Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunostimulatory sequences regulate interferon-inducible genes but not allergic airway responses.

RATIONALE 1018 ISS is a synthetic oligonucleotide containing immunostimulatory CpG motifs. In animal studies, 1018 ISS effectively inhibited Th2-mediated lung inflammation, including eosinophil infiltration, and airway hyperresponsiveness. OBJECTIVES To evaluate whether 1018 ISS has activity in subjects with allergic asthma. METHODS Forty subjects (n = 21, 1018 ISS; n = 19, placebo) were enrolled in a randomized, double-blind, placebo-controlled, parallel-group study to examine safety, pharmacologic activity, and efficacy of 1018 ISS on allergen-induced airway responses. Subjects received 36 mg of 1018 ISS or placebo by nebulization weekly for 4 wk. MEASUREMENTS Allergen inhalation challenge was performed 24 h after the 2nd and 4th doses to measure the early and late fall in FEV(1). Sputum cells and peripheral blood mononuclear cells were collected before and after dosing, and gene expression was measured by quantitative polymerase chain reaction. MAIN RESULTS Treatment with 1018 ISS significantly increased expression of interferon (IFN)-gamma and IFN-inducible genes, such as IFN-gamma-inducible 10 kD protein (IP10), monokine induced by IFN-gamma (MIG), IFN-stimulated gene (ISG)-54, monocyte chemotactic protein (MCP)-1, and MCP-2 from cells collected postdose (p < 0.05). There was no attenuation of the early or late decrease in FEV(1) after 1018 ISS compared with placebo, nor a reduction in allergen-induced sputum eosinophils or Th2-related gene expression measured in sputum cells. CONCLUSIONS This study demonstrated that 1018 ISS is safe and pharmacologically active in the respiratory tract of asthmatics but, at this dose regimen, did not inhibit a fall in FEV(1) or other key features of the response to inhaled allergen challenge. This suggests that induction of IFN and IFN-inducible genes alone is not sufficient to inhibit allergen-induced responses in asthmatic subjects.
Analysis of the Highly Diverse Gene Borders in Ebola Virus Reveals a Distinct Mechanism of Transcriptional Regulation

ABSTRACT Ebola virus (EBOV) belongs to the group of nonsegmented negative-sense RNA viruses. The seven EBOV genes are separated by variable gene borders, including short (4- or 5-nucleotide) intergenic regions (IRs), a single long (144-nucleotide) IR, and gene overlaps, where the neighboring gene end and start signals share five conserved nucleotides. The unique structure of the gene overlaps and the presence of a single long IR are conserved among all filoviruses. Here, we sought to determine the impact of the EBOV gene borders during viral transcription. We show that readthrough mRNA synthesis occurs in EBOV-infected cells irrespective of the structure of the gene border, indicating that the gene overlaps do not promote recognition of the gene end signal. However, two consecutive gene end signals at the VP24 gene might improve termination at the VP24-L gene border, ensuring efficient L gene expression. We further demonstrate that the long IR is not essential for but regulates transcription reinitiation in a length-dependent but sequence-independent manner. Mutational analysis of bicistronic minigenomes and recombinant EBOVs showed no direct correlation between IR length and reinitiation rates but demonstrated that specific IR lengths not found naturally in filoviruses profoundly inhibit downstream gene expression. Intriguingly, although truncation of the 144-nucleotide-long IR to 5 nucleotides did not substantially affect EBOV transcription, it led to a significant reduction of viral growth. IMPORTANCE Our current understanding of EBOV transcription regulation is limited due to the requirement for high-containment conditions to study this highly pathogenic virus. EBOV is thought to share many mechanistic features with well-analyzed prototype nonsegmented negative-sense RNA viruses. A single polymerase entry site at the 3′ end of the genome determines that transcription of the genes is mainly controlled by gene order and cis-acting signals found at the gene borders. Here, we examined the regulatory role of the structurally unique EBOV gene borders during viral transcription. Our data suggest that transcriptional regulation in EBOV is highly complex and differs from that in prototype viruses and further the understanding of this most fundamental process in the filovirus replication cycle. Moreover, our results with recombinant EBOVs suggest a novel role of the long IR found in all filovirus genomes during the viral replication cycle.
Bibliometrics/Citation networks

