Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Thymectomy on Human Peripheral Blood T Cell Pools in Myasthenia Gravis

The human thymus is required for establishment of the T cell pool in fetal life, but postnatal thymectomy does not lead to immunodeficiency in humans. Because thymectomy in humans is performed for treatment of myasthenia gravis (MG), we have studied patients with MG for effects of thymectomy on peripheral blood (PB) naive (CD45RA+, CD62L+) and memory (CD45RO+) T cells. We have also determined the effect of thymectomy on levels of PB cells containing signal joint TCR δ excision circles (TRECs), a molecular marker of thymus emigrants that have divided few times after leaving the thymus. In 17 nonthymectomized and 26 thymectomized MG patients studied at varying times after thymectomy (1 day to 41 years), we found no significant mean difference in PB T cell TREC levels between ages 40 and 80 years. However, both thymectomized and nonthymectomized MG patients had lower PB T cell TREC levels than did age-matched normal subjects (p < 0.0001 for both). These data demonstrated that MG itself or treatment for MG decreased thymopoiesis independent of thymectomy. Next, to control for disease activity and treatment, we prospectively studied 10 MG patients before and from 27 to 517 days after thymectomy. We found that thymectomy decreased CD4 or CD8 T cell TREC concentrations most when thymopoiesis was active before thymectomy (six of six patients), but had little effect in patients when thymopoiesis was minimal (four of four patients). In contrast, there was no significant effect of thymectomy on absolute numbers of naive PB T cells. Thus, in MG, removal of a thymus with active thymopoiesis resulted in a significant fall in PB TREC+ T cells postthymectomy.
Ventricular assist device in severe heart failure: effects on cytokines, complement and body weight.

AIMS Inflammatory and immune activation and body wasting are important features of end-stage chronic heart failure. It is not known whether restoration of cardiac output by assist device implantation can improve these abnormalities. METHODS We studied 48 patients (39 males; age 45+/-2 years) with NYHA class IV heart failure. All patients underwent ventricular assist device implantation for end-stage heart failure as a bridge to cardiac transplantation. Plasma levels of tumour necrosis factor alpha, and its receptors, interleukin-6, elastase, activated complement, and soluble CD14 receptors were measured at the time of operation and in survivors at 1 week (n=46), 40 days (n=35) and 90 days (n=26). Follow-up was for a minimum of 1 year. RESULTS One-year survival was 35% (95% CI: 22-49%). Body mass index was the only predictor of survival (body mass index >25 (n=16); survival 63 (39-86) %; body mass index <25 (n=32); survival 22 (7.5-36) %: P=0.003). Tumour necrosis factor alpha fell from 9.66+/-1.33 pg x ml(-1) to 4.2+/-1.0 at 1 week (P=0.008), but returned to pre-operative levels at 90 days. Interleukin-6, activated complement and elastase fell progressively to 40 days, but were rising at 90 days. There was no change in tumour necrosis factor receptor. There was a gradual rise in CD14 (3.99+/-0.15 microg x ml(-1) at baseline, 5.02+/-0.39 at 90 days, P=0.006). After surgery, body weight fell from 80+/-2 to 73+/-2 kg by 1 month (P<0.001) and to 72+/-2 kg at 90 days. CONCLUSIONS Ventricular assist device implantation results in a short-term fall in tumour necrosis factor alpha and interleukin-6, but no change in CD14 or tumour necrosis factor receptor, suggesting that the pathophysiological process resulting in inflammation was not altered by left ventricular assist device implantation. Low body mass index is related to poor outcome after assist device implantation, and no weight gain.
TinyLFU: A Highly Efficient Cache Admission Policy

This paper proposes to use a frequency based cache admission policy in order to boost the effectiveness of caches subject to skewed access distributions. Rather than deciding on which object to evict, TinyLFU decides, based on the recent access history, whether it is worth admitting an accessed object into the cache at the expense of the eviction candidate. Realizing this concept is enabled through a novel approximate LFU structure called TinyLFU, which maintains an approximate representation of the access frequency of recently accessed objects. TinyLFU is extremely compact and lightweight as it builds upon Bloom filter theory. The paper shows an analysis of the properties of TinyLFU including simulations of both synthetic workloads as well as YouTube and Wikipedia traces.
The structure of dimethylallyl tryptophan synthase reveals a common architecture of aromatic prenyltransferases in fungi and bacteria

