Miracle-dz/UniFAR-FTUs huggingface dataset:
Applications of arterial spin labeled MRI in the brain

Perfusion provides oxygen and nutrients to tissues and is closely tied to tissue function while disorders of perfusion are major sources of medical morbidity and mortality. It has been almost two decades since the use of arterial spin labeling (ASL) for noninvasive perfusion imaging was first reported. While initial ASL magnetic resonance imaging (MRI) studies focused primarily on technological development and validation, a number of robust ASL implementations have emerged, and ASL MRI is now also available commercially on several platforms. As a result, basic science and clinical applications of ASL MRI have begun to proliferate. Although ASL MRI can be carried out in any organ, most studies to date have focused on the brain. This review covers selected research and clinical applications of ASL MRI in the brain to illustrate its potential in both neuroscience research and clinical care. J. Magn. Reson. Imaging 2012;35:1026‐1037. © 2012 Wiley Periodicals, Inc.
Parallel sorting by over partitioning

A new approach to parallel sorting called Parallel Sorting by OverPartitioning (PSOP) is presented. The approach limits the communication cost by moving each element between processors at most once, and leads to good load balancing with high probability y. The PSOP framework can be applied to both comparison and non-comparison sorts. Implementations on the KSR1 and Hector shared memory multiprocessors show that PSOP achieves nearly linear speedup and outperforms alternative approaches. An analytical model for PSOP has been developed that predicts the performance within 10% accuracy.
Structural and Functional Characterization of Recombinant Interleukin-10 from Indian Major Carp Labeo rohita

Interleukin-10, an important regulator of both the innate and adaptive immune systems, is a multifunctional major cytokine. Though it is one of the major cytokines, IL-10 from the Indian major carp, Labeo rohita, has not yet been characterized. In the present study, we report large scale production and purification of biologically active recombinant IL-10 of L. rohita (rLrIL-10) using a heterologous expression system and its biophysical and functional characterization. High yield (~70 mg/L) of soluble rLrIL-10 was obtained at shake flask level. The rLrIL-10 was found to exist as a dimer. Far-UV CD spectroscopy showed presence of predominantly alpha helices. The tertiary structure of the purified rLrIL-10 was verified by fluorescence spectroscopy. Two-dimensional gel analysis revealed the presence of six isoforms of the rLrIL-10. The rLrIL-10 was biologically active and its administration significantly reduced serum proinflammatory cytokines, namely, interleukin 1β, TNFα, and IL-8, and augmented the NKEF transcript levels in spleen of L. rohita. Anti-inflammatory role of the rLrIL-10 was further established by inhibition of phagocytosis using NBT reduction assay in vitro. The data indicate that the dimeric alpha helical structure and function of IL-10 of L. rohita as a key regulator of anti-inflammatory response have remained conserved during evolution.
X-ray spectral variability in PG 1535+547: the changing look of a "soft X-ray weak" AGN

Context. PG 1535+547 is a bright Narrow Line Seyfert 1 galaxy, whose high-energy emission shows strong variability both in shape and flux. On the basis of ROSAT observations, it is classified as “soft X-ray weak quasi-stellar object (QSO)”, a class of objects whose X-ray-to-optical flux ratio is smaller than in typical QSOs. Their X-ray spectra are often characterized by highly-ionized, complex absorbers and/or reflection from the inner accretion disk, and the relative importance of the two is currently debated. Whatever the correct interpretation may be, the presence of such features implies that we are looking at matter located in the innermost regions of these AGN. Aims. We want to clarify the nature of the X-ray emission of PG 1535+547, and constrain the physical properties of its innermost regions, where this emission originates. Methods. We present new XMM-Newton observations of PG 1535+547 (90 ks exposure time, January 2006), from which we obtained two spectra European Photon Imaging Camera (EPIC) separated by about one week. We compare these spectra with those from a previous (November 2002) XMM-Newton observation. Results. These latest observations support the complex and variable nature of the X-ray emission of PG 1535+547. The broadband observed flux increases by a factor ∼2.3 in three years, and then decreases by a factor ∼1.3 in about one week. In the new spectra, strong absorption features at E < 3 keV and a complex spectral shape in the iron-line energy range are evident, coupled with a drop in the emission at higher energies. We describe all the different states in a consistent way, assuming either a warm absorber plus a relativistically-blurred ionized reflection, or a two-phase warm absorber partially covering the source with the addition of a scattered component. Conclusions. The observed variability can be ascribed mostly to warm absorbing gas in the innermost regions of PG 1535+547, which appears to vary in its physical properties on timescales of both years and days. In the blurred reflection scenario, all the analyzed states require a high fraction of reflection from the disk, calling for some mechanisms able to increase the reflection component with respect to the intrinsic continuum. Finally, the strong variability observed in the X-ray band opposed to a more constant emission at optical frequencies, changes the value of the X-ray-to-optical spectral index, implying that PG 1535+547 can not actually be classified as a soft X-ray weak active galactic nucleus (AGN).
Immune Modulation by Different Types of β2→1-Fructans Is Toll-Like Receptor Dependent