In addition to shaping social networks, for example, in terms of co-authorship relations, scientific communications induce and reproduce cognitive structures. Scientific literature is intellectually organized in terms of disciplines and specialties; these structures are reproduced and networked reflexively by making references to the authors, concepts and texts embedded in these literatures. The concept of a cognitive structure was introduced in social network analysis (SNA) in 1987 by David Krackhardt, but the focus in SNA has hitherto been on cognition as a psychological attribute of human agency. In bibliometrics, and in science and technology studies (STS) more generally, socio-cognitive structures refer to intellectual organization at the supra-individual level. This intellectual organization emerges and is reproduced by the collectives of authors who are organized not only in terms of inter-personal relations, but also more abstractly in terms of codes of communication that are field-specific. Citations can serve as indicators of this codification process.
Assessing the likelihood of severe side effects in radiotherapy

Ionizing radiation is a powerful tool to treat cancer. The curing effect is mainly based on the efficiency of ionizing radiation to kill the cancer cells and it is believed that DNA double‐strand breaks (DSBs) represent the most significant genetic lesion introduced by radiation that causes cell killing. One limitation in radiotherapy is the unavoidable damage delivered to the normal, noncancer cells that can give rise to side effects. The ultimate goal in treatment planning is to maximize cell killing in the tumor by minimizing damage induction in the normal tissue surrounding the tumor. The biological response to the induction of DSBs is largely affected by DSB repair processes and it has, therefore, been a long‐standing goal to determine a patient's DSB repair capacity to “individualize” treatment planning. A recently developed DSB repair assay that allows the assessment of patients' repair capacity under in vivo conditions may provide a new approach to predict individuals' responses to radiotherapy and may be able to contribute to improvements in treatment planning. © 2006 Wiley‐Liss, Inc.
Identification of a Photosystem II Phosphatase Involved in Light Acclimation in Arabidopsis[W]

Thylakoid protein phosphorylation plays a central role in the dynamic acclimation of the photosynthetic electron transfer chain to changing light conditions. This work identifies a protein phosphatase that is required for dephosphorylation of photosystem II subunits and counteracts the activity of the protein kinase STN8. Reversible protein phosphorylation plays a major role in the acclimation of the photosynthetic apparatus to changes in light. Two paralogous kinases phosphorylate subsets of thylakoid membrane proteins. STATE TRANSITION7 (STN7) phosphorylates LHCII, the light-harvesting antenna of photosystem II (PSII), to balance the activity of the two photosystems through state transitions. STN8, which is mainly involved in phosphorylation of PSII core subunits, influences folding of the thylakoid membranes and repair of PSII after photodamage. The rapid reversibility of these acclimatory responses requires the action of protein phosphatases. In a reverse genetic screen, we identified the chloroplast PP2C phosphatase, PHOTOSYSTEM II CORE PHOSPHATASE (PBCP), which is required for efficient dephosphorylation of PSII proteins. Its targets, identified by immunoblotting and mass spectrometry, largely coincide with those of the kinase STN8. The recombinant phosphatase is active in vitro on a synthetic substrate or on isolated thylakoids. Thylakoid folding is affected in the absence of PBCP, while its overexpression alters the kinetics of state transitions. PBCP and STN8 form an antagonistic kinase and phosphatase pair whose substrate specificity and physiological functions are distinct from those of STN7 and the counteracting phosphatase PROTEIN PHOSPHATASE1/THYLAKOID-ASSOCIATED PHOSPHATASE38, but their activities may overlap to some degree.
Quantitative assessment on coronary computed tomography angiography (CCTA) image quality: comparisons between genders and different tube voltage settings.