Ergot alkaloids are toxins and important pharmaceuticals that are produced biotechnologically on an industrial scale. The first committed step of ergot alkaloid biosynthesis is catalyzed by dimethylallyl tryptophan synthase (DMATS; EC 2.5.1.34). Orthologs of DMATS are found in many fungal genomes. We report here the x-ray structure of DMATS, determined at a resolution of 1.76 Å. A complex of DMATS from Aspergillus fumigatus with its aromatic substrate L-tryptophan and with an analogue of its isoprenoid substrate dimethylallyl diphosphate reveals the structural basis of this enzyme-catalyzed Friedel-Crafts reaction, which shows strict regiospecificity for position 4 of the indole nucleus of tryptophan as well as unusual independence of the presence of Mg2+ ions. The 3D structure of DMATS belongs to a rare β/α barrel fold, called prenyltransferase barrel, that was recently discovered in a small group of bacterial enzymes with no sequence similarity to DMATS. These bacterial enzymes catalyze the prenylation of aromatic substrates in the biosynthesis of secondary metabolites (i.e., a reaction similar to that of DMATS).
Reactive nitrogen chemistry in aerosol water as a source of sulfate during haze events in China

Multiphase chemistry of NO2 and alkaline matter in aerosol water explains rapid sulfate formation and severe haze in China. Fine-particle pollution associated with winter haze threatens the health of more than 400 million people in the North China Plain. Sulfate is a major component of fine haze particles. Record sulfate concentrations of up to ~300 μg m−3 were observed during the January 2013 winter haze event in Beijing. State-of-the-art air quality models that rely on sulfate production mechanisms requiring photochemical oxidants cannot predict these high levels because of the weak photochemistry activity during haze events. We find that the missing source of sulfate and particulate matter can be explained by reactive nitrogen chemistry in aerosol water. The aerosol water serves as a reactor, where the alkaline aerosol components trap SO2, which is oxidized by NO2 to form sulfate, whereby high reaction rates are sustained by the high neutralizing capacity of the atmosphere in northern China. This mechanism is self-amplifying because higher aerosol mass concentration corresponds to higher aerosol water content, leading to faster sulfate production and more severe haze pollution.
Voice Conversion of Non-aligned Data using Unit Selection

Voice conversion (VC) technology allows to transform the voice of the source speaker so that it is perceived as the voice of a target speaker. One of the applications of VC is speech-to-speech translation where the voice has to inform, not only about what is said, but also about who is the speaker. This paper introduces the different methods submitted by UPC to the TC-STAR second evaluation campaign. One method is based on the LPC model and the other on the Harmonic+Noise Model (HNM). Unit selection techniques are employed so that the methods no longer require parallel sentences during the training phase. We have applied these methods both to intra-lingual and cross-lingual voice conversion. Results from the TC-STAR evaluation show that the speaker identity is successfully transformed with all the methods. Further work is required to increase the quality of the voice so that it achieve the quality of current TTS voices.
A Graph-based Approach for Web Services Composition

The automatic web services composition plays an important role in the area of semantic web services. In fact, in a real life it is not usual to discover atomicweb services matching with the user’s query. So composing services fulfilling the query is needed. This paper discusses the web services composition model based on an oriented graph. It is based on Bcov algorithm (Benatallah.B et al., 2005a), initially defined for web services discovery and considered as the best cover problem, which it was mapped as the problem of computing the minimal transversals with minimum cost of a weighted hypergraph. We propose two algorithms handling the oriented graph reasoning for web service composition. At first glance, a basic composition version for Bcov algorithm is given. The algorithm composes services over the induced subgraphs of each transversal provided by Becov algorithm, and gives a covering ratio satisfying the query. The second algorithm used a composed services graph maintained by a web services provider. The composition in that case is based on Dijkstra algorithm, where for each two consecutive services in the best minimal transversal provided by Bcov algorithm, a shortest path is computed regarding the composed services graph.
The Role of Pleiotropy in the Maintenance of Sex in Yeast

