Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal and spatial dynamics of cerebral immune cell accumulation in stroke.

BACKGROUND AND PURPOSE Ischemic stroke leads to significant morbidity and mortality in the Western world. Early reperfusion strategies remain the treatment of choice but can initiate and augment an inflammatory response causing secondary brain damage. The understanding of postischemic inflammation is very limited. The objectives of this study were to define the temporal and spatial infiltration of immune cell populations and their activation patterns in a murine cerebral ischemia-reperfusion injury model. METHODS Transient middle cerebral artery occlusion was induced for 1 hour followed by 12-hour to 7-day reperfusion in C57/BL6 mice. Immunohistochemistry and flow cytometry were used to quantify the infiltrating immune cell subsets. RESULTS Accumulation of microglia and infiltration of the ischemic hemisphere by macrophages, lymphocytes, and dendritic cells (DCs) preceded the neutrophilic influx. DCs were found to increase 20-fold and constituted a substantial proportion of infiltrating cells. DCs exhibited a significant upregulation of major histocompatibility complex II and major histocompatibility complex II high-expressing DCs were found 100 times more abundant than in sham conditions. Upregulation of the costimulatory molecule CD80 was observed in DCs and microglial cells but did not further increase in major histocompatibility complex II high-expressing DCs. No lymphocyte activation was observed. Additionally, regulatory immune cells (natural killer T-cells, CD4(-)/CD8(-)T lymphocytes) cumulated in the ischemic hemisphere. CONCLUSIONS This study provides a detailed analysis of the temporal dynamics of immune cell accumulation in a rodent stroke model. The peculiar activation pattern and massive increase of antigen-presenting cells in temporal conjunction with regulatory cells might provide additional insight into poststroke immune regulation.
Properties of dust in the high-latitude translucent cloud L1780 - I. Spatially distinct dust populations and increased dust emissivity from ISO observations*

We have analyzed the properties of dust in the high galactic latitude translucent cloud Lynds 1780 using ISOPHOT maps at 100 μ m and 200 μ m and raster scans at 60 μ m, 80 μ m, 100 μ m, 120 μ m, 150 μ m and 200 μ m. In far-infrared (FIR) emission, the cloud has a single core that coincides with the maxima of visual extinction and 200 μ m optical depth. At the resolution of 3.0′, the maximum visual extinction is 4.0 mag. At the cloud core, the minimum temperature and the maximum 200 μ m optical depth are 14.9 ± 0.4 K and 2.0 ± 0.2 $\times$ 10 -3 , respectively, at the resolution of 1.5′. The cloud mass is estimated to be 18 $M_{\odot}$. The FIR observations, combined with IRAS observations, suggest the presence of different, spatially distinct dust grain populations in the cloud: the FIR core region is the realm of the “classical” large grains, whereas the very small grains and the PAHs have separate maxima on the Eastern side of the cold core, towards the “tail” of this cometary-shaped cloud. The color ratios indicate an overabundance of PAHs and VSGs in L1780. Our FIR observations combined with the optical extinction data indicate an increase of the emissivity of the big grain dust component in the cold core, suggesting grain coagulation or some other change in the properties of the large grains. Based on our observations, we also address the question, to what extent the 80 μ m emission and even the 100 μ m and the 120 μ m emission contain a contribution from the small-grain component.
Postweaning Multisystemic Wasting Syndrome (PMWS) in pigs with particular emphasis on the causative agent, the mode of transmission, the diagnostic tools and the control measures. A review

Summary Postweaning multisystemic wasting syndrome (PMWS) is a worldwide emerging disease of weaned piglets. The objective of this review is to summarize the current knowledge regarding PMWS, its causative agent, mode of transmission, diagnostic techniques to detect PCV‐2, the possible control measures, and the association of PMWS and PCV‐2 with porcine dermatitis and nephropathy syndrome (PDNS). The causative agent of PMWS is porcine circovirus type 2 (PCV‐2), however, not all pigs infected with PCV‐2 develop the syndrome. PCV‐2 is consistently associated with PMWS and PMWS is considered not to occur without it. Both the syndrome and the virus are not regarded as new. Co‐factors that could activate PCV‐2 to cause PMWS are considered. This enigmatic nature of both the syndrome and the virus is triggering a concern towards uncertainties of the viral transmission, its introduction in to the herd, effective tools of diagnosis, and control strategies.
Diversification of Rice Yellow Mottle Virus and Related Viruses Spans the History of Agriculture from the Neolithic to the Present

