Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling Prostate Deformation: SOFA versus Experiments

Needle insertion procedures are commonly used to treat and to diagnose prostate cancer. Surgical simulation systems can be used to estimate prostate deformation during pre- and intra-operative needle insertion planning. Such systems require a model that can accurately predict the prostate deformation in real time. In this study, we present a prostate model that incorporates the anatomy of the male pelvic region. The model is used to predict the prostate deformation during needle insertion and it is implemented in the Simulation Open Framework Architecture (SOFA). SOFA simulations are compared with experimental results for two scenarios: indentation and needle insertion. An experimental phantom is developed using anatomically accurate magnetic resonance images and populated with elasticity properties obtained from ultrasound-based Acoustic Radiation Force Impulse imaging technique. Markers are placed on the phantom surface to identify the deformation during indentation experiments. The root mean square error (RMSE) obtained in indentation experiments is 0.36 mm. During the needle insertion, the needle tip position is used to validate the model. The SOFA simulation resulted in a RMSE of 0.14 mm. The results of this study demonstrate that SOFA is a feasible option to be used in surgical simulations for pre-operative planning and training.
Protection of synapses against Alzheimer's-linked toxins: Insulin signaling prevents the pathogenic binding of Aβ oligomers

Synapse deterioration underlying severe memory loss in early Alzheimer's disease (AD) is thought to be caused by soluble amyloid beta (Aβ) oligomers. Mechanistically, soluble Aβ oligomers, also referred to as Aβ-derived diffusible ligands (ADDLs), act as highly specific pathogenic ligands, binding to sites localized at particular synapses. This binding triggers oxidative stress, loss of synaptic spines, and ectopic redistribution of receptors critical to plasticity and memory. We report here the existence of a protective mechanism that naturally shields synapses against ADDL-induced deterioration. Synapse pathology was investigated in mature cultures of hippocampal neurons. Before spine loss, ADDLs caused major downregulation of plasma membrane insulin receptors (IRs), via a mechanism sensitive to calcium calmodulin-dependent kinase II (CaMKII) and casein kinase II (CK2) inhibition. Most significantly, this loss of surface IRs, and ADDL-induced oxidative stress and synaptic spine deterioration, could be completely prevented by insulin. At submaximal insulin doses, protection was potentiated by rosiglitazone, an insulin-sensitizing drug used to treat type 2 diabetes. The mechanism of insulin protection entailed a marked reduction in pathogenic ADDL binding. Surprisingly, insulin failed to block ADDL binding when IR tyrosine kinase activity was inhibited; in fact, a significant increase in binding was caused by IR inhibition. The protective role of insulin thus derives from IR signaling-dependent downregulation of ADDL binding sites rather than ligand competition. The finding that synapse vulnerability to ADDLs can be mitigated by insulin suggests that bolstering brain insulin signaling, which can decline with aging and diabetes, could have significant potential to slow or deter AD pathogenesis.
Arterial stiffness in fertile women with metabolic syndrome

Abstract Introduction: Although metabolic syndrome (MetS) is evidently associated with the risk of cardiovascular disease (CVD), recently its use has been questioned. We studied the utility of MetS diagnosis when estimating individual CVD risk. Methods: We compared 27 fertile women with MetS and 27 counterparts without the syndrome, matched pairwise according to well-known risk factors of CVD. Pulse wave velocity (PWV) and central blood pressure (cBP) were determined noninvasively via a SphygmoCor device. Arterial compliance was measured noninvasively with an HDI/PulseWaveTMCR-2000 arterial tonometer. Results: PWV (7.1 ± 2.5 versus 6.5 ± 1.1 m/s, p = .037), and both systolic (120.9 ± 12.2 versus 111.5 ± 16.0 mmHg, p = .031) and diastolic cBP (81.3 ± 8.5 versus 74.1 ± 11.2 mmHg, p = .035) were higher in the MetS group. Systemic arterial compliance values were lower in both large (15.1 ± 8.0 versus 16.1 ± 4.4 mL/mmHg × 10, p = .034) and small arteries (7.1 ± 2.5 versus 9.3 ± 3.2 mL/mmHg ×100, p = .010) in women with MetS. Conclusions: Fertile women with MetS had increased arterial stiffness, as measured by three different methods. Our results highlight the utility of MetS when revealing increased individual CVD risks in fertile-aged women. Key messages Women with MetS have increased arterial stiffness when measured by different methods. MetS is a useful clinical tool to assess increased cardiovascular risk, particularly among fertile-aged women.
Projections from the periamygdaloid cortex to the amygdaloid complex, the hippocampal formation, and the parahippocampal region: A PHA‐L study in the rat