Introduction β2→1-fructans are dietary fibers. Main objectives of this study were 1) to demonstrate direct signalling of β2→1-fructans on immune cells, 2) to study whether this is mediated by the pattern recognition receptors Toll-like receptors (TLRs) and nucleotide-binding oligomerisation domain-containing proteins (NODs), and 3) to relate the observed effects to the chain length differences in β2→1-fructans. Methods Four different β2→1-fructan formulations were characterised for their chain length profile. Human peripheral blood mononuclear cells (PBMCs) were stimulated in vitro with β2→1-fructans, and production of IL-1Ra, IL-1β, IL-6, IL-10, IL-12p70, and TNF-α was analysed. Reporter cells for TLRs and NODs were incubated with β2→1-fructans and analysed for NF-κB/AP-1 activation. Results Cytokine production in human PBMCs was dose- and chain length-dependent. Strikingly, short chain enriched β2→1-fructans induced a regulatory cytokine balance compared to long chain enriched β2→1-fructans as measured by IL-10/IL-12 ratios. Activation of reporter cells showed that signalling was highly dependent on TLRs and their adapter, myeloid differentiation primary response protein 88 (MyD88). In human embryonic kidney reporter cells, TLR2 was prominently activated, while TLR4, 5, 7, 8, and NOD2 were mildly activated. Conclusions β2→1-fructans possess direct signalling capacity on human immune cells. By activating primarily TLR2, and to a lesser extent TLR4, 5, 7, 8, and NOD2, β2→1-fructan stimulation results in NF-κB/AP-1 activation. Chain length of β2→1-fructans is important for the induced activation pattern and IL-10/IL-12 ratios.
Decline in capture rate of stoats at high mouse densities in New Zealand Nothofagus forests

We present two statistical models documenting variations in density indices of stoats and of mice in New Zealand southern beech (Nothofagus spp.) forests. They confirm previous, simpler correlations showing that the summer capture rate of stoats increases with spring mouse density index up to about 20-25 mouse captures per 100 trap-nights (C/100TN). However, at much higher mouse densities (60-80 C/100TN), observed in the Grebe and Borland Valleys in southern Fiordland in 1979/80 and again in 1999/2000, fewer stoats were caught than expected. These models quantify a serious decline in capture rate of stoats during periods of high mouse abundance over the range 25-80 C/100TN. At such times, management strategies aiming to protect threatened birds by intensive lethal trapping of stoats during the nesting seasons may be least effective just when they are most needed.
Replacement Strategies in Steady State Genetic Algorithms: Static Environments

This paper investigates the eﬀects of a number of replacement strategies for use in steady state genetic algorithms. Some of these (deleting the oldest, worst or random members, or deletion by “Kill Tournament”) are well known from the literature. The last, “conservative” replacement was developed for use in time-varying problems and combines a Replace–Oldest strategy with modiﬁed selection tournaments, where one candidate is always the oldest member of the population. A Markov chain analysis is provided to model the expected time for a single member of the optimal class to take over ﬁnite populations. For strategies which replace the oldest member, a linear approximation is developed for the probability that it belongs to the optimal class. It is shown that under certain conditions this approximation yields a transition matrix which is identical to a strategy of deletion by binary Kill Tournament. Predicted and simulation results conﬁrm that without enforced elitism Replace– Random and Replace–Oldest strategies cannot guarantee takeover, and for a ﬁxed parent selection method the speed of takeover is dramatically altered by the choice of replacement strategy.
Microtiming Patterns and Interactions with Musical Properties in Samba Music