The mechanisms of evolution of plant viruses are being unraveled, yet the timescale of their evolution remains an enigma. To address this critical issue, the divergence time of plant viruses at the intra- and inter-specific levels was assessed. The time of the most recent common ancestor (TMRCA) of Rice yellow mottle virus (RYMV; genus Sobemovirus) was calculated by a Bayesian coalescent analysis of the coat protein sequences of 253 isolates collected between 1966 and 2006 from all over Africa. It is inferred that RYMV diversified approximately 200 years ago in Africa, i.e., centuries after rice was domesticated or introduced, and decades before epidemics were reported. The divergence time of sobemoviruses and viruses of related genera was subsequently assessed using the age of RYMV under a relaxed molecular clock for calibration. The divergence time between sobemoviruses and related viruses was estimated to be approximately 9,000 years, that between sobemoviruses and poleroviruses approximately 5,000 years, and that among sobemoviruses approximately 3,000 years. The TMRCA of closely related pairs of sobemoviruses, poleroviruses, and luteoviruses was approximately 500 years, which is a measure of the time associated with plant virus speciation. It is concluded that the diversification of RYMV and related viruses has spanned the history of agriculture, from the Neolithic age to the present.
Vector approximation based indexing for non-uniform high dimensional data sets

With the proliferation of multimedia data, there is increasing need to support the indexing and searching of high dimensional data. Recently, a vector approximation based technique called VAle has been proposed for indexing high dimensional data. It has been shown that the VAle is an e ective technique compared to the current approaches based on space and data partitioning. The VAle gives good performance especially when the data set is uniformly distributed. Real data sets are not uniformly distributed, are often clustered, and the dimensions of the feature vectors in real data sets are usually correlated. More careful analysis for nonuniform or correlated data is needed for e ectively indexing high dimensional data. We propose a solution to these problems and propose the VAle, a new technique for indexing high dimensional data sets based on vector approximations. We conclude with an evaluation of nearest neighbor queries and show that the VAle technique results in signi cant improvements over the current VAle approach for several real data sets.
Contrast and stability of the axon diameter index from microstructure imaging with diffusion MRI

The ActiveAx technique fits the minimal model of white matter diffusion to diffusion MRI data acquired using optimized protocols that provide orientationally invariant indices of axon diameter and density. We investigated how limitations of the available maximal gradient strength (Gmax) on a scanner influence the sensitivity to a range of axon diameters. Multishell high‐angular‐diffusion‐imaging (HARDI) protocols for Gmax of 60, 140, 200, and 300 mT/m were optimized for the pulsed‐gradient‐spin‐echo (PGSE) sequence. Data were acquired on a fixed monkey brain and Monte‐Carlo simulations supported the results. Increasing Gmax reduces within‐voxel variation of the axon diameter index and improves contrast beyond what is achievable with higher signal‐to‐noise ratio. Simulations reveal an upper bound on the axon diameter (∼10 μm) that pulsed‐gradient‐spin‐echo measurements are sensitive to, due to a trade‐off between short T2 and the long diffusion time needed to probe larger axon diameters. A lower bound (∼2.5 μm) slightly dependent on Gmax was evident, below which axon diameters are identifiable as small, but impossible to differentiate. These results emphasize the key‐role of Gmax for enhancing contrast between axon diameter distributions and are, therefore, relevant in general for microstructure imaging methods and highlight the need for increased Gmax on future commercial systems. Magn Reson Med 70:711–721, 2013. © 2012 Copenhagen University Hospital Hvidovre. Magnetic Resonance in Medicine Published by Wiley Periodicals, Inc. on behalf of International Society of Medicine in Resonance. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution, and reproduction in any medium, provided the original work is properly cited.
m-Berezin transform and compact operators