In facultatively sexual species, lineages that reproduce asexually for a period of time can accumulate mutations that reduce their ability to undergo sexual reproduction when sex is favorable. We propagated Saccharomyces cerevisiae asexually for ∼800 generations, after which we measured the change in sexual fitness, measured as the proportion of asci observed in sporulation medium. The sporulation rate in cultures propagated asexually at small population size declined by 8%, on average, over this time period, indicating that the majority of mutations that affect sporulation rate are deleterious. Interestingly, the sporulation rate in cultures propagated asexually at large population size improved by 11%, on average, indicating that selection on asexual function effectively eliminated most of the mutations deleterious to sporulation ability. These results suggest that pleiotropy between mutations' effects on asexual fitness and sexual fitness was predominantly positive, at least for the mutations accumulated in this experimental evolution study. A positive correlation between growth rate and sporulation rate among lines also provided evidence for positive pleiotropy. These results demonstrate that, at least under certain circumstances, selection acting on asexual fitness can help to maintain sexual function.
DMNI: A specialized network interface for NoC-based MPSoCs

Current proposals of NoC-based MPSoC adopt an NI (Network Interface) interconnected to a DMA (Direct Memory Access) module to enable the communication between processors through the NoC. The adoption of both modules decouples computation from communication, and a standard interface at the NI provides an abstract way for designers to connect new cores. However, this architecture is inherited from bus-based architectures and can be optimized, by removing unnecessary interfaces, signals, and registers. This paper presents a specialized communication interface for NoC-based MPSoCs, called DMNI (Direct Memory Network Interface). The DMNI merges the functionalities of the DMA and the NI into a single component, directly connecting the NoC router with the processor memory. To avoid stalls in the communication, the design of the DMNI supports simultaneous packet reception and transmission. A simplified and generic programming interface exposes the DMNI services to the software layer. Results show a reduction in the silicon area and performance improvement in the packet transmission.
Planck intermediate results. XXXVIII. E- and B-modes of dust polarization from the magnetized filamentary structure of the interstellar medium

The quest for a B-mode imprint from primordial gravity waves on the polarization of the cosmic microwave background (CMB) requires the characterization of foreground polarization from Galactic dust. We present a statistical study of the filamentary structure of the 353 GHz Planck Stokes maps at high Galactic latitude, relevant to the study of dust emission as a polarized foreground to the CMB. We filter the intensity and polarization maps to isolate filaments in the range of angular scales where the power asymmetry between E-modes and B-modes is observed. Using the Smoothed Hessian Major Axis Filament Finder, we identify 259 filaments at high Galactic latitude, with lengths larger or equal to 2\deg\ (corresponding to 3.5 pc in length for a typical distance of 100 pc). These filaments show a preferred orientation parallel to the magnetic field projected onto the plane of the sky, derived from their polarization angles. We present mean maps of the filaments in Stokes I, Q, U, E, and B, computed by stacking individual images rotated to align the orientations of the filaments. Combining the stacked images and the histogram of relative orientations, we estimate the mean polarization fraction of the filaments to be 11 %. Furthermore, we show that the correlation between the filaments and the magnetic field orientations may account for the E and B asymmetry and the $C_{\ell}^{TE}/C_{\ell}^{EE}$ ratio, reported in the power spectra analysis of the Planck 353 GHz polarization maps. Future models of the dust foreground for CMB polarization studies will need to take into account the observed correlation between the dust polarization and the structure of interstellar matter.
Intestinal gluconeogenesis and glucose transport according to body fuel availability in rats

