Miracle-dz/UniFAR-FTUs huggingface dataset:
First isolation of Mimivirus in a patient with pneumonia.

BACKGROUND Mimiviridae Mimivirus, including the largest known viruses, multiply in amoebae. Mimiviruses have been linked to pneumonia, but they have never been isolated from patients. To further understand the pathogenic role of these viruses, we aimed to isolate them from a patient presenting with pneumonia. METHODS We cultured, on Acanthamoeba polyphaga amoebae, pulmonary samples from 196 Tunisian patients with community-acquired pneumonia during the period 2009-2010. An improved technique was used for Mimivirus isolation, which used agar plates where the growth of giant viruses is revealed by the formation of lysis plaques. Mimivirus serology was tested by microimmunofluorescence and by bidimensional immunoproteomic analysis using Mimivirus strains, to identify specific immunoreactive proteins. The new Mimivirus strain genome sequencing was performed on Roche 454 GS FLX Titanium, then AB SOLiD instruments. RESULTS We successfully isolated a Mimivirus (LBA111), the largest virus ever isolated in a human sample, from a 72-year-old woman presenting with pneumonia. Electron microscopy revealed a Mimivirus-like virion with a size of 554 ± 10 nm. The LBA111 genome is 1.23 megabases, and it is closely related to that of Megavirus chilensis. Furthermore, the serum from the patient reacted specifically to the virus compared to controls. CONCLUSIONS This is the first Mimivirus isolated from a human specimen. The findings presented above together with previous works establish that mimiviruses can be associated with pneumonia. The common occurrence of these viruses in water and soil makes them probable global agents that are worthy of investigation.
The effects of framing of charitable solicitations on moral judgment

We study how the framing of the charitable “ask” affects moral judgment and thus how much to donate and to whom. We develop a theoretical framework grounded in insights developed by Adam Smith in his Theory of Moral Sentiments (1759) and psychological construal level theory. The framework rests on the effects of variations in the salience of donors’ financial interest and in their distance/detachment from the targets of their generosity. We hypothesize that (1) increasing the salience of donors’ self-interest will act like an increase in the price of giving, and (2) increasing the distance or detachment of the donor from the charitable targets induces substitution in giving towards the poor and the needy, away from cultural and other ordinary purposes. We design four modified dictator game experiments with seven local charitable organizations. In a conventional model an individual will make equivalent choices of donations, but if moral judgment is activated by framing, the choices will differ. In an experiment with a mixed withinand between-subjects design with 157 participants, we find empirical support for our hypotheses. Professor, Carlson School of Management, University of Minnesota, benne001@umn.edu Ph.D. Candidate, Economics Department, University of Minnesota, leung085@umn.edu Graduate Student, Psychology Department, New York University, xx619@nyu.edu
Phenotypic analysis of T lymphocytes isolated from non-small-cell lung cancer.

BACKGROUND The study of the nature of tumor-infiltrating lymphocytes (TIL) may provide insight into the complex issue of tumor-host interactions. METHODS Cytofluorometric analysis was performed to characterize the phenotypic profiles of TIL from non-small-cell lung cancers (NSCLC) and pulmonal metastases of different primary locations. An extensive panel of antibodies was used specific to different activation-associated molecules on T cells. In 10 patients, findings on the T cell phenotype of TIL were compared with the findings in peripheral blood lymphocytes (PBL) from the same patients. Furthermore, we investigated whether the measurement of the TIL phenotype might serve as a prognostic parameter correlating with survival of patients with NSCLC. RESULTS In contrast to PBL, T cells infiltrating lung tumors expressed significantly higher amounts of various activation antigens. However, the immunophenotype of TIL hardly differed among different histological subtypes and pulmonal metastases. Addressing the prognostic value of the lymphocytic composition of TIL, we found no significant difference in the survival of NSCLC with high or low percentages of T and natural killer cells, whereas high percentages of B cells were associated with increased survival (p = 0.05). Patients with high percentages of CD13+ tumor-infiltrating T cells had significantly poorer prognosis according to Cox's multivariate analysis. CONCLUSION Our results indicate that different tumor histologies within the lung are characterized by a 'similar' T cell phenotype, at least with respect to the surface molecules studied by us. The measurement of the expression of activation-associated markers on T cells may have prognostic value in the pathological evaluation of NSCLC.
An Arf6- and caveolae-dependent pathway links hemidesmosome remodeling and mechanoresponse

