Miracle-dz/UniFAR-FTUs huggingface dataset:
Raised LIGHT levels in pulmonary arterial hypertension: potential role in thrombus formation.

RATIONALE Thrombus formation and inflammation are involved in the pathogenesis of pulmonary arterial hypertension (PAH), and LIGHT (Lymphotoxin-like Inducible protein that competes with Glycoprotein D for Herpesvirus entry mediator on T lymphocytes) has been shown to promote vascular inflammation. OBJECTIVES We sought to investigate the role of the tumor necrosis factor superfamily ligand LIGHT in the pathogenesis of PAH. METHODS We studied 73 patients with severe PAH and 10 control subjects. LIGHT and pro- and antithrombotic markers were assessed by enzyme immunoassays. MEASUREMENTS AND MAIN RESULTS (1) Patients with idiopathic PAH (n = 21), patients with PAH related to risk factors or associated conditions (n = 31), and those with chronic thromboembolic PAH (n = 21) all had raised serum levels of LIGHT compared with control subjects (n = 10). (2) LIGHT levels in femoral artery were significantly related to mortality in the patients with PAH. (3) Immunostaining of LIGHT and its receptors was seen in alveolar macrophages, vascular smooth muscle cells, and endothelial cells in lungs from patients with PAH. (4) Thirteen patients received prostacyclin infusion (3 mo), and all showed hemodynamic improvement, accompanied by decreased LIGHT levels. (5) Prostacyclin abolished the release of LIGHT from activated platelets in vitro, suggesting that the decrease in LIGHT during prostacyclin therapy could involve direct effects on platelets. (6) LIGHT increased tissue factor and plasminogen activator inhibitor type 1 and decreased thrombomodulin levels in endothelial cells, inducing a prothrombotic state in these cells. CONCLUSIONS Our findings suggest prothrombotic effects of LIGHT in PAH involving endothelium-related mechanisms, potentially contributing to the progression of this disorder.
Upregulation of Bcl-xL Double-Positive Thymocytes through + CD8+ c-Myb Promotes the Survival of CD4

Mechanisms that regulate the lifespan of CD4 + CD8 + double-positive (DP) thymocytes help shape the peripheral T cell repertoire. However, the molecular mechanisms controlling DP thymocyte survival remain poorly understood. The Myb proto-oncogene encodes a transcription factor required during multiple stages of T cell development. We demonstrate that Myb mRNA expression is upregulated as thymocytes differentiate from the double-negative into the metabolically quiescent, small, preselection DP stage during T cell development. Using a conditional deletion mouse model, we demonstrate that Myb -deﬁcient DP thymocytes undergo premature apoptosis, resulting in a limited Tcr a repertoire biased toward 5 9 J a segment usage. Premature apoptosis occurs speciﬁcally in the small preselection DP compartment in an ab TCR-independent manner and is a consequence of decreased Bcl-xL expression. Forced Bcl-xL expression is able to rescue survival, and reintroduction of c-Myb restores both Bcl-xL expression and the small preselection DP compartment. We further demonstrate that c-Myb promotes transcription at the Bcl2l1 locus via a genetic pathway that is independent of the expression of T cell-speciﬁc factor-1 or ROR g t, two transcription factors that induce Bcl-xL expression in T cell development. Thus, Bcl-xL is a novel mediator of c-Myb activity during normal T cell development. The Journal of Immunology , 2010, 184: 2793–2804.
Tandem repeats finder: a program to analyze DNA sequences.

