Miracle-dz/UniFAR-FTUs huggingface dataset:
Norm theory: Comparing reality to its alternatives

A theory of norms and normality is presented and applied to some phenomena of emotional responses, social judgment, and conversations about causes. Norms are assumed to be constructed ad hoc by recruiting specific representations. Category norms are derived by recruiting exemplars. Specific objects or events generate their own norms by retrieval of similar experiences stored in memory or by construction of counterfactual alternatives. The normality of a stimulus is evaluated by comparing it to the norms that it evokes after the fact, rather than to precomputed expectations. Norm theory is applied in analyses of the enhanced emotional response to events that have abnormal causes, of the generation of predictions and inferences from observations of behavior, and of the role of norms in causal questions and answers. This article is concerned with category norms that represent knowledge of concepts and with stimulus norms that govern comparative judgments and designate experiences as surprising. In the tradition of adaptation level theory (Appley, 1971; Helson, 1964), the concept of norm is applied to events that range in complexity from single visual displays to social interactions. We first propose a model of an activation process that produces norms, then explore the role of norms in social cognition. The central idea of the present treatment is that norms are computed after the event rather than in advance. We sketch a supplement to the generally accepted idea that events in the stream of experience are interpreted and evaluated by consulting precomputed schemas and frames of reference. The view developed here is that each stimulus selectively recruits its own alternatives (Garner, 1962, 1970) and is interpreted in a rich context of remembered and constructed representations of what it could have been, might have been, or should have been. Thus, each event brings its own frame of reference into being. We also explore the idea that knowledge of categories (e.g., "encounters with Jim") can be derived on-line by selectively evoking stored representations of discrete episodes and exemplars. The present model assumes that a number of representations can be recruited in parallel, by either a stimulus event or an
Red and Problematic Green Phylogenetic Signals among Thousands of Nuclear Genes from the Photosynthetic and Apicomplexa-Related Chromera velia

The photosynthetic and basal apicomplexan Chromera velia was recently described, expanding the membership of this otherwise nonphotosynthetic group of parasite protists. Apicomplexans are alveolates with secondary plastids of red algal origin, but the evolutionary history of their nuclear genes is still actively discussed. Using deep sequencing of expressed genes, we investigated the phylogenetic affinities of a stringent filtered set of 3,151 expressed sequence tag-contigs by generating clusters with eukaryotic homologs and constructing phylogenetic trees and networks. The phylogenetic positioning of this alveolate alga was determined and sets of phyla-specific proteins extracted. Phylogenetic trees provided conflicting signals, with 444 trees grouping C. velia with the apicomplexans but 354 trees grouping C. velia with the alveolate oyster pathogen Perkinsus marinus, the latter signal being reinforced from the analysis of shared genes and overall sequence similarity. Among the 513 C. velia nuclear genes that reflect a photosynthetic ancestry and for which nuclear homologs were available both from red and green lineages, 263 indicated a red photosynthetic ancestry, whereas 250 indicated a green photosynthetic ancestry. The same 1:1 signal ratio was found among the putative 255 nuclear-encoded plastid proteins identified. This finding of red and green signals for the alveolate mirrors the result observed in the heterokont lineage and supports a common but not necessarily single origin for the plastid in heterokonts and alveolates. The inference of green endosymbiosis preceding red plastid acquisition in these lineages leads to worryingly complicated evolutionary scenarios, prompting the search for other explanations for the green phylogenetic signal and the amount of hosts involved.
Long-Term Asymmetric Hearing Affects Cochlear Implantation Outcomes Differently in Adults with Pre- and Postlingual Hearing Loss

In many countries, a single cochlear implant is offered as a treatment for a bilateral hearing loss. In cases where there is asymmetry in the amount of sound deprivation between the ears, there is a dilemma in choosing which ear should be implanted. In many clinics, the choice of ear has been guided by an assumption that the reorganisation of the auditory pathways caused by longer duration of deafness in one ear is associated with poorer implantation outcomes for that ear. This assumption, however, is mainly derived from studies of early childhood deafness. This study compared outcomes following implantation of the better or poorer ear in cases of long-term hearing asymmetries. Audiological records of 146 adults with bilateral hearing loss using a single hearing aid were reviewed. The unaided ear had 15 to 72 years of unaided severe to profound hearing loss before unilateral cochlear implantation. 98 received the implant in their long-term sound-deprived ear. A multiple regression analysis was conducted to assess the relative contribution of potential predictors to speech recognition performance after implantation. Duration of bilateral significant hearing loss and the presence of a prelingual hearing loss explained the majority of variance in speech recognition performance following cochlear implantation. For participants with postlingual hearing loss, similar outcomes were obtained by implanting either ear. With prelingual hearing loss, poorer outcomes were obtained when implanting the long-term sound-deprived ear, but the duration of the sound deprivation in the implanted ear did not reliably predict outcomes. Contrary to an apparent clinical consensus, duration of sound deprivation in one ear has limited value in predicting speech recognition outcomes of cochlear implantation in that ear. Outcomes of cochlear implantation are more closely related to the period of time for which the brain is deprived of auditory stimulation from both ears.
Montessori's Concept of Personality