Hemidesmosomes (HDs) are epithelial-specific cell-matrix adhesions, which stably anchor the intracellular keratin network to the extracellular matrix. Although their main role is to protect the epithelial sheet from external mechanical strain, how HDs respond to mechanical stress remains poorly understood. Here we identify a pathway essential for HD remodeling, and outline its role with respect to α6β4 integrin recycling. We find that α6β4 integrin chains localize to the plasma membrane/caveolae and Arf6+ endocytic compartments. Based on FRAP and endocytosis assays, integrin recycling between both sites requires the small GTPase Arf6 and its co-regulators GIT1/βPIX, but neither Caveolin1 (Cav1) nor Cavin1. Strikingly, when keratinocytes are stretched or hypo-osmotically shocked, α6β4 integrin accumulates at cell edges, whereas Cav1 disappears from it. This process, which is isotropic relative to the orientation of stretch, depends on Arf6, Cav1 and Cavin1. We propose that mechanically-induced HD growth involves the isotropic flattening of caveolae (known for their mechanical buffering role) associated with integrin diffusion and turnover.
Search performance is better predicted by tileability than presence of a unique basic feature

Traditional models of visual search such as feature integration theory (FIT; Treisman & Gelade, 1980), have suggested that a key factor determining task difficulty consists of whether or not the search target contains a “basic feature” not found in the other display items (distractors). Here we discriminate between such traditional models and our recent texture tiling model (TTM) of search (Rosenholtz, Huang, Raj, Balas, & Ilie, 2012b), by designing new experiments that directly pit these models against each other. Doing so is nontrivial, for two reasons. First, the visual representation in TTM is fully specified, and makes clear testable predictions, but its complexity makes getting intuitions difficult. Here we elucidate a rule of thumb for TTM, which enables us to easily design new and interesting search experiments. FIT, on the other hand, is somewhat ill-defined and hard to pin down. To get around this, rather than designing totally new search experiments, we start with five classic experiments that FIT already claims to explain: T among Ls, 2 among 5s, Q among Os, O among Qs, and an orientation/luminance-contrast conjunction search. We find that fairly subtle changes in these search tasks lead to significant changes in performance, in a direction predicted by TTM, providing definitive evidence in favor of the texture tiling model as opposed to traditional views of search.
Left ventricular global longitudinal strain in patients with heart failure with preserved ejection fraction: outcomes following an acute heart failure hospitalization

While abnormal resting LV GLS has been described in patients with chronic heart failure with preserved ejection fraction (HFpEF), its prognostic significance when measured during an acute heart failure hospitalization remains unclear. We assessed the association between left ventricular global longitudinal strain (LV GLS) and outcomes in patients hospitalized with acute HFpEF.
Tracking Virus-Specific CD4+ T Cells during and after Acute Hepatitis C Virus Infection

Background CD4+ T cell help is critical in maintaining antiviral immune responses and such help has been shown to be sustained in acute resolving hepatitis C. In contrast, in evolving chronic hepatitis C CD4+ T cell helper responses appear to be absent or short-lived, using functional assays. Methodology/Principal Findings Here we used a novel HLA-DR1 tetramer containing a highly targeted CD4+ T cell epitope from the hepatitis C virus non-structural protein 4 to track number and phenotype of hepatitis C virus specific CD4+ T cells in a cohort of seven HLA-DR1 positive patients with acute hepatitis C in comparison to patients with chronic or resolved hepatitis C. We observed peptide-specific T cells in all seven patients with acute hepatitis C regardless of outcome at frequencies up to 0.65% of CD4+ T cells. Among patients who transiently controlled virus replication we observed loss of function, and/or physical deletion of tetramer+ CD4+ T cells before viral recrudescence. In some patients with chronic hepatitis C very low numbers of tetramer+ cells were detectable in peripheral blood, compared to robust responses detected in spontaneous resolvers. Importantly we did not observe escape mutations in this key CD4+ T cell epitope in patients with evolving chronic hepatitis C. Conclusions/Significance During acute hepatitis C a CD4+ T cell response against this epitope is readily induced in most, if not all, HLA-DR1+ patients. This antiviral T cell population becomes functionally impaired or is deleted early in the course of disease in those where viremia persists.
Direct international normalized ratio determination using multicalibrators is more responsive than the conventional method for measuring prothrombin time

Direct international normalized ratio (INR) determination using certified INR plasmas was shown to improve precision and accuracy. We evaluated the utility of a multicalibrator in determining INR. INR values were measured in 493 blood samples from patients subjected to anticoagulation therapy (320) and control subjects (173). Study was performed using CA‐7000 coagulation analyzer (Sysmex, Japan) with Thromborel S (Dade Behring, Germany). Direct INR values were obtained using PT‐Multi Calibrator (Dade Behring) composed of five lyophilized calibrant plasmas. Conventional INR values were calculated from mean normal prothrombin time and instrument/reagent‐specific international sensitivity index (ISI). We compared the difference between the INR results obtained with the two methods. The mean INR value of direct INR method was significantly higher than that of conventional method. The differences in values (direct INR – conventional INR) generated using the two methods increased in proportion to the INR values. Elevation of INR was observed in data obtained with the direct INR method, compared with conventional INR values. Accordingly, we conclude that direct INR method is more responsive than conventional method in determining INR.
The Novel Evolution of the Sperm Whale Genome