A tandem repeat in DNA is two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats have been shown to cause human disease, may play a variety of regulatory and evolutionary roles and are important laboratory and analytic tools. Extensive knowledge about pattern size, copy number, mutational history, etc. for tandem repeats has been limited by the inability to easily detect them in genomic sequence data. In this paper, we present a new algorithm for finding tandem repeats which works without the need to specify either the pattern or pattern size. We model tandem repeats by percent identity and frequency of indels between adjacent pattern copies and use statistically based recognition criteria. We demonstrate the algorithm's speed and its ability to detect tandem repeats that have undergone extensive mutational change by analyzing four sequences: the human frataxin gene, the human beta T cellreceptor locus sequence and two yeast chromosomes. These sequences range in size from 3 kb up to 700 kb. A World Wide Web server interface atc3.biomath. mssm.edu/trf.html has been established for automated use of the program.
Minimax differential dynamic programming: application to a biped walking robot

We developed a robust control policy design method in high-dimensional state space by using differential dynamic programming with a minimax criterion. As an example, we applied our method to a simulated five link biped robot. The results show lower joint torques from the optimal control policy compared to a hand-tuned PD servo controller. Results also show that the simulated biped robot can successfully walk with unknown disturbances that cause controllers generated by standard differential dynamic programming and the hand-tuned PD servo to fail. Learning to compensate for modeling error and previously unknown disturbances in conjunction with robust control design is also demonstrated. We also applied proposed method to a real biped robot for optimizing swing leg trajectories.
Doppler radar wind field retrieval over the Po Valley

Although methods of using multiple Doppler radars to study wind fields have long been proposed, and many research studies have been made, very few operational radar operators adopt methods which require the use of spe- cific scanning strategies to allow the extraction of wind in- formation. Here we report a collaborative study on dual- Doppler radars based on two Doppler radars in the Po val- ley, Italy. Unusually, the radars are only about 90 km apart, though operated by the same authority. The wind field syn- theses are carried out on a 30 km by 30 km region where the two radars have overlapping scan coverage. An itera- tive method based on the linear wind model and the equation of mass continuity is used to construct the wind fields. The methodology has been validated by two different methods. The first method is to reconstruct the radial wind observed by each radar, and the second method is calculating and com- paring the along-track component with that derived from the observations. Both two comparisons show good agreement with the original data.
Surgical management of extensive burns treatment using allografts

Patients with extensive burns (TBSA over 45%) can benefit from treatment with split thickness skin allotransplants (skin bank or honorific donors). In this study, we present our protocols for the surgical treatment by using allografts. We emphasize the criteria for the staging of the procedures, the prioritisation of the areas that need to be grafted and the postoperative management. The treatment includes a serial excision grafting with simple grafts or the sandwich method, which implies the covering of the wound with a widely meshed autograft (6:1). This layer is covered by a 1,5:1 or 3:1 expanded mesh allograft.
Sparse Reconstruction for Quantitative Bioluminescence Tomography Based on the Incomplete Variables Truncated Conjugate Gradient Method References and Links

In this paper, we present an incomplete variables truncated conjugate gradient (IVTCG) method for bioluminescence tomography (BLT). Considering the sparse characteristic of the light source and insufficient surface measurement in the BLT scenarios, we combine a sparseness-inducing ( 1 norm) regularization term with a quadratic error term in the IVTCG-based framework for solving the inverse problem. By limiting the number of variables updated at each iterative and combining a variable splitting strategy to find the search direction more efficiently, it obtains fast and stable source reconstruction, even without a priori information of the permissible source region and multispectral measurements. Numerical experiments on a mouse atlas validate the effectiveness of the method. In vivo mouse experimental results further indicate its potential for a practical BLT system. Looking and listening to light: the evolution of whole-body photonic imaging, " Nat. Advances in in vivo bioluminescence imaging of gene expression, " Annu. " Hyperspectral and multispectral bioluminescence optical tomography for small animal imaging, " Phys. Med. Spectrally resolved bioluminescence tomography using the reciprocity approach, " Med. Fast iterative image reconstruction methods for fully 3D multispectral bioluminescence tomography, " Phys. Truncated total least squares method with a practical truncation parameter choice scheme for bioluminescence tomography inverse problem, " Int. A multilevel adaptive finite element algorithm for bioluminescence tomography, " Opt. An optimal permissible source region strategy for multispectral bioluminescence tomography, " Opt. A multi-phase level set framework for source reconstruction in bioluminescence tomography, " J. Algorithms for bioluminescence tomography incorporating anatomical information and reconstruction of tissue optical properties, " J. Source reconstruction for spectrally-resolved bioluminescence tomography with sparse a priori information, " Opt. Multilevel bioluminescence tomography based on radiative transfer equation Part 1: l1 regularization, " Opt. Sparse regularization-based reconstruction for bioluminescence tomography using a multilevel adaptive finite element method, " Int. J. The inverse source problem based on the radiative transfer equation in optical molecular imaging, " J. Quantitative bioluminescence tomography guided by diffuse optical tomography, " Opt. The finite element method for the propagation of light in scattering media: boundary and source conditions, " Med. Gradient projection for sparse reconstruction: Application to compressed sensing and other inverse problems, IEEE J. Select, " IEEE J. systems via trust region and the conjugate gradient methods, " SIAM J. Incomplete variables truncated conjugate gradient method for signal reconstruction in compressed sensing, " in preparation. Digimouse: a 3D whole body mouse atlas from CT and cryosection …
A comparative study of power control approaches for device-to-device communications

