengineered models of the functional units of human organs. With the capacity to mimic physiological microenvironments and vascular perfusion, OOC devices allow the reproduction of tissue- and organ-level functions. When considering drug testing, nephrotoxicity is a major cause of attrition during pre-clinical, clinical, and post-approval stages. Renal toxicity accounts for 19% of total dropouts during phase III drug evaluation—more than half the drugs abandoned because of safety concerns. Mimicking the functional unit of the kidney, namely the nephron, is therefore a crucial objective. Here we provide an extensive review of the studies focused on the development of a nephron-on-chip device.
Rapid Prototyping Design Acceleration Using a Novel Merging Methodology for Partial Configuration Streams of Xilinx Virtex-II FPGAs

RAM-based FPGAs have become very important for electronic designs in the last years since they are very flexible, provide high configurability and allow short turn around times. Especially in the field of rapid prototyping (RP) another feature plays an important rule: their infinite reprogrammability. These features help to create freely modifiable rapid prototyping systems, which allow both, changes in the hardware architecture as well as in software. However, handling the FPGA devices in the engineering process is not an easy issue and typically requires deep knowledge of the circuits themselves, their behavior and programming languages as VHDL or Verilog. Our approach presents the combination of a flexible and versatile FPGA-based rapid prototyping system and efficient configuration methodology for Xilinx Virtex-II FPGAs supplemented by an easy to use design support for time saving functional implementation and platform configuration
POLYMORPHONUCLEAR LEUKOCYTES IN IMMUNOLOGIC REACTIONS

Several experimental immunologic diseases apparently share a common pathway of mediation. To date these include the Arthus phenomenon in which cutaneous vessels are injured, the arteritis in serum sickness (1), and the glomerulitis in acute nephrotoxic nephritis (2). Damage occurs in each of these following the interaction of many factors, several of which are apparently common to all the reactions. These common mediators include (a) antibody and antigen that combine at a focal point in a blood vessel wall (3-6), (b) complement (C') that reacts with the immune complex (7-9, 1), and (c) polymorphonuclear leukocytes (PMN's) that accumulate at the site. Recent studies in this laboratory would suggest a complex of the 5th, 6th, and 7th components of C' is responsible, at least in part, for this accumulation of PMN's (10, 11). A release of PMN constituents may in turn, also bring about accumulation of more PMN's (12-14). Each of these events has been shown to be essential for full expression of the reaction. Considerable speculation exists as to the mechanism by which PMN's may injure blood vessel walls. In addition, little is known about the critical target in the vessel walls attacked by the PMN's. Several investigators have described permeability factors either released during incubation of PMN's in normal saline at 37°C (12) or contained within the cytoplasmic granules (13, 14). These factors have been shown to be cationic proteins (13, 14) and are capable of causing degranulation of rat mast cells (13). Other possible injurious agents within PMN's include the acid proteases or cathepsins (15). These are known to catabolize phagocytized immunologic reactants in Arthus reactions (16) or antigen and antibody in vitro (17). The possible roles played by these various
Holographic Algorithms

Complexity theory is built fundamentally on the notion of efficient reduction among computational problems. Classical reductions involve gadgets that map solution fragments of one problem to solution fragments of another in one-to-one, or possibly one-to-many, fashion. In this paper we propose a new kind of reduction that allows for gadgets with many-to-many correspondences, in which the individual correspondences among the solution fragments can no longer be identified. Their objective may be viewed as that of generating interference patterns among these solution fragments so as to conserve their sum. We show that such holographic reductions provide a method of translating a combinatorial problem to finite systems of polynomial equations with integer coefficients such that the number of solutions of the combinatorial problem can be counted in polynomial time if one of the systems has a solution over the complex numbers. We derive polynomial time algorithms in this way for a number of problems for which only exponential time algorithms were known before. General questions about complexity classes can also be formulated. If the method is applied to a P-complete problem, then polynomial systems can be obtained, the solvability of which would imply P$^{{\tiny{\#P}}}$ = NC2.
A low-cost attitude heading reference system by combination of GPS and magnetometers and MEMS inertial sensors for mobile applications