Organizing and clarifying Montessori's central concept of personality as the totality of an individual's potentiality, and her concept of character as the healthy organization of personality, this book concludes with a discussion of William Hear Kilpatrick's criticism of the Montessori System and David Norbert Campbell's analysis of that criticism.
A NEAR-INFRARED TRANSMISSION SPECTRUM FOR THE WARM SATURN HAT-P-12b

We present a Hubble Space Telescope Wide Field Camera-3 (WFC3) transmission spectrum for the transiting exoplanet HAT-P-12b. This warm (1000 K) sub-Saturn-mass planet has a smaller mass and a lower temperature than the hot Jupiters that have been studied so far. We find that the planet's measured transmission spectrum lacks the expected water absorption feature for a hydrogen-dominated atmosphere and is instead best described by a model with high-altitude clouds. Using a frequentist hypothesis testing procedure, we can rule out a hydrogen-dominated cloud-free atmosphere to 4. 9σ. When combined with other recent WFC3 studies, our observations suggest that clouds may be common in exoplanetary atmospheres.
Short-term oral pentoxifylline use increases choroidal blood flow in patients with age-related macular degeneration.

OBJECTIVE To study the ocular hemodynamic effects of a 3-month oral treatment with pentoxifylline in patients with nonexudative age-related macular degeneration. DESIGN Double-blind, placebo-controlled, randomized, parallel group study. SETTING Outpatient clinic of the Department of Ophthalmology, Vienna University, Vienna, Austria, that specializes in age-related macular degeneration. METHODS Forty patients with age-related macular degeneration received pentoxifylline (400 mg 3 times a day orally, n=20) or placebo (n=20) for 3 months. Retinal blood flow was assessed by scanning laser Doppler flowmetry and pulsatile choroidal blood flow was assessed by laser interferometric measurement of fundus pulsation amplitude. MAIN OUTCOME MEASURES Changes in retinal blood flow and fundus pulsation amplitude. RESULTS Four patients receiving pentoxifylline and 3 patients receiving placebo discontinued medication because of nausea. In the remaining subjects, the use of pentoxifylline increased ocular fundus pulsation amplitude (P<.001 vs placebo and baseline). The maximum increase was 28% after 3 months. In contrast, retinal blood flow was not changed by the use of pentoxifylline. CONCLUSIONS A 3-month course of oral pentoxifylline treatment increases choroidal but not retinal blood flow in patients with age-related macular degeneration. These data strongly support the concept that pentoxifylline might be useful in the treatment of age-related macular degeneration. Long-term clinical outcome trials are now warranted to test this hypothesis.
The XMM–Newton/2dF survey – I. X‐ray properties of normal galaxies

This paper explores the X-ray properties of 'normal' galaxies using a shallow (2-10 ks) XMM-Newton survey covering an area of 1.5 deg 2 . The X-ray survey overlaps with the 2dF Galaxy Redshift Survey. Compared with previous studies this has the advantage that high-quality spectra and spectral classifications (early-, late-type) exist for all galaxies to b j = 19.4. Moreover, sources with optical spectra revealing powerful active galactic nuclei (AGN) can easily be discarded from the normal galaxy sample used here. In particular, we present stacking analysis results for about 200 galaxies from the 2dF Galaxy Redshift Survey at a mean redshift of z 0.1. We detect a strong signal for the whole sample (6σ) in the soft 0.5-2 keV band corresponding to a flux of 7 × 10 - 1 6 erg s - 1 cm - 2 and a luminosity of 2 × 10 4 0 erg s - 1 . A statistically significant signal is also detected for both the early and late galaxy subsamples with X-ray luminosities of 3 x 10 4 0 and 5 x 10 3 9 erg s - 1 , respectively. In contrast, no signal is detected in the hard 2-8 keV band for any of the above samples. The mean L X /L B ratio of the spiral galaxy sample is found to be consistent with both local (<100 Mpc) and distant (z 1) samples (after accounting for differences in L B ), suggesting little or no evolution of the X-ray emission mechanisms relative to the optical. The 0.5-2 keV X-ray background (XRB) contribution of the spiral galaxy subsample at z 0.1 is estimated to be 0.4 per cent, in broad agreement with the XRB fractions estimated in previous studies. Assuming that star-forming galaxies evolve with redshift as (1 + z) k , the present data combined with previous studies suggest k < 3. The k values are constrained by the relatively low fraction of the soft X-ray background that remains unresolved by deep surveys (6-26 per cent). Higher k values will result in an overproduction of the soft X-ray background, given the fraction already attributed to AGN, groups and clusters. The mean X-ray emissivity of spiral galaxies at z 0.1 is also estimated and is found to be consistent within the uncertainties with that of local H II galaxy samples. Using the mean X-ray emissivity of the spiral galaxy subsample we estimate a global star formation density of 0.009 ′ 0.007 M O . yr - 1 Mpc - 3 at z 0.1. Although the uncertainty is large, this is lower than previous results based on galaxy samples selected at different wavelengths. Nevertheless, given the large uncertainties involved in converting X-ray luminosity to star formation rate the agreement is surprising.
Kernel-based Visualisation of Genes with the Gene Ontology