m-Berezin transforms are introduced for bounded operators on the Bergman space of the unit ball. The norm of the m-Berezin transform as a linear operator from the space of bounded operators to L8 is found. We show that the m-Berezin transforms are commuting with each other and Lipschitz with respect to the pseudo-hyperbolic distance on the unit ball. Using the m-Berezin transforms we show that a radial operator in the Toeplitz algebra is compact iff its Berezin transform vanishes on the boundary of the unit ball
Vertical Protocol Composition

The security of key exchange and secure channel protocols, such as TLS, has been studied intensively. However, only few works have considered what happens when the established keys are actuallyused -- to run some protocol securely over the established "channel". We call this a vertical protocol composition, and it is truly commonplace in today's communication with the diversity of VPNs and secure browser sessions. In fact, it is normal that we have several layers of secure channels: For instance, on top of a VPN-connection, a browser may establish another secure channel (possibly with a different end point). Even using the same protocol several times in such a stack of channels is not unusual: An application may very well establish another TLS channel over an established one. We call this self-composition. In fact, there is nothing that tells us that all these compositions are sound, i.e., that the combination cannot introduce attacks that the individual protocols in isolation do not have. In this work, we prove a composability result in the symbolic model that allows for arbitrary vertical composition (including self-composition). It holds for protocols from any suite of channel and application protocols that fulfills a number of sufficient preconditions. These preconditions are satisfied for many practically relevant protocols such as TLS.
On the mitigation of SET broadening effects in integrated circuits

Nowadays, the integrated circuits design and manufacturing process are decreasing the minimum transistor size and this advancement, accompanied by increasing operating frequencies and lower power supplies voltages, leads, on the one side, to the availability of fast and low power circuits with very small noise margins but, on the other side, makes integrated circuits more sensitive to Single Event Transient (SET) pulses that may be generated and propagated through the combinational logic, leading to misbehaviors. SETs are mainly generated by high-energy particles that strikes the circuit near a junction, resulting in a significant charge injection/depletion process, that may produce spurious pulses. These can propagate and change their shape traversing the combinational logic paths, sometimes being broadened and amplified sometimes being filtered. In this paper, we present a place and route algorithm for integrated circuit design, which is able to mitigate and filter the erroneous effects of SETs. The proposed solution has been experimentally evaluated by means of electrical pulse injection within logic resources of several benchmark Integrated Circuits (ICs) implemented in a Flash-based FPGA and by accurate timing analyses. Preliminary results confirm the mitigation of SET broadening effects by acting on physical place and route constraints. On the selected benchmark circuit the algorithm decreases the SET sensitiveness more than 70% with respect to not hardened circuits. Besides, the solution does not introduce any area overhead or delay penalties.
Genetic and Epigenetic Aspects of Polyploid Evolution in Plants

Polyploidy, the condition of possessing more than 2 complete chromosome sets in the same nucleus, is frequent in nature and has implications for a species' prospects for evolution. Newly formed polyploids, so-called neopolyploids, undergo a wide spectrum of genomic changes upon genome merger and duplication. Here, we review recent literature describing genomic and transcriptomic changes along the pathway from neoallopolyploid formation to the stabilization of species and diversification at the allopolyploid level. We begin by reviewing pathways of polyploid formation and discuss the effects of genome doubling and hybridization on chromosome pairing. We then review our knowledge of epigenetic changes in allopolyploids, followed by a consideration of the effects of these structural genomic and epigenetic changes on the transcriptional activity of genes in allopolyploids. We discuss the effects of changes in gene expression in polyploids with respect to current evolutionary theory. Finally, we draw attention to the general question of the relationships between genomic and transcriptomic alteration and incipient diversification among sibling polyploid lines and populations.
Whole blood viscosity issues VI: Association with blood salicylate level and gastrointestinal bleeding