This paper describes a prototype system for attitude and heading determination. A L1-only GPS receiver is integrated with microelectromechanical gyroscopes, accelerometers and magnetometers. In contrast to a multi-antenna/multi-receiver GPS attitude determination system, this system uses a single antenna/single receiver configuration to derive standalone velocity and acceleration solutions from the GPS L1 carrier phase measurements. No reference station is needed to form differences of carrier phase measurements for the velocity and acceleration calculation. The GPSderived acceleration is further used in the attitude determination by combination with the three-dimension acceleration sensed by the accelerometers. The magnetometers sense the Earth’s magnetic field intensity, and can give the heading estimation regardless of the status of the host platform. To satisfy real-time applications, infinite impulse response differentiators instead of finite impulse response differentiators are used to derive the acceleration from GPS. The algorithms have been implemented and their efficiency demonstrated by experiments.
TSKT-ORAM: A Two-Server k-ary Tree Oblivious RAM without Homomorphic Encryption

This paper proposes TSKT-oblivious RAM (ORAM), an efficient multi-server ORAM construction, to protect a client’s access pattern to outsourced data. TSKT-ORAM organizes each of the server storages as a k-ary tree and adopts XOR-based private information retrieval (PIR) and a novel delayed eviction technique to optimize both the data query and data eviction process. TSKT-ORAM is proven to protect the data access pattern privacy with a failure probability of 2 - 80 when system parameter k ≥ 128 . Meanwhile, given a constant-size local storage, when N (i.e., the total number of outsourced data blocks) ranges from 2 16 – 2 34 , the communication cost of TSKT-ORAM is only 22–46 data blocks. Asymptotic analysis and practical comparisons are conducted to show that TSKT-ORAM incurs lower communication cost, storage cost and access delay in practical scenarios than the compared state-of-the-art ORAM schemes.
Area efficient architectures for information integrity in cache memories

Information integrity in cache memories is a fundamental requirement for dependable computing. Conventional architectures for enhancing cache reliability using check codes make it difficult to trade between the level of data integrity and the chip area requirement. We focus on transient fault tolerance in primary cache memories and develop new architectural solutions to maximize fault coverage when the budgeted silicon area is not sufficient for the conventional configuration of an error checking code. The underlying idea is to exploit the corollary of reference locality in the organization and management of the code. A higher protection priority is dynamically assigned to the portions of the cache that are more error-prone and have a higher probability of access. The error-prone likelihood prediction is based on the access frequency. We evaluate the effectiveness of the proposed schemes using a trace-driven simulation combined with software error injection using four different fault manifestation models. From the simulation results, we show that for most benchmarks the proposed architectures are effective and area efficient for increasing the cache integrity under all four models.
Hybrid Exponential Particle Swarm Optimization K-Means Algorithm for Efficient Image Segmentation

The introduction of unsupervised learning techniques like K-means inside the domain of Image Processing plays a vital role in Image Segmentation. The hybridization of this Algorithm by using Swarm Intelligent techniques further more improves the efficiency. Various works on hybridization of Particle Swarm Optimization (PSO) with K-means have been proposed and are found to be efficient in Image Segmentation. However, the PSO has a problem of getting stagnated with the local optima. This results in the degradation of the Image Segmentation process in most cases. The main reason behind this problem is the constancy of the inertia weight. The inertia weight when varied dynamically and exponentially could afford a better performance in the process of finding better global optima. We use the Exponential Particle Swarm Optimization to enhance the K-means Algorithm. This shows a drastic improvement in the process of Image Segmentation. The experimental results obtained also add to this process enhancement. The EPSO K-means Algorithm is much efficient compared to its previous types.
Dendritic Cells Strongly Boost the Antitumor Activity of Adoptively Transferred T Cells In vivo