BACKGROUND This study was carried out to quantify and compare the quantitative image quality of coronary computed tomography angiography (CCTA) between genders as well as between different tube voltages scan protocols. METHODS Fifty-five cases of CCTA were collected retrospectively and all images including reformatted axial images at systolic and diastolic phases as well as images with curved multi planar reformation (cMPR) were obtained. Quantitative image quality including signal intensity, image noise, signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) of right coronary artery (RCA), left anterior descending artery (LAD), left circumflex artery (LCx) and left main artery (LM) were quantified using Analyze 12.0 software. RESULTS Six hundred and fifty-seven coronary arteries were evaluated. There were no significant differences in any quantitative image quality parameters between genders. 100 kilovoltage peak (kVp) scanning protocol produced images with significantly higher signal intensity compared to 120 kVp scanning protocol (P<0.001) in all coronary arteries in all types of images. Higher SNR was also observed in 100 kVp scan protocol in all coronary arteries except in LCx where 120 kVp showed better SNR than 100 kVp. CONCLUSIONS There were no significant differences in image quality of CCTA between genders and different tube voltages. Lower tube voltage (100 kVp) scanning protocol is recommended in clinical practice to reduce the radiation dose to patient.
An Event-Based Abductive Model of Update

The Katsuno and Mendelzon theory of belief update has been proposed as a reasonable model for revising beliefs about a changing world. However, the semantics of update relies on information which is not readily available. We describe an alternative semantical view of update in which observations are incorporated into a belief set by: a) explaining the observation in terms of a set of plausible events that might have caused that observation; and b) predicting further consequences of those explanations. We also allow the possibility of conditional explanations. We show that this picture naturally induces an update operator under certain assumptions. However, we argue that these assumptions are not always reasonable, and they restrict our ability to integrate update with other forms of revision when reasoning about action.
Analysis of Direct Shipping Policies in an Inventory-Routing Problem with Discrete Shipping Times

We consider the problem in which several products have to be shipped from a supplier to a set of retailers over an infinite time horizon. Each product is made available at the supplier and absorbed by each retailer at given constant production and consumption rates. For each product, the unit inventory cost at the supplier is equal to the unit inventory cost at the retailers. Shipments can be performed in each discrete time instant by a fleet of vehicles of given transportation capacity, and routing is allowed. The aim is to determine shipping policies that minimize the sum of transportation cost and inventory cost both at the supplier and at the retailers. We study direct shipping policies, i.e., policies in which each retailer is served independently. We show the worst-case performance of the best single, best double, best triple, best frequency-based, and optimal direct shipping policies. In each of these policies each link is optimized independently. We prove that, in the worst case, the ratio between the cost of the optimal direct shipping policy and the optimal cost of the problem in which routing is allowed---i.e., the worst-case performance bound of this policy---is not greater than two whenever the unit volume on each link is not lower than 1/4 of the vehicle capacity. Moreover, if the unit volume is not lower than the capacity, the bound is about 1.21. These bounds are tight and obtained by applying frequency-based policies that make use of at most three different shipping frequencies and cannot be improved by allowing more frequencies or using time-based policies on each link. Computational results show that the best among the frequency-based direct shipping policies used to obtain the worst-case results gives an average percent increase error, with respect to a lower bound on the optimal cost of the problem in which routing is allowed, of 6.44% on a large set of randomly generated problem instances.
Non‐immune chronic idiopathic neutropenia of adult: an overview

