Miracle-dz/UniFAR-FTUs huggingface dataset:
The appearance of T cells bearing self-reactive T cell receptor in the livers of mice injected with bacteria

We demonstrated in the present study that with bacterial stimulation, an increased number of alpha/beta T cells proliferated in the liver of mice and that even T cells bearing self-reactive T cell receptor (TCR) (or forbidden T cell clones), as estimated by anti-V beta monoclonal antibodies in conjunction with immunofluorescence tests, appeared in the liver and, to some extent, in the periphery. The majority (greater than 80%) of forbidden clones induced had double-negative CD4-8- phenotype. In a syngeneic mixed lymphocyte reaction, these T cells appear to be self-reactive. Such forbidden clones and normal T cells in the liver showed a two-peak pattern of TCR expression, which consisted of alpha/beta TCR dull and bright positive cells, as seen in the thymus. A systematic analysis of TCR staining patterns in the various organs was then carried out. T cells from not only the thymus but also the liver had the two-peak pattern of alpha/beta TCR, whereas all of the other peripheral lymphoid organs had a single-peak pattern of TCR. However, T cells in the liver were not comprised of double-positive CD4+8+ cells, which predominantly reside in the thymus. The present results therefore suggest that T cell proliferation in the liver might reflect a major extrathymic pathway for T cell differentiation and that this hepatic pathway has the ability to produce T cells bearing self- reactive TCR under bacterial stimulation, probably due to the lack of a double-positive stage for negative selection.
Healing of experimental aneurysms. II: Platelet extracts can increase the thickness of the neointima at the neck of treated aneurysms.

PURPOSE To assess the effect of platelet extracts (PE) on neointima formation following gelfoam packing of experimental porcine aneurysms. A strategy involving the local delivery of platelet growth factors may potentially improve long term results of endovascular treatment of aneurysms. METHODS Bilateral lateral wall common carotid aneurysms were constructed on 30 pigs. A collagen sponge containing a PE rich in growth factors was used to pack one aneurysm with the controlateral lesion being embolized with a sponge containing NaCl 0.9% (22 animals). In 8 animals, a control sponge was used on both sides. Animals were sacrificed at 1, 2, 3, 4 and 9 weeks and the thickness of the neointima covering the neck of PE-treated aneurysms was measured in 5 locations for each lesion at 2 and 3 weeks and compared with the control aneurysm of the same animal. Morphometric data was analysed using the paired Student's t-test. RESULTS The thickness of the neointima was significantly increased in lesions treated with PE as compared to control lesions at 2 weeks (p = 0.008, n = 9). There was no significant difference at 3 weeks (p = 0.99, n = 9). There was no significant difference between lesions of control animals (p = 0.95, n = 8). CONCLUSION PE rich in growth factors can increase the thickness of the neointima at the neck of treated experimental porcine aneurysms at 2 weeks, but had no effect at 3 weeks. This accelerated neointimal formation may have some value in improving healing following endovascular treatment. This hypothesis could not be supported with this experimental model which has a spontaneous tendency to heal. Further studies using an animal model which reproduces the clinical problem of recurrences may help to define the role of the local delivery of growth factors in combination with coils in a strategy designed to improve results of endovascular treatment.
Phase Response Curves of a Molecular Model Oscillator: Implications for Mutual Coupling of Paired Oscillators

