Miracle-dz/UniFAR-FTUs huggingface dataset:
Fungi: the neglected allergenic sources

Allergic diseases are considered the epidemics of the twentieth century estimated to affect more than 30% of the population in industrialized countries with a still increasing incidence. During the past two decades, the application of molecular biology allowed cloning, production and characterization of hundreds of recombinant allergens. In turn, knowledge about molecular, chemical and biologically relevant allergens contributed to increase our understanding of the mechanisms underlying IgE‐mediated type I hypersensitivity reactions. It has been largely demonstrated that fungi are potent sources of allergenic molecules covering a vast variety of molecular structures including enzymes, toxins, cell wall components and phylogenetically highly conserved cross‐reactive proteins. Despite the large knowledge accumulated and the compelling evidence for an involvement of fungal allergens in the pathophysiology of allergic diseases, fungi as a prominent source of allergens are still largely neglected in basic research as well as in clinical practice. This review aims to highlight the impact of fungal allergens with focus on asthma and atopic dermatitis.
Characterization of the Interaction of Sclerostin with the Low Density Lipoprotein Receptor-related Protein (LRP) Family of Wnt Co-receptors*

Background: Sclerostin, an inhibitor of Wnt signaling, binds to the β-propeller domain-containing Wnt co-receptors LRP6 and LRP4. Results: An NXI motif in sclerostin mediates interactions with LRP6 (but not LRP4) and blocks Wnt1 signaling. Conclusion: The sclerostin/LRP6 interaction shares features with the well characterized nidogen/laminin interaction. Significance: NXI motifs are important in mediating interactions with β-propeller containing proteins. LRP5 and LRP6 are proteins predicted to contain four six-bladed β-propeller domains and both bind the bone-specific Wnt signaling antagonist sclerostin. Here, we report the crystal structure of the amino-terminal region of LRP6 and using NMR show that the ability of sclerostin to bind to this molecule is mediated by the central core of sclerostin and does not involve the amino- and carboxyl-terminal flexible arm regions. We show that this structured core region interacts with LRP5 and LRP6 via an NXI motif (found in the sequence PNAIG) within a flexible loop region (loop 2) within the central core region. This sequence is related closely to a previously identified motif in laminin that mediates its interaction with the β-propeller domain of nidogen. However, the NXI motif is not involved in the interaction of sclerostin with LRP4 (another β-propeller containing protein in the LRP family). A peptide derived from the loop 2 region of sclerostin blocked the interaction of sclerostin with LRP5/6 and also inhibited Wnt1 but not Wnt3A or Wnt9B signaling. This suggests that these Wnts interact with LRP6 in different ways.
Distributed EZ (string processing language)

EZ is a system that integrates traditional operating systems and programming languages into a very-high-level persistent string processing language. The authors describe the design and initial implementation of a distributed memory manager that distributes EZ's virtual address space transparently among a network of homogeneous computers. The design adapts the techniques used in recent implementation of shared virtual memory for use in EZ's persistent environment. Unlike most implementations of shared virtual memory, control information is distributed and migrates. This memory manager works in concert with a distributed mark-and-sweep garbage collector, which is also concurrent and real-time. This collector trades time for space and minimal disruption of mutators, which reduces communication costs. <<ETX>>
Definitional and human constraints on structural annotation of English*

Abstract The limits on predictability and refinement of English structural annotation are examined by comparing independent annotations, by experienced analysts using the same detailed published guidelines, of a common sample of written texts. Three conclusions emerge. First, while it is not easy to define watertight boundaries between the categories of a comprehensive structural annotation scheme, limits on inter-annotator agreement are in practice set more by the difficulty of conforming to a well-defined scheme than by the difficulty of making a scheme well defined. Secondly, although usage is often structurally ambiguous, commonly the alternative analyses are logical distinctions without a practical difference – which raises questions about the role of grammar in human linguistic behaviour. Finally, one specific area of annotation is strikingly more problematic than any other area examined, though this area (classifying the functions of clause-constituents) seems a particularly significant one for human language use. These findings should be of interest both to computational linguists and to students of language as an aspect of human cognition.
Functional disconnection of the semantic networks in schizophrenia