Device-to-device (D2D) communications integrated into cellular networks is a means to take advantage of the proximity of devices and thereby to increase the user bitrates and system capacity. D2D communications has recently been proposed for the 3GPP Long Term Evolution (LTE) system as a method to increase the spectrum- and energy-efficiency. Such systems support a wide range of power control schemes based on a combination of open-loop and closed-loop components and there is a need to set the associated control parameters such that spectrum- and energy-efficiency targets are met. In this paper we study the performance of various power control strategies applicable to D2D communications in LTE networks and compare them with a utility function maximization approach that balances spectrum efficiency and the total transmission power. Our reference scheme is based on a fully distributed algorithm that iteratively sets the signal-to-interference-plus-noise (SINR) targets and corresponding transmit power levels. We find that the LTE-based power control approach performs close to the optimal scheme provided that the associated parameters are properly set1.
Recognition of Bird Species from their Sounds using Data Reduction Techniques

This paper deals with techniques for automatic recognition of bird species based on audio recordings of their sounds. Perceptual features, Mel-frequency cepstral coefficients are extracted from the sound files. For dimensionality reduction Mean computation, Principal Component Analysis and Vector Quantization is used and compared. Classification is carried out using k-nearest neighbour classifier. In our experiment, classification accuracy of 82% is achieved for the classification of ten bird species.
Interleukin-1␤ Enhances Interleukin-1 Receptor Antagonist Content in Human Somatotroph Adenoma Cell Cultures*