Abstract In this study, we focus on the interaction between microtiming patterns and several musical properties: intensity, meter and spectral characteristics. The data-set of 106 musical audio excerpts is processed by means of an auditory model and then divided into several spectral regions and metric levels. The resulting segments are described in terms of their musical properties, over which patterns of peak positions and their intensities are sought. A clustering algorithm is used to systematize the process of pattern detection. The results confirm previously reported anticipations of the third and fourth semiquavers in a beat. We also argue that these patterns of microtiming deviations interact with different profiles of intensities that change according to the metrical structure and spectral characteristics. In particular, we suggest two new findings: (i) a small delay of microtiming positions at the lower end of the spectrum on the first semiquaver of each beat and (ii) systematic forms ofaccelerando and ritardando at a microtiming level covering two-beat and four-beat phrases. The results demonstrate the importance of multidimensional interactions with timing aspects of music. However, more research isneeded in order to find proper representations for rhythm and microtiming aspects in such contexts.
Transcriptome Analysis of Neisseria meningitidis during Infection

ABSTRACT Neisseria meningitidis is the cause of septicemia and meningococcal meningitis. During the course of infection, N. meningitidis encounters multiple environments within its host, which makes rapid adaptation to environmental changes a crucial factor for neisserial pathogenicity. Employing oligonucleotide-based DNA microarrays, we analyzed the transcriptome of N. meningitidis during two key steps of meningococcal infection, i.e., the interaction with epithelial cells (HeLa cells) and endothelial cells (human brain microvascular endothelial cells). Seventy-two genes were differentially regulated after contact with epithelial cells, and 48 genes were differentially regulated after contact with endothelial cells, including a considerable proportion of well-known virulence genes. While a considerable number of genes were in concordance between bacteria adherent to both cell types, we identified several open reading frames that were differentially regulated in only one system. The data obtained with this novel approach may provide insight into the pathogenicity mechanisms of N. meningitidis and could demonstrate the importance of gene regulation on the transcriptional level during different stages of meningococcal infection.
Angiogenesis Impairment in Diabetes: Role of Methylglyoxal-Induced Receptor for Advanced Glycation Endproducts, Autophagy and Vascular Endothelial Growth Factor Receptor 2

Diabetes impairs physiological angiogenesis by molecular mechanisms that are not fully understood. Methylglyoxal (MGO), a metabolite of glycolysis, is increased in patients with diabetes. This study defined the role of MGO in angiogenesis impairment and tested the mechanism in diabetic animals. Endothelial cells and mouse aortas were subjected to Western blot analysis of vascular endothelial growth factor receptor 2 (VEGFR2) protein levels and angiogenesis evaluation by endothelial cell tube formation/migration and aortic ring assays. Incubation with MGO reduced VEGFR2 protein, but not mRNA, levels in a time and dose dependent manner. Genetic knockdown of the receptor for advanced glycation endproducts (RAGE) attenuated the reduction of VEGFR2. Overexpression of Glyoxalase 1, the enzyme that detoxifies MGO, reduced the MGO-protein adducts and prevented VEGFR2 reduction. The VEGFR2 reduction was associated with impaired angiogenesis. Suppression of autophagy either by inhibitors or siRNA, but not of the proteasome and caspase, normalized both the VEGFR2 protein levels and angiogenesis. Conversely, induction of autophagy either by rapamycin or overexpression of LC3 and Beclin-1 reduced VEGFR2 and angiogenesis. MGO increased endothelial LC3B and Beclin-1, markers of autophagy, which were accompanied by an increase of both autophagic flux (LC3 punctae) and co-immunoprecipitation of VEGFR2 with LC3. Pharmacological or genetic suppression of peroxynitrite (ONOO−) generation not only blocked the autophagy but also reversed the reduction of VEGFR2 and angiogenesis. Like MGO-treated aortas from normglycemic C57BL/6J mice, aortas from diabetic db/db and Akita mice presented reductions of angiogenesis or VEGFR2. Administration of either autophagy inhibitor ex vivo or superoxide scavenger in vivo abolished the reductions. Taken together, MGO reduces endothelial angiogenesis through RAGE-mediated, ONOO–dependent and autophagy-induced VEGFR2 degradation, which may represent a new mechanism for diabetic angiogenesis impairment.
Apolipoprotein J expression in human ocular surface epithelium.