Patients with schizophrenia exhibit deficits in semantic processing, which can form the basis of thought disorders. The objective of this study was to explore functional connectivity between the activated areas during semantic processing in schizophrenia. Twelve patients with schizophrenia and 12 healthy controls were studied with [15O]H2O positron-emission tomography during semantic judgment. The expected activation in the left inferior occipitotemporal cortex significantly correlated with several other regional activations in normal study participants, but with no other regional activations in patients with schizophrenia. This finding suggests that schizophrenia involves a disconnection of semantic networks. The resultant distortion in semantic processing may have an impact on thought disorders.
A New Approach to Coin Recognition using Neural Pattern Analysis

In business transactions, to enable computers to recognize coins and other different forms of currency has become an essential process. If the computers are able to perform such recognitions, monetary transactions becomes much easier in all forms of trade. Keeping all the necessary factors in mind we have created a system that could easily identify the numeral in the coins. To limit the scope of this problem, our research focuses on recognizing the exact numeral in a 1-rupee, 2-rupee and 5-rupee Indian coin. The proposed system focuses only on the numerals rather than the use of other images presented in the front and rear side of the coin. In the proposed approach coin images are acquired and numeral in the coins are extracted. Unlike other edge detection process, the coin edges are not sharp and gradually become dull by years of usage. Moreover, numeral edges are same as the background pixel value, which increases the complexity of edge detection process. Hence statistical color threshold method is suggested and implemented in the coin recognition process. After finding the Cartesian co-ordinates of numeral in the coins, the sub image of the numeral is extracted from the given coin image. This sub image is used for character recognition process. In this phase, rotation-invariant character recognition is carried out by multi channel Gabor filter and back propagation network methods. The overall collection contains 72 images in which skewed images are acquired in various angles of rotation varying from 30 degrees onwards.
On catastrophic nature of network performance degradation induced by traffic correlations

Although it is evident that traffic correlations may have significant performance impacts on networks, it is still not clear how correlated traffic may deteriorate network performance. This paper demonstrates the catastrophic nature of network performance degradation induced by traffic correlations, that is, as long as the correlation time is large enough, bistability may appear in network behavior, which may cause the network to change abruptly from one stable state to another. This catastrophic behavior may have significant impacts on traffic control and engineering.
Stray flux and its influence on protection relays

Current transformers (CT) normally have excellent performance when applied correctly under conditions for which they were designed. While the common operating conditions affecting CT performance are usually recognized and properly considered, there is one factor, the importance of which is sometimes underestimated or even overlooked entirely. This is the effect of external stray flux produced by: (a) abrupt bends of the CT primary conductor at very close distance from the CT location; (b) high-current busses adjacent to the CT; and (c) other sources of magnetic fields near the CT (e.g. CTs installed within power transformer or shunt reactor tank). If a CT is applied incorrectly (e.g. without considering the existence of stray fluxes) the secondary CT current can be, under certain circumstances, entirely different from the primary CT current which then can easily cause unwanted operations of sensitive protection relays like for example differential protection.
A proposal for treatment of invasive thymoma

Eleven patients with invasive thymoma were treated with radiotherapy. All patients had gross anterior mediastinal tumors that invaded the adjacent structures, four of whom showed intrathoracic dissemination. Before radiotherapy, only one had macroscopic complete resection of the tumor, and another had partial resection; the other nine patients underwent biopsy only. All 11 patients achieved complete remission after radiotherapy, eight of whom have been free from relapse for 31 to 202 months. Three patients experienced recurrence within the thorax but outside the radiation fields. Even after whole mediastinal irradiation, recurrence could occur in the pleural cavity. Therefore, extended radiation fields including the entire hemithorax is recommended. Intensive combination chemotherapy was administered for two patients with recurrence and they achieved complete remission. A possible role of intensive chemotherapy in induction phase for invasive thymomas is discussed.
Free fatty acid availability and temperature regulation in cold water.