Increasing evidence indicates that the accessory medulla is the circadian pacemaker controlling locomotor activity rhythms in insects. A prominent group of neurons of this neuropil shows immunoreactivity to the peptide pigment-dispersing hormone (PDH). In Drosophila melanogaster, the PDH immunoreactive (PDH-ir) lateral neurons, which also express the clock genes period and timeless, are assumed to be circadian pacemaker cells themselves. In other insects, such as Leucophaea maderae, a subset of apparently homologue PDH-ir cells is a candidate for the circadian coupling pathway of the bilaterally symmetric clocks. Although knowledge about molecular mechanisms of the circadian clockwork is increasing rapidly, very little is known about mechanisms of circadian coupling. The authors 4used a computer model, based on the molecular feedback loop of the clock genes in D. melanogaster, to test the hypothesis that release of pigment-dispersing hormone is involved in the coupling between bilaterally paired oscillators. They can show that a combination of all-delay- and all-advance-type interactions between two model oscillators matches best the experimental findings on mutual pacemaker coupling in L. maderae. The model predicts that PDH affects the phosphorylation rate of clock genes and that in addition to PDH, another neuroactive substance is involved in the coupling pathway, via an all-advance type of interaction. The model suggests that PDH and light pulses, represented by two distinct classes of phase response curves, have different targets in the oscillatory feedback loop and are, therefore, likely to act in separate input pathways to the clock.
The Protein Expression Level of a Heterogeneous Gene Inserted in LIPI-1 of the Listeria ivanovii Genome Relies on Its Insertion Orientation

Due to its capability to multiply in either phagocytic or nonphagocytic cells, and to subsequently elicit a robust cellular immune response, Listeria ivanovii (LI) is thought to be feasible for developing bacteria-based live attenuated vaccines. We previously generated several recombinant LI strains expressing Mycobacterium tuberculosis antigens. Since the expression level of heterogeneous protein was sometimes very low, we attempted to elucidate the principle of heterogeneous protein expression in such recombinant LI strains. In this study, we inserted the M. tuberculosis antigen gene Rv0129c into LI strains at the same site as the genome but with a different insertion orientation. RT-qPCR and Western blot showed that when the insertion orientation of the heterogeneous gene was opposite to the LIorfXYZ gene in the Listeria pathogenicity island 1 in the bacterial genome, the heterogeneous gene could be transcribed well but the protein expression level seemed limited, both in vitro and in vivo. When inserted at an orientation consistent with LIorfXYZ at the same site in the genome, the expected 43-kD protein was observed in vitro as well as in a mouse model. Bacterial virulence was found to have decreased after recombination. This work confirms that the protein expression level of the heterogenous gene in such genome-recombinant LI-based vaccines is related to its inserted orientation in the bacterial genome, and a foreign gene inserted at this position of LIPI-1 will abolish Listeria virulence without affecting its growth.
MSV-Driven Floorplanning

Power consumption has become a crucial problem in modern circuit design. Multiple supply voltage (MSV) design is introduced to provide higher flexibility in controlling the power and performance tradeoff. One important requirement of MSV design is that timing constraints of the circuit must be satisfied after voltage assignment of the cells. In this article, we develop two algorithms to solve the voltage assignment problem under timing constraints, namely, min-cost flow (MCF) and value-oriented branch-and-bound (VOBB). In the MCF algorithm, the voltage assignment problem is formulated as a convex cost dual network flow problem, and can be solved optimally in polynomial time under certain conditions by calling a MCF solver. The VOBB algorithm, which is a VOBB-based searching method, solves the voltage assignment problem optimally in general cases by employing the MCF algorithm and a linear programming solver as subroutines. At last, we propose a MSV-driven floorplanning framework that optimizes power consumption and physical layout of a circuit simultaneously during the floorplanning stage, by embedding the MCF algorithm into a simulated annealing-based floorplanner and applying the VOBB algorithm as a postprocessing step. We compared our approach with the latest works on this problem, and the experimental results show that, using our approach, significant improvement on power saving can be achieved in much less running time, which confirms the effectiveness and efficiency of our method.
Prevalence of osteoporosis in Iran: A meta-analysis