PURPOSE Apolipoprotein J (apoJ) expression has been detected in various mouse mucosal epithelial cells, as well as in the human ciliary body, retina, vitreous humor, and aqueous humor. The purpose of this study was to determine the expression and localization pattern of apoJ mRNA transcripts and protein in the human ocular surface epithelium. METHODS The expression of apoJ mRNA in corneal and conjunctival epithelial cells was investigated by reverse-transcriptase polymerase chain reaction (RT-PCR). mRNA localization in the corneal epithelium and protein localization in corneal and conjunctival epithelia were analyzed by in situ hybridization and immunohistochemistry, respectively. RESULTS The RT-PCR studies demonstrated the expression of apoJ mRNA transcripts in corneal and conjunctival epithelial cells. In situ hybridization analysis revealed that apoJ mRNA signals were detected in all layers of the corneal epithelium, most prominently in the basal cells. Immunohistochemical analysis revealed positive immunostaining for apoJ in the apical cell layers of corneal and conjunctival epithelia. CONCLUSIONS ApoJ is synthesized by and localized in the ocular surface epithelium. This suggests a role for this protein at the tear-ocular surface interface.
Wavelet Denoising of Infrared Spectra

The application of wavelet denoising to infrared spectra was investigated. Six different wavelet denoising methods (SURE, VISU, HYBRID, MINMAX, MAD and WAVELET PACKETS) were applied to pure infrared spectra with various added levels of homo- and heteroscedastic noise. The performances of the wavelet denoising methods were compared with the standard Fourier and moving mean filtering in terms of root mean square errors between the pure and denoised spectra and visual quality of the denoised spectrum. The use of predictive ability as a possible objective criterion for denoising performance was also investigated. The main conclusion is that for very low signal-to-noise ratios (S/N) the standard denoising methods (Fourier and moving mean) are comparable to the more sophisticated methods. At higher S/N levels the wavelet denoising methods, in particular the HYBRID and VISU methods, are better. Wavelet methods are also better in restoring the visual quality of the denoised infrared spectra.
The Impact of Trade Liberalization on Wage Inequality: Evidence from Argentina

Wage inequality in Argentina greatly increased during the nineties. During this period, a rapid and deep process of trade liberalization was implemented. In this paper we study whether trade liberalization played any role in shaping the Argentine wage structure during the nineties. Specifically, we test whether those sectors where import penetration deepened are also the sectors where, ceteris paribus, a higher increase in wage inequality is observed. Even though we find some evidence that supports this hypothesis, as has been found for some developed economies, trade deepening can only explain a relatively small proportion of the observed rise in wage inequality.
Pacific and Indian Ocean climate signals in a tree‐ring record of Java monsoon drought