The purpose of this study was to investigate whether a reduced availability of plasma free fatty acids (FFA) would impair human temperature regulation during cold exposure. Seven seminude male subjects were immersed on two occasions in 18 degrees C water for 90 min or until their rectal temperature (Tre) decreased to 35.5 degrees C. The immersion occurred after 2 h of intermittent oral ingestion of either nicotinic acid (NIC) or a placebo (PLAC). Plasma FFA levels immediately before the immersion were significantly lower in NIC (87 +/- 15 mumol/l) than in PLAC (655 +/- 116 mumol/l, P less than 0.05). Although FFA levels increased by 73% in NIC during the immersion (P less than 0.05), they remained significantly lower than in PLAC (151 +/- 19 vs. 716 +/- 74 mumol/l, P less than 0.05) throughout the immersion. Muscle glycogen concentrations in the vastus lateralis decreased after cold water immersion in both trials (P less than 0.05), but the rate of glycogen utilization was similar, averaging 1.00 +/- 0.27 mmol glucose unit.kg dry muscle-1.min-1). Plasma glucose levels were significantly reduced after immersion in both trials (P less than 0.05), this decrease being greater in NIC (1.3 +/- 0.2 mmol/l) than in PLAC (0.7 +/- 0.1 mmol/l, P less than 0.05). O2 uptake increased to 3.8 +/- 0.3 times preimmersion values in both trials (P less than 0.05). Mean respiratory exchange ratio (RER) immediately before the immersion was greater in NIC (0.87 +/- 0.02) than in PLAC (0.77 +/- 0.01, P less than 0.05). Cold exposure increased RER in PLAC but not in NIC. (ABSTRACT TRUNCATED AT 250 WORDS)
Making Progress Toward Individualized Medicine in the Treatment of Psychosis.

Current treatment algorithms for the management of psychosis do not take into account the substantial interindividual variability in response to antipsychotic drugs. Clinicians have no alternative but to choose antipsychotics based on trial and error, often resulting in prolonging patients’ suffering. What if a brief brain scan or a blood test prior to starting an antipsychotic were sufficient to provide an accurate measure of how likelyan individual was to respond to a specific medication and could thus guide treatment decisions? Two articles in this issue report on advances toward individualized medicine in the treatment of psychosis. In order to develop a biomarker of treatment response with clinical utility, researchers must first demonstrate a robust association between the biomarker and clinical outcome, and then must replicate these findings in independent cohorts. Based on converging evidence implicating the striatum as critical to antipsychotic response, Sarpal et al. (1) hypothesized that functional connectivity between the striatum and other brain regions could be established as a biomarker indexing the likelihood that an individual will respond to treatment. Functional connectivity leverages the temporal coherence of low-frequency fluctuations in the blood-oxygen-level-dependent signal between remote brain regionsobtainedduringresting-statefunctionalMRItoallow inferences on coordinated brain activity (Figure 1). The authors obtained a 5-minute resting-state scan in a group of first-episode psychosis patients (the “discovery cohort” )a t the initiation of a 12-week randomized trial with either risperidone or aripiprazole and determined the response to treatment at the end of the trial. By regressing treatment response values with baseline functional connectivity, striatal connectivity to 91 brain regions was identified to be predictive of subsequent response to treatment. For each participant, a striatal connectivity index was calculated by summing the strength of the functional connectivity between the striatum and each of these regions. This index was found to be significantly different between treatment responders and nonresponders. To validate this putative biomarker, similar resting-state scans were then obtained in a diagnostically heterogeneous group of patients who were hospitalized for an acute exacerbation of psychosis (“the generalization co
Optical Observations of XTE J1118+480 during the 2000 Outburst

We report on photometric and spectroscopic observations of a possible halo black-hole X-ray nova, XTE J1118 + 480 (= KV UMa) during outburst. Our photometric monitoring during the main outburst revealed that the optical maximum as well as the onset of the outburst precede those in the X-ray region. This indicates that the event was an “outside-in” type outburst and that its optical flux was dominated by viscous heating, itself, and not the effect of X-ray irradiation. Based on these results, we suggest an outburst scenario analogous to superoutbursts in SU UMa-type dwarf novae. This scenario predicts a superhump phenomenon, which we indeed detected throughout the outburst. We determined its period to be 0.170529± 0.000006 d, which is slightly longer than the orbital periods suggested from spectroscopic observations. We have furthermore revealed the first evidence of a continuous period decreasing in X-ray novae. The most prominent feature in our optical spectrum is a double-peak He II 4686 Å emission line having an asymmetric profile with an outstanding blue side peak. Using a Doppler mapping method, we found that the He II emission originates from the accretion disk, which particularly concentrates on the hot spot. The time that the blue peak becomes strongest corresponds to a superhump peak. This implies that we see an elongated side of an eccentric disk at that time and, hence, it may cause an asymmetric emission profile. Substituting the observed fractional superhump excess for a theoretically expected relation between it and the mass ratio, we estimate that the black-hole mass is larger than 9.5M . XTE J1118 + 480 thus has a large mass of a compact object compared with the typical black-hole X-ray novae.
Reconstitution and Molecular Analysis of an Active Human Immunodeficiency Virus Type 1 Nef/p21-Activated Kinase 2 Complex