The periamygdaloid cortex, an amygdaloid region that processes olfactory information, projects to the hippocampal formation and parahippocampal region. To elucidate the topographic details of these projections, pathways were anterogradely traced using Phaseolus vulgaris leukoagglutinin (PHA‐L) in 14 rats. First, we investigated the intradivisional, interdivisional, and intra‐amygdaloid connections of various subfields [periamygdaloid subfield (PAC), medial subfield (PACm), sulcal subfield (PACs)] of the periamygdaloid cortex. Thereafter, we focused on projections to the hippocampal formation (dentate gyrus, hippocampus proper, subiculum) and to the parahippocampal region (presubiculum, parasubiculum, entorhinal, and perirhinal and postrhinal cortices). The PACm had the heaviest intradivisional projections and it also originated light interdivisional projections to other periamygdaloid subfields. Projections from the other subfields converged in the PACs. All subfields provided substantial intra‐amygdaloid projections to the medial and posterior cortical nuclei. In addition, the PAC subfield projected to the ventrolateral and medial divisions of the lateral nucleus. The heaviest periamygdalohippocampal projections originated in the PACm and PACs, which projected moderately to the temporal end of the stratum lacunosum moleculare of the CA1 subfield and to the molecular layer of the ventral subiculum. The PACm also projected moderately to the temporal CA3 subfield. The heaviest projections to the entorhinal cortex originated in the PACs and terminated in the amygdalo‐entorhinal, ventral intermediate, and medial subfields. Area 35 of the perirhinal cortex was lightly innervated by the PAC subfield. Thus, these connections might allow for olfactory information entering the amygdala to become associated with signals from other sensory modalities that enter the amygdala via other nuclei. Further, the periamygdalohippocampal pathways might form one route by which the amygdala modulates memory formation and retrieval in the medial temporal lobe memory system. These pathways can also facilitate the spread of seizure activity from the amygdala to the hippocampal and parahippocampal regions in temporal lobe epilepsy. © 2003 Wiley‐Liss, Inc.
Plasmonic Photon Sorters and Their Potential for Use in Compact Multispectral Imagers at Visible and Infrared Wavelengths

Abstract : Spectral imaging extracts rich information from the incoming light and has many military applications. Polarimetric imaging is also an active field of study with many potential applications. Many sensor technologies exist for spectral and polarimetric imaging, but these generally involve scanning or subsampling, since the dataset is three-dimensional while photodetector arrays are at most two-dimensional. Recently, it has been shown how surface plasmons may be used to sort photons arriving at a detector array by placing plasmonic antenna structures on top of the array. Each antenna structure concentrates light of a particular wavelength and/or polarization onto one detector element. Importantly, the antennas of a group of neighbouring detector elements are overlapped to form a superpixel capable of separating different components of the incoming light. Thus photons of different wavelengths arriving at the same location on the antenna structure may be routed to different detector elements. This has potential for use in snapshot multispectral and polarimetric imaging. The photon sorting capability has been demonstrated experimentally in the visible spectral range. No fundamental difficulties are expected in translating these results into the thermal infrared spectral range. Indeed, the antenna structures for thermal infrared wavelengths will be easier to fabricate due to the relatively long wavelength. The photon sorter concept has some specific issues and limitations, most importantly the polarization-dependent coupling efficiency which leads to reflection loss of a large fraction of the incoming light. However this may not be problematic in the 8 to 12 m spectral range, where the number of photons per frame time is usually larger than the charge collection capacity of a photovoltaic detector.
Slow Computing Simulation of Bio-plausible Control

Abstract : In order to implement control methods on low power, size-constrained systems, significant departures from standard approaches are needed. We look to biology for inspiration and focus on the problem of attitude stabilization through visual input alone. Bio-plausibility broadly refers to the ability of an operation to be carried out on a neural substrate or a parallel asynchronously operating computation scheme. One method of realizing such an asynchronous, parallel computing capability in power-constrained systems is by making use of low-throughput, energy-efficient computing elements; this is referred to as a slow computing architecture. In this work, we evaluate the capacity of bio-plausible control laws for attitude stabilization on a slow computing architecture. The Gillespie Stochastic Simulation Algorithm (SSA) from chemical kinetics is modified to simulate a slow computing system. We approximate how sparse the system's visual information may be while remaining controllable and producing attitude stabilization. Gaussian noise is added to the simulation of visual input values, and the interaction of noise and sparsity is explored. The bio-plausible approach to stabilization is intended to replace more power-consumptive methods. In simulation, low power processing of visual input data produced effective attitude stabilization for a range of noise and sparsity.
Bayesian analysis of birth weight and litter size in Baluchi sheep using Gibbs sampling.