Abstract: There is strong evidence that non‐immune chronic idiopathic neutropenia of adult is a cytokine‐mediated syndrome characterized by (a) neutropenia of varying degree associated with a low number of lineage‐specific CD34+ cells and increased production of inhibitors of hematopoiesis, including transforming growth factor‐β1 and tumor necrosis factor‐α; (b) lymphopenia due to selective loss of primed/memory T‐cells and NK cells; (c) increased splenic volume on ultrasonography in 48.1% of patients; (d) osteopenia and/or osteoporosis in 60.0% of patients; (e) anemia, mostly of the type of anemia of chronic disease, in 15.6% of patients; (f) features of chronic antigenic stimulation, including increased proportion of bone marrow plasma cells, increased serum levels of IgG1 and/or IgA, increased frequency of monoclonal gammopathy of undetermined significance, increased frequency of antinuclear antibodies with specific reactivity, and increased serum levels of circulating immune complexes; and (g) increased concentrations of a variety of macrophage‐derived pro‐inflammatory cytokines and chemokines capable of affecting bone metabolism, bone marrow function, and leukocyte trafficking. All these findings are suggestive of the existence of an unrecognized low‐grade chronic inflammatory process which may be involved in the pathogenesis of the disorder. Neutropenia in these patients is probably the result of a combination of at least three factors, reduced neutrophil production in bone marrow, enhanced neutrophil extravasation, and increased sequestration and/or extravasation of neutrophils into the spleen.
Lara, Silvia Hunold, and Joseli Maria Nunes Mendonça, eds. Direitos e justiças no Brasil: Ensaios de história social. São Paulo: Editora da UNICAMP, 2006. Notes. 543 pp.

Este livro é uma introdução ao pensamento de Vilém Flusser (1920–1991), um fi lósofo de grande originalidade e, de certo modo, profético. Analisando a superação de espaço e tempo, agora uma possibilidade aberta pela internet e pela relação intrínseca entre homem e máquina, Flusser reconhece novas categorias de experiências, de observação e análise, de conhecimento e de comunicação e, consequentemente, uma nova concepção de ser. Os autores vêm de diferentes países. Gustavo Bernardo é professor da Universidade Estadual do Rio de Janeiro, Rainer Guldin é professor da Università della Svizzera Italiana, em Lugano, e Arne Finger é professora da University of Connecticut. Guldin e Finger editam o jornal virtual Flusser Studies www . fl usserstudies.net, uma referência básica sobre o pensamento e a obra de Vilém Flusser. O livro tem uma organização amigável para o leitor. A Introdução, escrita por Gustavo Bernardo, dá detalhes de como ele foi concebido e realizado. Nela é insinuado que antecipa uma desejada publicação das obras completas de Vilém Fusser. Seguem-se seis capítulos, uma bibliografi a (de obras de Flusser, de obras sobre Flusser e de obras de apoio) e fotos de Flusser e família e dos autores. Vilém Flusser viveu a maior e mais importante parte de sua vida no Brasil. Nasceu em Praga em 12 de maio de 1920, de uma família judia, com apreciável nível intelectual. Em 1939 emigrou para Londres e logo todos decidiram emigrar para o Brasil. Passaram a viver em São Paulo, onde Flusser associou-se ao emergente Instituto Brasileiro de Filosofi a, fundado por Miguel Reale, e passou a publicar na Revista Brasileira de Filosofi a e no prestigioso Suplemento Literário do jornal O Estado de São Paulo. Em 1972 os Flusser mudaram-se para a França. Vilém morreu em 27 de novembro de 1991, em um acidente de automóvel, retornando de uma conferência em sua cidade natal. Seu ensaio autobiográfi co, Bodenlos. Uma autobiografi a fi losófi ca (publicada em 1992, em alemão), revela uma forma de nomadismo. A palavra bodenlos tem um signifi cado amplo em alemão: sem chão, sem terra, sem fundamento. Flusser não só rejeita o topocentrismo, mas igualmente a subordinação a uma língua materna. Seus escritos são em alemão, português, inglês e francês. Interpreto sua concepção de
Multi-element analysis of airborne particulate matter from different work tasks during subsea tunnel rehabilitation work