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) Nef activation of p21-activated kinase 2 (PAK-2) was recapitulated in a cell-free system consisting of in vitro-transcribed RNA, rabbit reticulocyte lysate, and microsomal membranes on the basis of the following observations: (i) Nef associated with a kinase endogenous to the rabbit reticulocyte lysate that was identified as PAK-2, (ii) Nef-associated kinase activity was detected with Nefs from HIV-1SF2, HIV-1YU2, and SIVmac239, (iii) kinase activation was not detected with a myristoylation-defective Nef (HIV-1SF2NefG2A) or with a Nef defective in PAK-2 activation but fully competent in other Nef functions (HIV-1SF2NefF195I), and (iv) Nef-associated kinase activation required activated endogenous p21 GTPases (Rac1 or Cdc42). The cell-free system was used to analyze the mechanism of Nef activation of PAK-2. First, studies suggest that the p21 GTPases may act transiently to enhance Nef activation of PAK-2 in vitro. Second, addition of wortmannin to the cell-free system demonstrated that Nef activation of PAK-2 does not require PI 3-kinase activity. Third, ultracentrifugation analysis revealed that whereas the majority of Nef and PAK-2 partitioned to the supernatant, Nef-associated PAK-2 activity partitioned to the membrane-containing pellet as a low-abundance complex. Lastly, Nef activation of PAK-2 in vitro requires addition of microsomal membranes either during or after translation of the Nef RNA. These results are consistent with a model in which activation of PAK-2 by Nef occurs by recruiting PAK-2 to membranes. As demonstrated herein, the cell-free system is a new and important tool in the investigation of the mechanism of PAK-2 activation by Nef.
Aldolase provides an unusual binding site for thrombospondin-related anonymous protein in the invasion machinery of the malaria parasite

An actomyosin motor located underneath the plasma membrane drives motility and host-cell invasion of apicomplexan parasites such as Plasmodium falciparum and Plasmodium vivax, the causative agents of malaria. Aldolase connects the motor actin filaments to transmembrane adhesive proteins of the thrombospondin-related anonymous protein (TRAP) family and transduces the motor force across the parasite surface. The TRAP–aldolase interaction is a distinctive and critical trait of host hepatocyte invasion by Plasmodium sporozoites, with a likely similar interaction crucial for erythrocyte invasion by merozoites. Here, we describe 2.4-Å and 2.7-Å structures of P. falciparum aldolase (PfAldo) obtained from crystals grown in the presence of the C-terminal hexapeptide of TRAP from Plasmodium berghei. The indole ring of the critical penultimate Trp-residue of TRAP fits snugly into a newly formed hydrophobic pocket, which is exclusively delimited by hydrophilic residues: two arginines, one glutamate, and one glutamine. Comparison with the unliganded PfAldo structure shows that the two arginines adopt new side-chain rotamers, whereas a 25-residue subdomain, forming a helix–loop–helix unit, shifts upon binding the TRAP-tail. The structural data are in agreement with decreased TRAP binding after mutagenesis of PfAldo residues in and near the induced TRAP-binding pocket. Remarkably, the TRAP- and actin-binding sites of PfAldo seem to overlap, suggesting that both the plasticity of the aldolase active-site region and the multimeric nature of the enzyme are crucial for its intriguing nonenzymatic function in the invasion machinery of the malaria parasite.
Challenges and Rewards of Interaction Proteomics *