Variance and covariance components for birth weight (BWT), as a lamb trait, and litter size measured on ewes in the first, second, and third parities (LS1 through LS3) were estimated using a Bayesian application of the Gibbs sampler. Data came from Baluchi sheep born between 1966 and 1989 at the Abbasabad sheep breeding station, located northeast of Mashhad, Iran. There were 10,406 records of BWT recorded for all ewe lambs and for ram lambs that later became sires or maternal grandsires. All lambs that later became dams had records of LS1 through LS3. Separate bivariate analyses were done for each combination of BWT and one of the three variables LS1 through LS3. The Gibbs sampler with data augmentation was used to draw samples from the marginal posterior distribution for sire, maternal grandsire, and residual variances and the covariance between the sire and maternal grandsire for BWT, variances for the sire and residual variances for the litter size traits, and the covariances between sire effects for different trait combinations, sire and maternal grandsire effects for different combinations of BWT and LS1 through LS3, and the residual covariations between traits. Although most of the densities of estimates were slightly skewed, they seemed to fit the normal distribution well, because the mean, mode, and median were similar. Direct and maternal heritabilities for BWT were relatively high with marginal posterior modes of . 14 and . 13, respectively. The average of the three direct-maternal genetic correlation estimates for BWT was low, . 10, but had a high standard deviation. Heritability increased from LS1 to LS3 and was relatively high, . 29 to . 37. Direct genetic correlations between BWT and LS1 and between BWT and LS3 were negative, -. 32 and -. 43, respectively. Otherwise, the same correlation between BWT and LS2 was positive and low, . 06. Genetic correlations between maternal effects for BWT and direct effects for LS1 through LS3 were all highly negative and consistent for all parities, circa -. 75. Environmental correlations between BWT and LS1 through LS3 were relatively low and ranged from . 18 to . 29 and had high standard errors.
A laboratory model of a dual active bridge DC-DC converter for a smart user network

The paper presents an application of a dual active bridge DC-DC converter for a smart user network that is a microgrid with a DC-powered local network (or DC bus). In such a microgrid the DC-DC converter connects a battery energy storage system to the DC bus. In a previous paper, the authors demonstrated that the DC-DC converter is able to assure a stable DC bus voltage to a reference value; performance was evaluated by means of numerical experiment using Simplorer. In this paper the DC-DC converter is further investigated using a 400W laboratory model of a smart user network; the laboratory results demonstrate that the converter provides a high level of reliability and resilience against disturbances.
Efficient SMC inference in Semi-Markov models by compressing the belief state

Hidden semi - Markov models allow state transitions (actions) to have arbitrary duration distributions. Sequential Monte Carlo (SMC) methods provide an approximate inference for Semi-Markov models. In real-world applications with huge discrete state spaces and long-running actions with flat duration distributions, even SMC methods cannot efficiently approximate the posterior distribution. We propose a compression of the belief state to track significantly many more states with the same computational complexity. A piecewise approximation of the starting time distribution using log-linear models with constant-time online changepoint detection is used. The effect of the approach is analysed and discussed for three different datasets.
Personalized recommendation of live programs in cable television

Aiming at reducing the overload of cable television information and the difficulty to pinpoint users, this research employs the directed preview method of CATV's live programs which is grounded in labels. Long-term and short-term models of users' viewing behaviors and models of period preference are constructed accurately and can multi-dimensionally describe users' viewing behaviors. Based on labels, the research propounds the TOPN method of recommendation of live program, which could increase the accuracy rate of recommendation to 40%.
Long-term liver allograft survival induced by combined treatment with rAAV-hCTLA4Ig gene transfer and low-dose FK5061

Background. Recombinant adeno-associated virus vector (rAAV) is a promising vehicle for gene delivery, but few reports have documented its application in solid organ transplantation. In a rat orthotopic liver transplantation model, we investigated the efficacy of rAAV-mediated human cytotoxic T-lymphocyte-associated antigen 4 and immunoglobulin G (hCTLA4Ig) gene transfer to induce long-term allograft survival. Methods. Dark Agouti and Lewis rats were used as donors and recipients, respectively, in six experimental groups: (a) syngeneic control, (b) no treatment, (c) rAAV-green fluorescent protein, (d) rAAV-hCTLA4Ig, (e) low-dose FK506 for 7 days, and (f) rAAV-hCTLA4Ig and low-dose FK506 for 7 days. Results. The liver allografts were rejected within 10 days when no treatment was given or rAAV-green fluorescent protein was delivered. rAAV-hCTLA4Ig transduction slightly prolonged the survival time to 11 days. Long-term survival was achieved using the combined treatment of rAAV-hCTLA4Ig and low-dose FK506, whereas grafts were rejected on day 33 in the low-dose FK506 group. A sustained hCTLA4 level in plasma was detected in the combined treatment group from day 5 to day 180. On postoperative day 5, combined treatment significantly decreased the interleukin-2 and interferon-&ggr; protein levels in the grafts and the number of infiltrating B, T, CD25+, CD4+, CD8+, and NK cells. Conclusion. This study shows that rAAV-hCTLA4Ig gene transfer combined with low-dose FK506 can achieve long-term liver allograft survival.
RNA-dependent RNA polymerase consensus sequence of the L-A double-stranded RNA virus: definition of essential domains.