Abstract The sperm whale, made famous by Moby Dick, is one of the most fascinating of all ocean-dwelling species given their unique life history, novel physiological adaptations to hunting squid at extreme ocean depths, and their position as one of the earliest branching toothed whales (Odontoceti). We assembled the sperm whale (Physeter macrocephalus) genome and resequenced individuals from multiple ocean basins to identify new candidate genes for adaptation to an aquatic environment and infer demographic history. Genes crucial for skin integrity appeared to be particularly important in both the sperm whale and other cetaceans. We also find sperm whales experienced a steep population decline during the early Pleistocene epoch. These genomic data add new comparative insight into the evolution of whales.
Textural and sensorial properties of cookies prepared by partial substitution of wheat flour with unripe banana (Musa x paradisiaca var. Tanduk and Musa acuminata var. Emas) flour

The textural and sensorial properties of the cookies prepared by partial substitution of wheat flour with two types of unripe banana flour (UBF) were studied. The green matured unripe banana (Musa x paradisiaca var. Tanduk and Musa acuminata var. Emas) was used to partially substitute the usage of wheat flour at 0% (control), 25% and 50% level in the formulated plain cookies. Textural (hardness) and sensorial properties were conducted on all samples. Substitution of UBF to formulation of cookies had increased the hardness of cookies (ranging from 967 N to 1665 N) compared to the control except for substitution of Emas banana flour (EBF) at 50% which was not significantly difference (p > 0.05) with control sample. The substitution of 25% of Tanduk banana flour (TBF) showed the highest mean score in overall acceptability (6.81 ± 1.18) compared to all treated samples. TBF substitution is feasible up to 50% substitution while for EBF, the substitution only up to 25% level in this study.
Laser material processing

Abstract Light amplification by stimulated emission of radiation (laser) is a coherent and monochromatic source of electromagnetic radiation that can propagate in a straight line with negligible divergence. As a result, laser finds diverse applications ranging from mere mundane to most sophisticated uses either for totally commercial or purely scientific purposes, and from life saving to life threatening causes. High power lasers can produce intense heating and perform various manufacturing operations or material processing. The present contribution provides an overview of the application of high power laser only for material processing in engineering applications, and intentionally excludes the scope of application of laser in metrology, biomedical technology, spectroscopy, etc. The manufacturing processes covered have been broadly divided into four major categories, namely, laser assisted forming, joining, machining and surface engineering. Besides discussing the scope and principle of these processes, each section enumerates a detailed update of literature, scientific issues and technological innovations. At the beginning, a brief introduction to different types of lasers and their general applications, fundamentals of laser–matter interaction and classification of laser material processing has been provided. The entire discussion primarily focuses on correlating the properties with processing parameters and microstructure and composition of the material.
Firms and the Global Crisis: French Exports in the Turmoil

Global trade contracted quickly and severely during the global crisis. This paper uses a unique dataset of French firms to match export data to firm-level credit constraints and shows that most of the 2008-2009 trade collapse was due to the unprecedented demand shock and to product characteristics. While all firms have been affected by the crisis, the effect on large firms has been mainly at the intensive margin and has resulted in a smaller portfolio of products being offered to export destinations. The effect on smaller exporters has been to reduce the range of destinations served or to stop exporting altogether. Credit constraints have been an added aggravation for firms active in high financial dependence sectors. However, the share of credit constrained firms is small and their number has not increased hugely during the crisis, with the result that the overall impact of credit constraints on trade has been limited.
Which Institutional Investors Trade Based on Private Information About Earnings and Returns?

Recent work suggests that institutional investors execute profitable trades based on private information about earnings and returns. We provide new evidence on the prevalence and sources of such informed trading by (1) testing for the creation and liquidation of positions based on private information, (2) introducing private information proxies that reflect the size and nature of an institution's position in each portfolio firm, and (3) using a methodology that examines multiple investor characteristics simultaneously at the institution-firm level. We find that changes in ownership by institutions with large positions in a firm are consistent with informed trading. However, other previously documented proxies for private information produce results more consistent with risk-based trading (e.g., investment style) or insignificant in the presence of other proxies (e.g., fiduciary type). We also find that informed trading is more prevalent in small firms and when the large positions are taken by investment advisers and large institutions.
Solubility phenomena related to normal and pathological biomineralization processes