Dendritic cells (DCs) have been well characterized for their ability to initiate cell-mediated immune responses by stimulating naive T cells. However, the use of DCs to stimulate antigen-activated T cells in vivo has not been investigated. In this study, we determined whether DC vaccination could improve the efficacy of activated, adoptively transferred T cells to induce an enhanced antitumor immune response. Mice bearing B16 melanoma tumors expressing the gp100 tumor antigen were treated with cultured, activated T cells transgenic for a T-cell receptor specifically recognizing gp100, with or without concurrent peptide-pulsed DC vaccination. In this model, antigen-specific DC vaccination induced cytokine production, enhanced proliferation, and increased tumor infiltration of adoptively transferred T cells. Furthermore, the combination of DC vaccination and adoptive T-cell transfer led to a more robust antitumor response than the use of each treatment individually. Collectively, these findings illuminate a new potential application for DCs in the in vivo stimulation of adoptively transferred T cells and may be a useful approach for the immunotherapy of cancer.
Crosstalk minimization in logic synthesis for PLAs

We propose a maximum crosstalk effect minimization algorithm that takes logic synthesis into consideration for PLA structures. To minimize the crosstalk effect, a technique for permuting wire is used which contains the following steps. First, product terms are partitioned into long and short sets, and then the product terms in the long and short sets are interleaved. After that, we take advantage of the crosstalk immunity of product terms in the long set to further reduce the maximum coupling capacitance of the PLA. Finally, synthesis techniques such as local and global transformations are taken into consideration to search for a better result. The experiments demonstrate that our algorithm can effectively minimize the maximum coupling capacitance of a circuit by 51% as compared with the original area-minimized PLA without crosstalk effect minimization.
Differential diagnosis of thyroid nodules with US elastography using carotid artery pulsation.

PURPOSE To explore the sensitivity and specificity of ultrasonographic (US) elastography using carotid arterial pulsation as the compression source for differential diagnosis of thyroid nodules. MATERIALS AND METHODS This HIPAA-compliant study was approved by the ethics committee of the institution, and all patients provided written informed consent. Fifty-eight patients (13 men and 45 women [mean age, 51 years; range, 20-76 years]) were enrolled. A short US examination and elastography with pulsation of the carotid artery used as the thyroid compression source were performed before fine-needle aspiration. Baseband US data were downloaded for off-line analysis. Elastographic maps and the thyroid stiffness index were calculated. The Kruskal-Wallis nonparametric rank sum test was used to assess equality of population medians among the different types of thyroid nodules; the R software environment was used for statistical computing and graphics (http://www.r-project.org/). RESULTS Thyroid stiffness index calculated with elastography using carotid arterial pulsation as the compression source was effective in helping distinguish between papillary carcinomas (n = 10) and other lesions (n = 43) because papillary carcinomas were stiffer than other lesions (P < .0039). CONCLUSION It is possible to distinguish between papillary carcinomas and other lesions with the thyroid stiffness index calculated from US elastography using carotid arterial pulsation.
On the mechanical factors which determine the output of the ventricles

THE working capacity of a pump is measured by its output. In the heart the output has to undergo large alterations with varying conditions of the body, and its measurement is therefore the most important quantitative determinat.ion connected with this organ. Most of the previous researches on this subject have been carried out on the whole animal, and in view of the difficulty of controlling the different factors involved under these circumstances it is not surprising that considerable discrepancies exist between the views of different workers as to the relative importance of the various factors involved. Thus whereas Zun tz m and his pupils describe great variations in the outpuit associated with exercise, and Krogh (2) has actually measured these variations in marl, Yandell Henderson (3), as a result of a number of careful experiinents, considers it impossible for the heart to more than double its output under any circumstances, though Krogh finds variations in the output of the left ventricle between 2 8 and 21 litres per minute. It seemed to us that the whole question might be put on a securer basis if investigated on the heart-lung preparation as used in this laboratory, where all the mechanical factors of the circulation are under strict control. The results obtained in this way should give us somie idea of the capabilities of the heart as a pump, which might serve to explain the behaviour of this organ in the intact animal. It has been shown lately by Mark walder (4) and one of us that, provided the venous inflow be maintained constant, the ouitput of the left ventricle is within wide limits irndependent of the arterial resistance, the small falling off in the output with rise of pressure, observed in previous experiments, being fully accounted for by the increased leakage from the aorta through the coronary system of vessels as the arterial pressure rises. Knowlton