In addition to the well-known modulation of immune and inflam-matory responses, the interleukin-1 (IL-1) system has been shown to be involved in the regulation of anterior pituitary hormone secretion and growth. We previously demonstrated that IL-1 receptor antagonist (IL-1ra) is expressed in human pituitary adenomas cultured in vitro. In the present study, we investigated the regulation of IL-1ra protein by IL-1␤ (1–100 U/mL) in human somatotroph adenomas (n ϭ 9) cultured for 12– 48 h. IL-1␤ significantly enhanced the concentration of IL-1ra dose dependently in the somatotroph adenoma cell lysates, whereas IL-1ra concentrations remained unchanged in the culture supernatants. Furthermore, basal IL-1ra concentrations were significantly higher in the cell lysates compared with the corresponding culture supernatants. The regulation of IL-1ra in somatotroph adenoma cells is different from human cultured monocytes, in which IL-1␤ significantly stimulated IL-1ra secretion into the culture su-pernatants, and no change of intracellular IL-1ra content was observed. Incubation of the somatotroph adenoma cells with 100 U/mL IL-1␤ did not result in a change of GH concentrations in the culture supernatants. Enhancement of intracellular IL-1ra protein by IL-1␤ may represent a mechanism intrinsic to somatotroph adenoma cells to counterregulate the response to IL-1␤ on hormone secretion or cellular growth. C YTOKINES have been demonstrated to be critically involved in neuroendocrine-immune interactions (reviewed in Refs. 1 and 2). The anterior pituitary gland not only represents a target but also a site of origin of cytokines. Among other cytokines, production of the inflammatory cy-tokine interleukin-1 (IL-1) was demonstrated in rat and mouse pituitary, increasing after treatment with bacterial lipopolysaccharide of the animals (3, 4). Furthermore, IL-1 receptors and messenger RNA (mRNA) were characterized in mouse and rat anterior pituitary cells as well as mouse AtT-20 corticotrophs (57). Because the predominant sub-population of mouse anterior pituitary cells that express types I and II IL-1 receptors corresponds to GH-synthesizing cells (7), somatotrophs may be a preferential target for IL-1 actions within the pituitary. As for the human anterior pituitary , IL-1␤ expression was detected in pituitary adenomas (8) by RT-PCR of RNA. IL-6 synthesis, secretion, and im-munoreactivity have been detected in human pituitary ad-enomas (9). Moreover, we have described IL-2 and IL-2 receptor expression by human corticotroph adenoma cells and murine AtT-20 corticotrophs (10) and also detected mRNA expression of the intracellular IL-1 receptor antagonist (IL-1ra) by RT-PCR in human pituitary adenomas as well as IL-1ra colocalized with ACTH and GH immunoreactivity …
Controlled hierarchical filtering: Model of neocortical sensory processing

A model of sensory information processing is presented. The model assumes that learning of internal (hidden) generative models, which can predict the future and evaluate the precision of that prediction, is of central importance for information extraction. Furthermore, the model makes a bridge to goal-oriented systems and builds upon the structural similarity between the architecture of a robust controller and that of the hippocampal entorhinal loop. This generative control architecture is mapped to the neocortex and to the hippocampal entorhinal loop. Implicit memory phenomena; priming and prototype learning are emerging features of the model. Mathematical theorems ensure stability and attractive learning properties of the architecture. Connections to reinforcement learning are also established: both the control network, and the network with a hidden model converge to (near) optimal policy under suitable conditions. Falsifying predictions, including the role of the feedback connections between neocortical areas are made.
Robust backstepping tracking controller for low speed PMSM positioning system: Design, analysis, and implementation

This article is concerned with the design and implementation of a robust position trajectory tracking controller for a permanent magnet synchronous motor (PMSM). The information on the angular position, provided by a classical resolver, is here complemented with an observer based phase lock loop (PLL) circuit which accurately renders the position and the angular velocity of the rotor. A Backstepping control law is designed from the input-output linearization of the PMSM model, written in d-q coordinates. This controller is adapted through a load torque and friction reduced order observer to ensure high closed loop performance of the motor. An input-state stability analysis of the entire system is also provided. Co-simulation via the MATLAB/Simulink-PSIM package, including realistic measurement disturbances, are used to investigate the stability and accuracy of the proposed control algorithm. The simulation results are examined and confirmed through laboratory experiments.
Mitochondrial Complex I Inhibitor Rotenone Induces Apoptosis through Enhancing Mitochondrial Reactive Oxygen Species Production*

Inhibition of mitochondrial respiratory chain complex I by rotenone had been found to induce cell death in a variety of cells. However, the mechanism is still elusive. Because reactive oxygen species (ROS) play an important role in apoptosis and inhibition of mitochondrial respiratory chain complex I by rotenone was thought to be able to elevate mitochondrial ROS production, we investigated the relationship between rotenone-induced apoptosis and mitochondrial reactive oxygen species. Rotenone was able to induce mitochondrial complex I substrate-supported mitochondrial ROS production both in isolated mitochondria from HL-60 cells as well as in cultured cells. Rotenone-induced apoptosis was confirmed by DNA fragmentation, cytochrome c release, and caspase 3 activity. A quantitative correlation between rotenone-induced apoptosis and rotenone-induced mitochondrial ROS production was identified. Rotenone-induced apoptosis was inhibited by treatment with antioxidants (glutathione, N-acetylcysteine, and vitamin C). The role of rotenone-induced mitochondrial ROS in apoptosis was also confirmed by the finding that HT1080 cells overexpressing magnesium superoxide dismutase were more resistant to rotenone-induced apoptosis than control cells. These results suggest that rotenone is able to induce apoptosis via enhancing the amount of mitochondrial reactive oxygen species production.
Percutaneous endoscopic gastrostomy: 30-day mortality trends and risk factors.