Intestinal hexose absorption and gluconeogenesis have been studied in relation to refeeding after two different fasting phases: a long period of protein sparing during which energy expenditure is derived from lipid oxidation (phase II), and a later phase characterized by a rise in plasma corticosterone triggering protein catabolism (phase III). Such a switch in body fuel uses, leading to changes in body reserves and gluconeogenic precursors, could modulate intestinal gluconeogenesis and glucose transport. The gene and protein levels, and the cellular localization of the sodium–glucose cotransporter SGLT1, and of GLUT5 and GLUT2, as well as that of the key gluconeogenic enzymes phosphoenolpyruvate carboxykinase (PEPCK) and glucose‐6‐phosphatase (Glc6Pase) were measured. PEPCK and Glc6Pase activities were also determined. In phase III fasted rats, SGLT1 was up‐regulated and intestinal glucose uptake rates were higher than in phase II fasted and fed rats. PEPCK and Glc6Pase mRNA, protein levels and activities also increased in phase III. GLUT5 and GLUT2 were down‐regulated throughout the fast, but increased after refeeding, with GLUT2 recruited to the apical membrane. The increase in SGLT1 expression during phase III may allow glucose absorption at low concentrations as soon as food is available. Furthermore, an increased epithelial permeability due to fasting may induce a paracellular movement of glucose. In the absence of intestinal GLUT2 during fasting, Glc6Pase could be involved in glucose release to the bloodstream via membrane trafficking. Finally, refeeding triggered GLUT2 and GLUT5 synthesis and apical recruitment of GLUT2, to absorb larger amounts of hexoses.
Sphingolipids Are Dual Specific Drug Targets for the Management of Pulmonary Infections: Perspective

Sphingolipids are the major constituent of the mucus secreted by the cells of epithelial linings of lungs where they maintain the barrier functions and prevent microbial invasion. Sphingolipids are interconvertible, and their primary and secondary metabolites have both structural and functional roles. Out of several sphingolipid metabolites, sphingosine-1 phosphate (S1P) and ceramide are central molecules and decisive for sphingolipid signaling. These are produced by enzymatic activity of sphingosine kinase-1 (SK-1) upon the challenge with either biological or physiological stresses. S1P and ceramide rheostat are important for the progression of various pathologies, which are manifested by inflammatory cascade. S1P is a well-established secondary messenger and associated with various neuronal, metabolic, and inflammatory diseases other than respiratory infections such as Chlamydia pneumoniae, Streptococcus pneumoniae, and Mycobacterium tuberculosis. These pathogens are known to exploit sphingolipid metabolism for their opportunistic survival. Decreased sphingosine kinase activity/S1P content in the lung and peripheral blood of tuberculosis patients clearly indicated a dysregulation of sphingolipid metabolism during infection and suggest that sphingolipid metabolism is important for management of infection by the host. Our previous study has demonstrated that gain of SK-1 activity is important for the maturation of phagolysosomal compartment, innate activation of macrophages, and subsequent control of mycobacterial replication/growth in macrophages. Furthermore, S1P-mediated amelioration of lung pathology and disease severity in TB patients is believed to be mediated by the selective activation or rearrangement of various S1P receptors (S1PR) particularly S1PR2, which has been effective in controlling respiratory fungal pathogens. Therefore, such specificity of S1P–S1PR would be paramount for triggering inflammatory events, subsequent activation, and fostering bactericidal potential in macrophages for the control of TB. In this review, we have discussed and emphasized that sphingolipids may represent effective novel, yet dual specific drug targets for controlling pulmonary infections.
Generation of OAM Beams Using Phased Array in the Microwave Band

A system is proposed to generate vortex electromagnetic (EM) beams in the microwave band, which generates high-order vortex beams at the X-frequency band for the first time. First, the orbital angular momentum (OAM)-generating system is designed and the signal model based on the uniform circular array is presented. Subsequently, the mathematical model with array error contributions is established and, comprehensively, numerical simulations are conducted to analyze how amplitude and phase errors affect the radiation field and the EM vortex imaging. The experimental results validate that the proposed system can readily generate vortex beams of high quality, which are in agreement with the simulated results. The work paves the way to applications of OAM-carrying beams as well as a novel information-rich radar paradigm.
Quantitative Proteomics Analysis of the Nuclear Fraction of Human CD4+ Cells in the Early Phases of IL-4-induced Th2 Differentiation