Background: This series on whole blood viscosity issues has been trying to elucidate the sensitivity, specificity and usefulness of the laboratory parameter in clinical practice. The postulation has been that since antiplatelet is used in the management of stasis, of which blood viscosity is an index, the latter would be useful laboratory indication and/or contraindication. Aim: The aim of this study was to observe whether blood level of acetylsalicylic acid differs with the level of whole blood viscosity. Patients and Methods: Out of the ten years database, 538 cases that were concomitantly tested for haematocrit, total proteins and blood level of salicylate were selected for this study. A separate nine cases of positive faecal occult blood tests were audited for blood viscosity and reviewed. Results: A statistically significant difference is observed with lower blood viscosity being associated with higher salicylate level in comparison of the former between the highest vs. lowest quartiles (p < 0.002). This observation demonstrates the effect of aspirin in lowering blood stasis. Reviewing the positive faecal occult blood cases indicate that gastrointestinal bleeding is characterized by relative hypoviscosity and that hyperviscosity is not present during bleeding complications. Conclusion: The findings affirm that whole blood viscosity is a valid clinical laboratory parameter for evidence-based contraindication, indication and monitoring of antiplatelet medication. It calls for better appreciation and clinical utility of whole blood viscosity, which (in the absence of viscometer) can now be extrapolated from haematocrit and total proteins.
Study on Analysis of Peripheral Biomarkers for Alzheimer’s Disease Diagnosis

Many factors are involved in Alzheimer’s disease (AD) pathology including tau phosphorylation, amyloid β protein (Aβ) accumulation, lipid dysregulation, oxidative stress, and inflammation. The markers of these pathological processes in cerebral spinal fluid are used currently for AD diagnosis. However, peripheral biomarkers are the need of the hour for large population screening for AD. The main objective of the present study is to evaluate the peripheral levels of redox markers, lipid peroxidation (LPO) indicators, and pathological markers in AD patients. Blood was collected from AD patients (n = 45), controls (n = 45), and analyzed for pathological markers of AD including Aβ42 and tau, LPO, and redox indicators. Plasma Aβ42 was significantly (P < 0.001) elevated while total tau was decreased in AD compared to controls. Hydroxynonenal (HNE) and malondialdehyde (MDA) were higher (P < 0.001) in AD patients pointing the enhanced LPO in AD pathology. Receiver operating characteristic curve (ROC) analysis indicated that HNE is a better indicator of LPO compared to MDA. Plasma glutathione (GSH) level was significantly (P < 0.001) low while oxidized glutathione (GSSG) level was higher (P < 0.001) in AD patients with corresponding decrease in GSH/GSSG ratio (P < 0.001). ROC analysis indicated that GSH/GSSG ratio can be used as reliable indicator for redox imbalance in AD with a cutoff value of <8.73 (sensitivity 91.1%, specificity 97.8%). Correlation analysis revealed a positive correlation for both HNE and MDA with Aβ42 and a negative correlation with total tau. Negative correlation was observed between GSH/GSSG ratio and LPO markers. While oxidative stress has been implicated in pathology of various neurodegenerative disorders, the present study pinpoints the direct link between LPO and Aβ production in plasma of AD patients. Normally, at low amyloid concentration in body fluids, this peptide shown to function as a strong metal chelating antioxidant. However, when the Aβ production enhanced as in AD, through gain of functional transformation, Aβ evolves into prooxidant, thereby enhancing oxidative stress and LPO. Altered redox status with enhanced LPO observed in AD blood could contribute to the oxidation and S-glutathionylation proteins, which has to be addressed in future studies.
Serogroup-Specific Bacterial Engineered Glycoproteins as Novel Antigenic Targets for Diagnosis of Shiga Toxin-Producing-Escherichia coli-Associated Hemolytic-Uremic Syndrome