BACKGROUND AND AIMS 30-day Percutaneous endoscopic gastrostomy (PEG) mortality of 8% (1992). Recent concerns suggest that mortality may have increased, prompting a comparison of current practice with that reported earlier. MATERIALS AND METHODS Data regarding PEG insertion with relation to case mix, complications, 30-day mortality and associated risk factors, in 2002, in a British University Hospital was compared with that in 1992. Logistic regression analysis was used to determine factors independently predictive of 30-day mortality. RESULTS In 2002, 112 patients (70% males, mean age 67.5 years; 1992: 63.6 years) underwent PEG. The 30-day mortality increased significantly from 8% (1992) to 22% (2002), P= 0.03. During this time, PEG insertion rate increased ten-fold, however, procedure-related mortality decreased from 2% to nil. In terms of percentage, the indications for PEG in 1992 and 2002 respectively were: cerebrovascular disease (33/25), head and neck tumours (16/24), motor neuron disease (27/11, P= 0.01). The proportion of PEGs for non-evidence-based indications increased from 16% in 1992 to 31% in 2002, P= 0.048. The number of PEGs placed radiologically increased (0/17, P= 0.02). Radiological patients received less antibiotic prophylaxis (P< 0.001) and had more PEG site infections than standard placement, P= 0.04. Multivariate analysis identified nil by mouth > or = 7 days or 11.4 (CI 3.2-41.7), albumin< or = 30 g/L or 12 (2.2-66.7) and > 1 cardiac factor or 5.1 (1.02-25.6) as independent predictors of 30-day mortality. CONCLUSIONS The ten-fold rise in the PEG insertion rate has been accompanied by a three-fold rise in 30-day mortality. This may reflect a lowered threshold of PEG insertion. The risk factors identified may help decision-making in cases where the risk-benefit relationship is not clear-cut.
ENDOSCOPIC INSERTION OF TYMPANOSTOMY TUBE IN CHILDREN Aso

This study is meant for determining the safety of endoscopy followed by grommet insertion into the middle ear. Traditionally, otoscopy, or the surgery using microscope has been the preferred method of Myringology. But given the limitations of using microscope, surgical interventions such as postauricular access have turned popular for treating the ailments of middle ear. A sum total of 178 cases of otitis media with effusion who had to undergo myringotomy along with or without tympanostomy tube insertion i.e. grommet were studied. The minimum age of the subject was 2.6 years while the maximum age was 44 years. The patients consisted of both male and female patients. 89 cases corresponded to that of right ear while another 89 cases were indications of left ear. The result derived from this study is clearly an indicative of the fact that the comparatively novice practice of endoscopy in grommet insertion is quite safe and also provides an edge in the live demonstrations and group teaching methods. However, the study also determines that although, this method is apparently safer and efficient, there is no proof of patients have any gains during post operative care and hearing efficiency when compared to other traditional methods.
On Solving Controlled Markov Set-Chains via Multi-Policy Improvement

We present formal methods of improving multiple policies for solving controlled Markov set-chains with infinite-horizon iscounted reward criteria. The multi-policy improvement methods follow the spirit of parallel rollout for solving Markov decision processes (MDPs). In particular, these methods are useful for on-line control of Markov set-chains and for approximately solving MDPs via state aggregation. We further discuss issues on designing a policy-iteration type algorithm based on our policy improvement methods.