We used stable isotope labeling with 4-plex iTRAQ (isobaric tags for relative and absolute quantification) reagents and LC-MS/MS to investigate proteomic changes in the nucleus of activated human CD4+ cells during the early stages of Th2 cell differentiation. The effects of IL-4 stimulation upon activated naïve CD4+ cells were measured in the nuclear fractions from 6 and 24 h in three biological replicates, each using pooled cord blood samples derived from seven or more individuals. In these analyses, in the order of 800 proteins were detected with two or more peptides and quantified in three biological replicates. In addition to consistent differences observed with the nuclear localization/expression of established human Th2 and Th1 markers, there were changes that suggested the involvement of several proteins either only recently reported or otherwise not known in this context. These included SATB1 and among the novel changes detected and validated an IL-4-induced increase in the level of YB1. This unique data set from human cord blood CD4+ T cells details an extensive list of protein determinations that compares with and complements previous data determined from the Jurkat cell nucleus.
Therapeutic benefit of ciliary neurotrophic factor in progressive motor neuronopathy depends on the route of delivery

Ciliary neurotrophic factor (CNTF) has demonstrated therapeutic effects in several mouse mutants with motoneuronal degeneration. However, the poor bioavailability and toxic side effects of recombinant CNTF protein have complicated its use in patients with amyotrophic lateral sclerosis. CNTF gene transfer strategies were developed but faced the question of whether CNTF should be delivered to motoneuron cell bodies or to their axons or muscle targets. To address this issue, we have used an adenoviral vector (AdCNTF) coding for a secretable form of CNTF and compared different routes of its administration in the mouse mutant progressive motor neuronopathy (pmn). Intramuscular, intravenous, and intracerebroventricular injections of AdCNTF or the control vector AdlacZ resulted in transgene expression in skeletal muscle fibers, hepatocytes, and ependymal cells, respectively, as determined by histochemistry and reverse transcription–polymerase chain reaction. AdCNTF intramuscularly treated and intravenously treated pmn mice showed a 25% increase in mean life span and a reduced degeneration of phrenic myelinated nerve fibers, which correlated with elevated CNTF serum bioactivities. In contrast, intracerebroventricular AdCNTF administration did not affect the mean life span or motor axonal degeneration of pmn mice. The differential efficacy of peripheral and central CNTF vector administrations might be of interest for future studies in human motor neuron diseases. Ann Neurol 1999;45:296–304
Phosphorylation of Adducin by Rho-Kinase Plays a Crucial Role in Cell Motility

Adducin is a membrane skeletal protein that binds to actin filaments (F-actin) and thereby promotes the association of spectrin with F-actin to form a spectrin-actin meshwork beneath plasma membranes such as ruffling membranes. Rho-associated kinase (Rho- kinase), which is activated by the small guanosine triphosphatase Rho, phosphorylates α-adducin and thereby enhances the F-actin–binding activity of α-adducin in vitro. Here we identified the sites of phosphorylation of α-adducin by Rho-kinase as Thr445 and Thr480. We prepared antibody that specifically recognized α-adducin phosphorylated at Thr445, and found by use of this antibody that Rho-kinase phosphorylated α-adducin at Thr445 in COS7 cells in a Rho-dependent manner. Phosphorylated α-adducin accumulated in the membrane ruffling area of Madin-Darby canine kidney (MDCK) epithelial cells and the leading edge of scattering cells during the action of tetradecanoylphorbol-13-acetate (TPA) or hepatocyte growth factor (HGF). The microinjection of Botulinum C3 ADP-ribosyl-transferase, dominant negative Rho-kinase, or α-adducinT445A,T480A (substitution of Thr445 and Thr480 by Ala) inhibited the TPA-induced membrane ruffling in MDCK cells and wound-induced migra- tion in NRK49F cells. α-AdducinT445D,T480D (substi- tution of Thr445 and Thr480 by Asp), but not α-adducinT445A,T480A, counteracted the inhibitory effect of the dominant negative Rho-kinase on the TPA-induced membrane ruffling in MDCK cells. Taken together, these results indicate that Rho-kinase phosphorylates α-adducin downstream of Rho in vivo, and that the phosphorylation of adducin by Rho-kinase plays a crucial role in the regulation of membrane ruffling and cell motility.