ABSTRACT Human infection with Shiga toxin-producing Escherichia coli (STEC) is a major cause of postdiarrheal hemolytic-uremic syndrome (HUS), a life-threatening condition characterized by hemolytic anemia, thrombocytopenia, and acute renal failure. E. coli O157:H7 is the dominant STEC serotype associated with HUS worldwide, although non-O157 STEC serogroups can cause a similar disease. The detection of anti-O157 E. coli lipopolysaccharide (LPS) antibodies in combination with stool culture and detection of free fecal Shiga toxin considerably improves the diagnosis of STEC infections. In the present study, we exploited a bacterial glycoengineering technology to develop recombinant glycoproteins consisting of the O157, O145, or O121 polysaccharide attached to a carrier protein as serogroup-specific antigens for the serological diagnosis of STEC-associated HUS. Our results demonstrate that using these antigens in indirect ELISAs (glyco-iELISAs), it is possible to clearly discriminate between STEC O157-, O145-, and O121-infected patients and healthy children, as well as to confirm the diagnosis in HUS patients for whom the classical diagnostic procedures failed. Interestingly, a specific IgM response was detected in almost all the analyzed samples, indicating that it is possible to detect the infection in the early stages of the disease. Additionally, in all the culture-positive HUS patients, the serotype identified by glyco-iELISAs was in accordance with the serotype of the isolated strain, indicating that these antigens are valuable not only for diagnosing HUS caused by the O157, O145, and O121 serogroups but also for serotyping and guiding the subsequent steps to confirm diagnosis.
Private decayed predicate sums on streams

In many monitoring applications, recent data is more important than distant data. How does this affect privacy of data analysis? We study a general class of data analyses --- predicate sums --- in this context. Formally, we study the problem of estimating predicate sums privately, for sliding windows and other decay models. While we require accuracy in analysis with respect to the decayed sums, we still want differential privacy for the entire past. This is challenging because window sums are not monotonic or even near-monotonic as the problems studied previously [DPNR10]. We present accurate ε-differentially private algorithms for decayed sums. For window and exponential decay sums, our algorithms are accurate up to additive 1/ε and polylog terms in the range of the computed function; for polynomial decay sums which are technically more challenging because partial solutions do not compose easily, our algorithms incur additional relative error. Our algorithm for polynomial decay sums generalizes to arbitrary decay sum functions. The algorithm crucially relies on our solution for the window sum problem as a subroutine. Further, we show lower bounds, tight within polylog factors and tight with respect to the dependence on the probability of error. Our results are obtained via a natural dyadic tree we maintain, but the crux is we treat the tree data structure in non-uniform manner. We also extend our study and consider the "dual" question of maintaining conventional running sums on the entire data thus far, but when privacy constraints expire with time. We define a new model of privacy with expiration and consider the problems of designing accurate running sum and linear map algorithms in this model. Now the goal is to design algorithms whose accuracy guarantees scale with the size of the privacy window. We reduce running sum with a privacy window W to window sum without privacy expiration, and characterize the accuracy of output perturbation for general linear maps with privacy window W.
A new five-parameter MOS transistor mismatch model

A new five-parameter MOS transistor mismatch model is introduced capable of predicting transistor mismatch with very high accuracy for ohmic and saturation regions, including short-channel transistors. The new model is based on splitting the contribution of the mobility degradation parameter mismatch /spl Delta//spl theta/ into two components, and modulating them as the transistor transitions from ohmic to saturation regions. The model is tested for a wide range of transistor sizes (30), and shows excellent precision, never reported before for such a wide range of transistor sizes, including short-channel transistors.
Cyclin D1 as a Target for the Proliferative Effects of PTH and PTHrP in Early Osteoblastic Cells

PTHrP induced a proliferative cyclin D1 activation in low‐density osteoblastic cells. The process was PKA and MAPK dependent and involved both AP‐1 and CRE sites. In ectopic ossicles generated from implanted bone marrow stromal cells, PTH upregulated cyclin D1 after acute or intermittent anabolic treatment. These data suggest a positive role of PTH and PTHrP in the cell cycle of early osteoblasts.