ABSTRACT Tunnel rehabilitation work involves exposure to various air contaminants, including airborne particulate matter (APM). Little is known on the contents of different chemical components of APM generated during tunnel work. The objective of the present study was to characterize exposure to APM and various elements for different job categories in different size fractions of APM during a subsea tunnel rehabilitation project carried out in Western Norway. Personal as well as stationary samples of inhalable, thoracic and respirable dust were collected from workers divided into 11 different job categories based on work operations performed, and air concentrations of a range of elements were determined using high-resolution inductively coupled plasma-mass spectrometry (HR-ICP-MS). Overall, APM concentrations were low, but with some measurements exceeding the American Conference of Governmental Industrial Hygienists (ACGIH) Threshold Limit Value (TLV) for inhalable particles, and considerable proportions of respirable and especially inhalable APM exceeding 10% of the TLVs. For most elements, air concentrations measured were quite low, in the ng/m3 range, except for the major crustal elements Si, Fe, Al, and Mg, which were found to be in the µg/m3 range. Asphalt millers overall had the highest exposure levels for APM and most measured elements; for instance, mean concentrations of V, Rb, and Mn were 380, 210, and 2000 ng/m3 in inhalable and 33, 44, and 310 ng/m3 in respirable APM. Mounting PVC membrane seemed to generate elevated levels of Cr, Zn, Sn, Pb, Sb, As, Mn, Fe, and Ni, whereas typical bedrock elements were elevated during drilling activities compared to the low exposed categories lead car drivers, foremen/surveyors, drivers of heavy-duty vehicles, and electricians. Overall, stationary samples contained lower amounts of dust and elemental constituents compared to personal samples. Elemental air concentrations were highly variable with occasional elevated values for APM and certain elements, particularly Cr and Zn.
How Exemplary Computer-Using Teachers Differ From Other Teachers: Implications for Realizing the Po

AbstractUsing national survey data from 3rd- through 12th-grade teachers of academic subjects, 45 teachers out of 516 were identified as being exemplary computer-using teachers. Four factors in the teaching environment made exemplary computer users more likely to be present: collegiality among users, school support for using computers for consequential activities, resources allocated to staff development and computer coordination, and smaller class sizes. Also found were certain factors in teachers’ backgrounds that were related to the probability of their being designated as exemplary users (e.g., if they were liberal arts majors rather than education majors) and showed that only among exemplary users were major changes in content coverage accomplished. The presence of exemplary users in a school did not result in fewer problems for administrators—just different ones. Contrary to expectations, exemplary teachers were not overrepresented in high socioeconomic communities, nor did they disproportionately t.
Mode-Locked Fibre Lasers with High-Energy Pulses

The recent explosive development of the physics and technology of fibre lasers as well as a vast expansion of their application areas greatly stimulate the quest for and the study of more advanced operational modes of such lasers, including generation of ultra-short and high-energy pulses. Since the invention of the laser researchers have continuously strived to generate shorter laser pulses. Simultaneously achieving a short duration and a high pulse energy is certainly more challenging than improving one of these parameters independently. However, it is this combination that becomes increasingly important in a wide range of scientific, technological, medical, and other applications. High energies and ultra-short pulse durations are both associated with high field intensity that often makes physical system non-linear. In fibre lasers, there are specific properties relevant to both shortening of the pulse duration and increasing their energy. The main obstacles on the road to shorter pulses are a relatively high dispersion and non-linearity of fibre resonators. In addition, the path to high-energy ultra-short pulses is, typically, further complicated by relatively low energy damage thresholds of standard fibre components, such as splitters, isolators, and so forth. While the effects of dispersion can be compensated by different rather advanced means, the nonlinear effects in fibres are much more difficult to manage. Thus, nonlinearity plays a critical role in the design of advanced fibre laser systems, but paradoxically, it is somewhat undesirable to many engineers because of its very limited controllability. Substantial efforts have been made to reduce the resonator nonlinearity, e.g. by using large-mode-area fibres, and this direction presents an important modern trend in laser technology. On the other hand, understanding and mastering nonlinear physical fibre systems offer the potential to enable a new generation of laser concepts. Therefore, it is of great importance to study physics and engineering design of laser systems based on nonlinear photonic technologies. In particular, new nonlinear approaches and solutions pave a way for development of advanced mode-locked fibre lasers with ultra-short high-energy pulses. Presently, passive mode locking is one of the key methods of ultra-short pulse (USP) generation. As recently as a few years ago, femtoand pico-second pulses extracted directly from the master oscillator operating in a passive mode-locking regime had relatively low energies, typically, not exceeding at few dozens of nJ and, in some special cases, hundreds