Background: Several studies have investigated the prevalence of osteoporosis among general population in several parts of Iran. However, the results have been inconsistent. This meta-analysis was conducted to estimate the overall prevalence of osteoporosis. Materials and Methods: International and national electronic databases were searched until April 2012, including Web of Knowledge, Medline, Scopus, Ovid, ScienceDirect, Science Information Database, IranMedex, MagIran, as well the relevant conference databases. The reference lists of included studies were screened as well. The cross-sectional studies addressing the prevalence of osteoporosis among Iranian general population were retrieved irrespective of age and sex. Bone mineral density (BMD) based on T-score was classified as follows: (a) normal (T-score ≥−1); (b) osteopenia (–2.5SD < T-score <−1SD); (c) osteoporosis (T-score ≤–2.5). Study quality was assessed using the recommended checklist of STROBE. Results: Of 2598 retrieved studies, 31 studies comprising 34,814 people was used for meta-analysis. The overall prevalence of osteoporosis in lumbar spine was 0.17 (95% CI: 0.13, 0.20) and that of osteopenia was 0.35 (95% CI: 0.30, 0.39). The prevalence was higher in older age groups, in women, and in the northern regions of the country, with an increasing trend in recent years. Conclusion: This meta-analysis indicated that osteoporosis and osteopenia are common problems among Iranian population older than 30 years. Furthermore, increasing trend of the diseases in recent years is promising a critical public health problem in Iran in the near future. However, due to the heterogeneity between the studies’ results, further evidence based on a national survey is needed to estimate the exact prevalence of the diseases in the country.
Microsomal Prostaglandin Synthase-1–Derived Prostaglandin E2 Protects Against Angiotensin II–Induced Hypertension via Inhibition of Oxidative Stress

Prostaglandin (PG) E2 has an established role in the regulation of vascular tone and reactivity. The present study examined the role and mechanism of microsomal PG synthase-1 (mPGES-1) in vascular response to angiotensin II (Ang II) infusion. A 7-day Ang II infusion at 0.35 mg/kg per day via osmotic minipump had no obvious effect on mean arterial blood pressure in mPGES-1+/+ mice but induced a marked hypertensive response in mPGES-1−/− mice, associated with a parallel increase in urinary 8-isoprostane excretion and aortic NADPH oxidase activity and mRNA expression of p47phox, gp91phox, and Nox1. The hypertension in mPGES-1−/− mice was completely prevented by Tempol treatment and was fully restored on termination of the antioxidant. Apocynin induced a similar blood pressure–lowering effect as Tempol. The Ang II infusion induced mRNA expression of mPGES-1, as well as mPGES-2 and cytosolic PGE synthase in the aortas as assessed by real-time RT-PCR. Immunohistochemistry revealed remarkably enhanced immunoreactivity of mPGES-1 mostly in vascular smooth muscle cells. In cultured vascular smooth muscle cells, Ang II exerted a direct stimulatory effect on reactive oxygen species production, NADPH oxidase activity, and expression of p47phox, gp91phox, and Nox1 that were all inhibited by PGE2. The −/− mice also exhibited enhanced renal hemodynamic response to acute Ang II infusion at 150 nmol/kg per minute via a jugular vein over a period of 40 minutes. These results suggest that mPGES-1–derived PGE2 buffers Ang II–induced vasoconstriction via inhibition of NADPH oxidase–dependent reactive oxygen species production.
Nanomechanics of silk: the fundamentals of a strong, tough and versatile material

Spider silk is a remarkable material that provides a template for upscaling molecular properties to the macroscale. In this article we review fundamental aspects of the mechanisms behind these behaviors, discuss the molecular makeup, chemical designs, and how these integrate in a complex arrangement to form webs, cocoons and other material architectures. Moreover, this review paper explores the unique ability of silk to tolerate various kinds of defects, in a way enabling this material platform to serve as one of the most resilient materials in nature. We conclude the discussion with a summary of key scaling laws, an attempt model and define hierarchical length-scales, and the translation to synthetic materials.
Divide and conquer skeleton on GPU