The L-A double-stranded RNA virus of Saccharomyces cerevisiae makes a gag-pol fusion protein by a -1 ribosomal frameshift. The pol amino acid sequence includes consensus patterns typical of the RNA-dependent RNA polymerases (EC 2.7.7.48) of (+) strand and double-stranded RNA viruses of animals and plants. We have carried out "alanine-scanning mutagenesis" of the region of L-A including the two most conserved polymerase motifs, SG.T. NT.N (. = any amino acid) and GDD. By constructing and analyzing 46 different mutations in and around the RNA polymerase consensus regions, we have precisely defined the extent of domains and specific residues essential for viral replication. Assuming that this highly conserved region has a common secondary structure among different viruses, we predict a largely beta-sheet structure.
A scalable architecture for massive Multi-Player Online Games using peer-to-peer overlay

Today, Massive Multi-player Online Game (MMOG) has taken an important part in the field of entertainment. But its increasing requirement of resources has brought a heavy burden to the game server. To address this problem, we propose a Structured Multi-Agent (SMA) model which divides the resources into groups by the Area of Interest (AOI) and builds itself on the pastry protocol. Then, every other agent can get the resources from the manager located by the pastry. Moreover, an algorithm called Assignment of Resource Processing License (ARPL) is implemented to constitute the core of SMA model. This algorithm guarantees the consistency of all resources by assigning events to the agents who have the processing licenses of resources. Through comparing with another P2P MMOG model, fine performance is indicated on SMA.
Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor

Significance This work reports unique insights into IF2 function during eubacterial translation initiation by addressing the function of the N domain within the structure of the full-length factor in isolated form or ribosome bound, using crystallography, SAXS, cryo-EM, fast kinetics, and single molecule fluorescence. Translation initiation factor 2 (IF2) promotes 30S initiation complex (IC) formation and 50S subunit joining, which produces the 70S IC. The architecture of full-length IF2, determined by small angle X-ray diffraction and cryo electron microscopy, reveals a more extended conformation of IF2 in solution and on the ribosome than in the crystal. The N-terminal domain is only partially visible in the 30S IC, but in the 70S IC, it stabilizes interactions between IF2 and the L7/L12 stalk of the 50S, and on its deletion, proper N-formyl-methionyl(fMet)-tRNAfMet positioning and efficient transpeptidation are affected. Accordingly, fast kinetics and single-molecule fluorescence data indicate that the N terminus promotes 70S IC formation by stabilizing the productive sampling of the 50S subunit during 30S IC joining. Together, our data highlight the dynamics of IF2-dependent ribosomal subunit joining and the role played by the N terminus of IF2 in this process.
Delay-aware VNF placement and chaining based on a flexible resource allocation approach

Network Function Virtualization (NFV) is a promising technology that is receiving significant attention in both academia and the industry. NFV paradigm proposes to decouple Network Functions (NFs) from dedicated hardware equipment, offering a better sharing of physical resources and providing more flexibility to network operators. However, in such environment, efficient management mechanisms are crucial to address the problem of Placement and Chaining of Virtual Network Functions (PC-VNF). In this paper, we introduce a PC-VNF model based on a flexible resource allocation approach that takes into account service requirements in terms of latency, in addition to traditional connectivity and resource utilization. This is particularly important for emerging 5G services such as ultrareliable, low latency and massive machine type communications. The end-to-end performance needs to meet the user expectations as well as service requirements to provide the desired QoS/QoE. Our main goal is to determine the optimal VNF placement minimizing resource consumption while providing specific latency (i.e., end-to-end delay) and avoiding violation of Service Level Agreements (SLA) by constraining allocated resources to a given VNF to reach its required performance. Results show that our approach achieves the required latency with better resources utilization compared to the classical approaches, with a reduction of up to 40% of resource consumption and a higher rate of accepted requests by recovering 15 to 60 % of the rejected requests.