Biomineralization, which refers to the complex processes by which organisms form minerals, is frequently associated with a high degree of regulation on different hierarchical levels [1,2]. ‘Biologically controlled’ mineralization, in which extra-, inter- and intracellular activities direct the nucleation, growth and morphology of minerals that form ‘normal’ biomaterials such as bone and teeth [1,2], is fundamentally different from ‘biologically induced’ mineralization, which occurs as a result of interactions between biological activity (affecting e.g. the pH and composition of secretion products) and the environment [1,2]. Since there is little control of the biological system over the type and habit of minerals deposited, these vary as greatly as the environments in which they form and are often poorly defined, heterogeneous and porous [1,2]. Biologically induced mineralization is commonly associated with various bacterial activities and with epicellular mineralization in marine environments, occasionally leading to the complete encrustation of organisms, that sink subsequently and form sediments [1,2]. However, its characteristic features are also typical for uncontrolled ‘pathological’ crystallization resulting in painful or even life threatening conditions such as calculi formation (renal, biliary, pancreatic or sublingual), development of gout or arteriosclerosis, tissue calcification associated with cancer, etc.
TX Task: Automatic Detection of Focus Organisms in Biomedical Publications

In biomedical information extraction (IE), a central problem is the disambiguation of ambiguous names for domain specific entities, such as proteins, genes, etc. One important dimension of ambiguity is the organism to which the entities belong: in order to disambiguate an ambiguous entity name (e.g. a protein), it is often necessary to identify the specific organism to which it refers. In this paper we present an approach to the detection and disambiguation of the focus organism(s), i.e. the organism(s) which are the subject of the research described in scientific papers, which can then be used for the disambiguation of other entities. The results are evaluated against a gold standard derived from IntAct annotations. The evaluation suggests that the results may already be useful within a curation environment and are certainly a baseline for more complex approaches.
THE EFFECT OF WATER-SOLUBLE POLYMERS ON THE MICROSTRUCTURE AND PROPERTIES OF FREEZE-CAST ALUMINA CERAMICS

Porous ceramics can be divided into three separate classes based on their pore size: microporous ceramics with pores less than 2 nm, mesoporous ceramics with pores in the range of 2-50 nm and macroporous ceramics with pores that are greater than 50 nm. In particular, macroporous ceramics are used in a variety of applications such as refractories, molten metal filtration, diesel particulate filters, heterogeneous catalyst supports and biomedical scaffolds.Freeze casting is a novel method used to create macroporous ceramics. In this method growing ice crystals act as a template for the pores and are solidified, often directionally, through a ceramic dispersion and removed from the green body through a freeze drying procedure. This method has attracted some attention over the past few years due to its relative simplicity, flexibility and environmental friendliness. On top of this freeze casting is capable of producing materials with high pore volume fractions, which is an advantage over processing by packing and necking of particles, where the pore volume fraction is typically less than 50%. Many of the basic processing variables that affect the freeze cast microstructure, such as the temperature gradient, interfacial velocity and solid loading of the dispersion have been well established in the literature. On the other hand, areas such as the effect of additives on the microstructure and mechanical properties have not been covered in great detail.In this study the concept of constitutional supercooling from basic solidification theory is used to explain the effects of two water-soluble polymers, polyethylene glycol and polyvinyl alcohol, on the microstructure of freeze cast alumina ceramics. In addition, changes in the observed microstructure will be related to experimentally determined values of permeability and compressive strength.
Comparison between resting state fMRI networks and responsive cortical stimulations in glioma patients

To validate the functional relevance of resting state networks (RSNs) by means of a comparison of resting state connectivity (RSC) between language regions elicited by direct cortical stimulation versus RSC between random regions; and to evaluate the accuracy of resting state fMRI in surgical planning by assessing the overlap between RSNs and intraoperative functional mapping results.
Treatment of psoriatic arthritis with traditional DMARD’s and novel therapies: approaches and recommendations

ABSTRACT Introduction: Recent advances in the therapeutics of psoriatic arthritis (PsA) have provided more options to clinicians managing PsA. The purpose of this review is to update the reader on treatment options for PsA using conventional synthetic disease modifying agents (csDMARDs) and novel therapies including tumour necrosis factor alpha inhibitors, interleukin 12/23 inhibitor (ustekinumab), the interleukin 17 antagonists including secukinumab, brodalumab, ixekizumab, and the phosphodiesterase-4 inhibitor, apremilast. Areas covered: We reviewed published articles on the treatment of PsA. Our main sources of data included treatment recommendations, registry studies, systematic literature reviews, major randomised controlled trials for more recently approved drugs, and abstracts from the American College of Rheumatology and EULAR meetings. Expert commentary: An overview of the evidence for the use of various pharmacotherapeutic agents for treatment of this heterogeneous disease was compiled. Treatment options for the various domains of PsA are also discussed.