Parallelism is a suitable approach for speeding up the massive computations of applications, but parallel programming is difficult yet. Algorithmic skeleton is a parallel programming model that provides a high level of abstraction for programmers. This approach uses the pre-defined components to facilitate easier parallel programming. Divide and conquer (DC) is an appropriate parallel pattern for implementation as a skeleton. The solution of the original problem is obtained by dividing it into smaller sub-problems and solving them in parallel. Today, graphics processor unit (GPU) is an attractive computational processor for doing tasks in parallel, because it has a large number of process units. In this paper, divide and conquer skeleton on GPU has been proposed and named OC_GFV. DC_GPU is a divide and conquer skeleton that is implemented on GPU that using a consistent programming interface in C++ for easier parallel programming. Performance of this skeleton has been evaluated by mergesort and sobeledge detection. The results show that obtained speedup at this skeleton is more than 2 on GPU.
ADAPTIVE KERNEL ALGORITHMS FOR TIME SERIES PREDICTION Summary

The article describes two kernel algorithms of the regression function estimation, that are used for the time series prediction. First of them (HASKE) has its own heuristic of the h parameter evaluation. The second (HKSVR) connects SVM and the HASKE in such way that it is based on the HASKE heuristic of local neighborhood evaluation.
Full TCP/IP in 8 Bits

We describe two small and portable TCP/IP implementations fulfilling the subset of RFC1122 requirements needed for full host-to-host interoperability. Our TCP/IP implementations do not sacrifice any of TCP’s mechanisms such as urgent data or congestion control. They support IP fragment reassembly and the number of multiple simultaneous connections is limited only by the avaliable RAM. Despite being small and simple, our implementations do not require their peers to have complex, full-size stacks, but can communicate with peers running a similarly light-weight stack. The code size is on the order of 10 kilobytes and RAM usage can be configured to be as low as a few hundred bytes.
Evidencing the Role of Erythrocytic Apoptosis in Malarial Anemia

In the last decade it has become clear that, similarly to nucleated cells, enucleated red blood cells (RBCs) are susceptible to programmed apoptotic cell death. Erythrocytic apoptosis seems to play a role in physiological clearance of aged RBCs, but it may also be implicated in anemia of different etiological sources including drug therapy and infectious diseases. In malaria, severe anemia is a common complication leading to death of children and pregnant women living in malaria-endemic regions of Africa. The pathogenesis of malarial anemia is multifactorial and involves both ineffective production of RBCs by the bone marrow and premature elimination of non-parasitized RBCs, phenomena potentially associated with apoptosis. In the present overview, we discuss evidences associating erythrocytic apoptosis with the pathogenesis of severe malarial anemia, as well as with regulation of parasite clearance in malaria. Efforts to understand the role of erythrocytic apoptosis in malarial anemia can help to identify potential targets for therapeutic intervention based on apoptotic pathways and consequently, mitigate the harmful impact of malaria in global public health.
Analysis of Improved Cyclostationary Spectrum Sensing with SLC Diversity over Composite Multipath Fading-Lognormal Shadowing Channels

Spectrum sensing is a key technical challenge for cognitive radio (CR). It is well known that multi-cycle cyclostationarity (MC) detector is a powerful method for spectrum sensing. However, conventional MC detector is difficult to implement due to its high computational complexity. This paper pays attention to the fact that the computation complexity can be reduced by simplifying the test statistic of conventional MC detector. Based on this simplification process, an improved MC detector is proposed. Compared with the conventional one, the proposed detector has the low-computational complexity and sufficient-accuracy on sensing performance. Subsequently, the sensing performances are further investigated for the cases of Rayleigh, Nakagami-m, Rician, composite Rayleigh fading-lognormal shadowing and composite Nakagami fading-lognormal shadowing channels, respectively. Furthermore, the square-law combining (SLC) is introduced to improve the detection capability over fading-shadowing channels. The corresponding closed-form expressions of average detection probability are derived for each case by the moment generation function (MGF) approach. Finally, illustrative and analytical results show that the efficiency and reliability of proposed detector and the improvement on sensing performance by SLC over composite fading-shadowing channels.
Effect of Gaussian Channel Estimation Error on IBI Cancellation and Circular Property Loss Restoration for Broadband DS-CDMA Combining FDE Without CP Insertion (無線通信システム)