The recent explosion of high throughput experimental technologies for characterizing protein interactions has generated large amounts of data describing interactions between thousands of proteins and producing genome scale views of protein assemblies. The systems level views afforded by these data hold great promise of leading to new knowledge but also involve many challenges. Deriving meaningful biological conclusions from these views crucially depends on our understanding of the approximation and biases that enter into deriving and interpreting the data. The challenges and rewards of interaction proteomics are reviewed here using as an example the latest comprehensive high throughput analyses of protein interactions in yeast.
Expression patterns and potential roles of SIRT1 in human medulloblastoma cells in vivo and in vitro

Medulloblastoma is a primitive neuroectodermal tumor, which originates in the cerebellum, presumably due to the alterations of some neurogenetic elements. Sirtuin 1 (SIRT1), a class III histone deacetylase (HDAC), regulates differentiation of neuronal stem cells but its status in medulloblastomas remains largely unknown. The current study aimed to address this issue by checking SIRT1 expression in noncancerous cerebellar tissues, medulloblastoma tissues and established cell lines. The roles of SIRT1 in proliferation and survival of UW228‐3 medulloblastoma cells were analyzed by SIRT1 small interfering RNA (siRNA) transfection and SIRT1 inhibitor nicotinamide treatment. The results revealed that the frequency of SIRT1 expression in medulloblastoma tissues was 64.17% (77/120), while only one out of seven tumor‐surrounding noncancerous cerebellar tissues showed restricted SIRT1 expression in the cells within the granule layer. Of the three morphological subtypes, the rates of SIRT1 detection in the large cell/anaplastic cell (79.07%; 34/43) and the classic medulloblastomas (60.29%; 41/68) are higher than that (22.22%; 2/9) in nodular/desmoplastic medulloblastomas (P < 0.01 and P < 0.05, respectively). Heterogeneous SIRT1 expression was commonly observed in classic medulloblastoma. Inhibition of SIRT1 expression by siRNA arrested 64.96% of UW228‐3 medulloblastoma cells in the gap 1 (G1) phase and induced 14.53% of cells to apoptosis at the 48‐h time point. Similarly, inhibition of SIRT1 enzymatic activity with nicotinamide brought about G1 arrest and apoptosis in a dose‐related fashion. Our data thus indicate: (i) that SIRT1 may act as a G1‐phase promoter and a survival factor in medulloblastoma cells; and (ii) that SIRT1 expression is correlated with the formation and prognosis of human medulloblastomas. In this context, SIRT1 would be a potential therapeutic target of medulloblastomas.
A CRIANÇA NA LÍNGUA. ERROS DE GÊNERO COMO MARCAS DE SUBJETIVAÇÃO

Cet article a pour but rendre hommage a Claudia Lemos, qui depuis mon doctorat dont elle a ete le directeur de recherche, m’a ouvert les chemins que j’ai parcourus pendant 25 ans, dans le Projeto de Aquisicao da Linguagem. Il s’agit de presenter sous le titre “l’Enfant dans la Langue” quelques aspects de l’etude du genre. Comme la plupart de nos publications, nous mettons en valeur un decoupage methodologique qui choisit la “faute” et non pas le “correct” comme la donnee de l’election. Dans cette etude nous analysons un fait particulier de l’acquisition du portugais, par lequel l’enfant refuse une forme linguistique, en la remplacant par une autre flexion de genre pour la faire conformer au sexe de l’entite qui est nommee. Notre objet est envisage en deux axes: sur le plan de la langue (les formes par lesquelles le genre se realise) et sur le plan du discours (le fonctionnement discursif auquel il se prete). Dans le cas des reprises, il s’agit de repondre a des questions telles que: quand peut-on entrevoir des situations ou l’enfant se tourne vers l’enonce precedent, en produisant une modification qui affecte le genre du mot? Qu’est-ce que cela represente en termes du rapport de l’enfant avec la langue? La description, a partir de la notion d’autonymie (Rey-Debove 1997, Authier- Revuz 1995) fera apparaitre un changement de position du sujet (De Lemos 1997). Les donnees montrent que les petits – âges de 2 a 5 ans – s’engagent dans un processus de subjectivation, manifeste par des alterations morphologiques non-usuelles, portant sur des mots qui les concernet, soit en tant que filles, soit en tant que garcons.