Extreme climate conditions have dramatic socio‐economic impacts on human populations across the tropics. In Indonesia, severe drought and floods have been associated with El Niño‐Southern Oscillation (ENSO) events that originate in the tropical Indo‐Pacific region. Recently, an Indian Ocean dipole mode (IOD) in sea surface temperature (SST) has been proposed as another potential cause of drought and flood extremes in western Indonesia and elsewhere around the Indian Ocean rim. The nature of such variability and its degree of independence from the ENSO system are topics of recent debate, but understanding is hampered by the scarcity of long instrumental records for the tropics. Here, we describe a tree‐ring reconstruction of the Palmer Drought Severity Index (PDSI) for Java, Indonesia, that preserves a history of ENSO and IOD‐related extremes over the past 217 years. Extreme Javan droughts correspond well to known ENSO and IOD events in recent decades, and most extreme droughts before this recent period can be explained by known ENSO episodes. Coral proxies from regions near or within the two poles of the IOD show good agreement with Javan PDSI extremes over the past ∼150 years. The El Niño of 1877, in conjunction with a positive IOD, was one of the most intense and widespread episodes of the past two centuries, based on instrumental and proxy data from across the tropical Indo‐Pacific and Asian monsoon regions. Although Java droughts typically show the expected association with El Niño‐like conditions and failed Indian monsoons, others (mainly linked to positive IOD conditions) co‐occur with a strengthened Indian monsoon, suggesting linkages between the Indian monsoon, Indonesian drought and Indian Ocean climatic variability. The close associations between the Java PDSI, ENSO and Indian Ocean climate are consistent with the hypothesis that interannual ENSO to decadal ENSO‐like modes interact to generate dipole‐like Indian Ocean variability. Copyright © 2008 Royal Meteorological Society
An information reconciliation protocol for secret-key agreement with small leakage

We report on a highly efficient information reconciliation protocol for the binary symmetric channel (BSC) with feedback, proposed to be used in the context of secret-key agreement. This is a variant of the so-called Cascade protocol. Simulations determine efficiencies, defined by the ratio of actual transmitted information to the necessary amount of information, of approximately 1.025 for a frame length of 214 bits and a frame error rate of typically 10-4. The proposed algorithm works for any BSC parameter between 0 and 0.5.
Developmental Cognitive Neuroscience Neural Correlates of Self-perceptions in Adolescents with Major Depressive Disorder

Alteration in self-perception is a salient feature in major depression. Hyperactivity of anterior corti-cal midline regions has been implicated in this phenomenon in depressed adults. Here, we extend this work to depressed adolescents during a developmental time when neuronal circuitry underlying the sense of self matures by using task-based functional magnetic resonance imaging (fMRI) and connec-tivity analyses. Twenty-three depressed adolescents and 18 healthy controls (HC) viewed positive and negative trait words in a scanner and judged whether each word described them ('self' condition) or was a good trait to have ('general' condition). Self-perception scores were based on participants' endorsements of positive and negative traits during the fMRI task. Depressed adolescents exhibited more negative self-perceptions than HC. Both groups activated cortical midline regions in response to self-judgments compared to general-judgments. However, depressed adolescents recruited the posterior cingulate cor-tex/precuneus more for positive self-judgments. Additionally, local connectivity of the dorsal medial prefrontal cortex was reduced during self-reflection in depressed adolescents. Our findings highlight differences in self-referential processing network function between depressed and healthy adolescents and support the need for further investigation of brain mechanisms associated with the self, as they may be paramount to understanding the etiology and development of major depressive disorder.
Upside-down stomach – results of mini-invasive surgical therapy

Aim The authors evaluate the results of mini-invasive therapy in patients diagnosed with upside-down stomach. Material and methods From 1998 to 2008, a total of 27 patients diagnosed with upside-down stomach were surgically treated at the 1st Department of Surgery, University Hospital Olomouc. Before the operation, patients were examined endoscopically and a barium swallow was performed. In all 27 patients (100%), the operation was performed electively laparoscopically. The principle of the operation in all cases was reposition of the stomach into the abdominal cavity, resection of the hernial sac and hiatoplasty. In addition, in 15 patients (56%) with reflux symptoms or endoscopic findings of reflux oesophagitis, fundoplication in Nissen's modification was also performed. Fundopexy was indicated in 12 patients (44%). Results In all patients (100%), the operation was performed mini-invasively; conversion to an open procedure was never necessary. In 3 cases (11%), the left pleural cavity was opened during the operation; this was treated by introducing a chest drain. The operation mortality in the patient set was zero; morbidity was 11%. A year after the operation, patients were re-examined, and follow-up endoscopy and barium swallow were performed. Conclusions In all patients diagnosed with upside-down stomach, surgical treatment is indicated due to the risk of developing severe complications. Mini-invasive surgical therapy in the hands of an experienced surgeon is a safe procedure which offers patients all the benefits of mini-invasive therapy with promising short- and long-term results.