In broadband DS-CDMA uplink transmission using frequency-domain equalization (FDE) without cyclic prefix (CP) insertion, the transmission performance degrades due to inter block interference (IBI) and circular property loss. The schemes were proposed to solve the problems of IBI and circular property loss in our previous study with the assumption of perfect channel estimation. In this paper, the Gaussian error channel model is used and the effect of estimating accuracy on the bit error rate (BER) is discussed. The requirement for practical channel estimation is also given based on the result. KeywordsDS-CDMA, MMSE-FDE, IBI cancellation, Circular property loss restoration, Gaussian error
Health and Quality of Life Outcomes

Objective: QoL data were routinely collected in a randomised controlled trial (RCT), which employed a reminder system, retrieving about 50% of data originally missing. The objective was to use this unique feature to evaluate possible missingness mechanisms and to assess the accuracy of simple imputation methods. Methods: Those patients responding after reminder were regarded as providing missing responses. A hypothesis test and a logistic regression approach were used to evaluate the missingness mechanism. Simple imputation procedures were carried out on these missing scores and the results compared to the actual observed scores. Results: The hypothesis test and logistic regression approaches suggested the reminder data were missing not at random (MNAR). Reminder-response data showed that simple imputation procedures utilising information collected close to the point of imputation (last value carried forward, next value carried backward and last-and-next), were the best methods in this setting. However, although these methods were the best of the simple imputation procedures considered, they were not sufficiently accurate to be confident of obtaining unbiased results under imputation. Conclusion: The use of the reminder data enabled the conclusion of possible MNAR data. Evaluating this mechanism was important in determining if imputation was useful. Simple imputation was shown to be inadequate if MNAR are likely and alternative strategies should be considered. Background Missing data are a common occurrence in any area of research, and are especially problematic in quality of life (QoL) studies. Data may be missing for a variety of reasons. If these reasons relate to the QoL of the patient, the missingness is informative. Simply excluding those with missing data from the analysis ("complete case analysis"), will bias the results if those who did not respond had significantly lower (or higher) QoL scores than those who did respond. Rubin [1] defines three main mechanisms of missing data: missing completely at random (MCAR), missing at random (MAR) and missing not at random (MNAR). MCAR Published: 4 August 2008 Health and Quality of Life Outcomes 2008, 6:57 doi:10.1186/1477-7525-6-57 Received: 11 February 2008 Accepted: 4 August 2008 This article is available from: http://www.hqlo. com/content/6/1/57 © 2008 Fielding et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Validation of MODIS MCD45A1 product to identify burned areas in Acre State - Amazon forest

Burned areas map is essential in many applications and the orbital sensors have been used to monitor fires for many years, providing a better understanding of processes at different scales and being the only practical technique to estimate fires in large areas. However, remote sensing methods have limitations that could cause errors in the final products. Therefore, the objective of this work is to evaluate the MCD45A1 burned area product derived from MODIS sensor in Amazon tropical forest by comparing this dataset with the reference data derived from the mapping of burned areas in Acre State/Brazil acquired by TM sensor aboard of Landsat 5 and with a fieldwork that took place in November 2011. The results showed that de MCD45A1 product presented 93% of omission errors in 2010 and 96% in 2011 year in relation to reference data, presenting a low confidence in identifying the burned areas in Amazon region.
Backstepping control for an induction motor with an adaptive Backstepping rotor flux observer

This paper deals with the synthesis of a stabilizing Backstepping nonlinear control provided with an adaptive Backstepping observer to estimate the rotor flux of an Induction Machine (IM). This approach is based on the vector control strategy by replacing the existing conventional controller with a Backstepping control in order to more quickly bring back the q-axis flux towards zero and to reduce the effect of the motor parameters variations. To observe the rotor flux, we have introduced an observer based on the Backstepping theory provided with an adaptive mechanism of rotor resistance. The design principle of the controlled system is established using the Lyapunov stability theory.