With the development of microarray--based high-- throughput technologies for examining genetic and biological information en masse, biologists are now faced with making sense of large lists of genes identified from their biological experiments. There is a vital need for "system biology" approaches which can allow biologists to see new or unanticipated potential relationships which will lead to new hypotheses and eventual new knowledge. Finding and understanding relationships in this data is a problem well suited to visualisation. We augment genes with their associated terms from the Gene Ontology and visualise them using kernel Principal Component Analysis with both specialised linear and Gaussian kernels. Our results show that this method can correctly visualise genes by their functional relationships and we describe the difference between using the linear and Gaussian kernels on the problem.
Stripe smuts of grasses: one lineage or high levels of polyphyly?

Stripe smut of grasses, Ustilago striiformis s.l. , is a complex of smut fungi widely distributed over temperate and subtropical regions. The disease results in the shredding and death of leaf tissue following the rupture of elongated sori. Nearly 100 different grass species in more than 30 genera are infected by stripe smut. During the last two centuries more than 30 smut taxa have been described from members of this complex. The present study attempts to clarify the taxonomy and phylogeny of stripe smuts on grasses by analysing both morphological and molecular data. More than 200 specimens from different continents and host plants were examined. DNA was extracted from teliospores of 23 specimens from different hosts collected in Europe, Asia, and North America. The ITS and LSU regions of ribosomal DNA were amplified and used in phylogenetic analyses. The results of Maximum Parsimony and Bayesian analyses demonstrated that there are several lineages of stripe smut fungi. Analyses of morphological characters assessed with light and scanning electron microscopy showed high support for the differentiation of two clades as distinct from U. striiformis s.l. , i.e., U. nunavutica sp. nov. and U. bromina. Two additional clades, U. striiformis s.str. on Holcus and a clade containing specimens from Elymus, were identified with molecular data although morphological differences were not apparent. Descriptions are given for each species.
Partial replacement of an infected arterial graft by a new prosthetic polytetrafluoroethylene segment: a new therapeutic option.

PURPOSE As the title suggests, this is an account of treating infected arterial grafts other than by the accepted methods of complete graft removal and revascularization with autogenous material or extraanatomic bypass. METHODS Since 1973, 42 patients with infected arterial grafts (n = 35) or autogenous reconstructions (n = 7) were seen with false aneurysm, hemorrhage, or perigraft or perianastomotic pus and were treated by removal of the infected graft and immediate adjacent or in situ revascularization by polytetrafluoroethylene (PTFE) in 39 cases and Dacron in three cases. Management plan included (1) removal of only the obviously infected part of the original graft, (2) obliteration of the infected anastomotic site, and (3) placement of the new PTFE graft in an adjacent clean or debrided route. So treated were 15 aortic Dacron grafts, 20 PTFE grafts (2 iliofemoral, 3 femorofemoral, and 15 femorodistal), and 7 autogenous reconstructions with bleeding. Partial graft salvage was attempted in 10 of 15 Dacron and 19 of 20 PTFE grafts. RESULTS Four patients required further removal of the original infected graft (three Dacron, one PTFE), giving an ultimate success rate of 7 of 15 Dacron and 18 of 20 PTFE grafts; two patients required further obliteration of the original adjacent infected arterial segment because of rebleeding. An additional PTFE segment was joined successfully to incorporated PTFE in all six repeat operations. Initial failure did not prejudice the outcome; direct arterial flow to at least midthigh level was preserved in 37 of the 42 patients for a mean period of 40 months (range 9 to 130 months). Three of the new PTFE grafts occluded and became infected, which led to amputation and one death at a secondary operation. Visceral complications caused the only two other deaths in the aortic group. Five late amputations (four below the knee and one above the knee) were required because of femorodistal graft occlusion. CONCLUSIONS Partial removal of infected grafts with adjacent or in situ replacement by PTFE is possible, simplifies management, and permits maintenance of distal circulation with low morbidity and mortality rates.
Colorectal Cancer-Specific Cytochrome P450 2W1: Intracellular Localization, Glycosylation, and Catalytic Activity

Cytochrome P450 2W1 (CYP2W1) is expressed at high levels in colorectal cancer cells. Moreover, we have shown previously that a higher tumor expression is associated with less survival. In this study, we characterize post-translational modification, inverted endoplasmic reticulum (ER) topology, and catalytic activity of CYP2W1. The analysis of colorectal normal and cancer tissues and CYP2W1 overexpressing human embryonic kidney (HEK) 293 cells showed that a fraction of CYP2W1 is modified by N-glycosylation. Bioinformatic analysis identified Asn177 as the only possible glycosylation site of CYP2W1, which was supported by the inability of an N177A mutant to be glycosylated in HEK 293 cells. Analysis of the membrane topology indicated that unlike other cytochromes P450, CYP2W1 in HEK 293-transfected cells and in nontransfected Caco2TC7 and HepG2 cells is oriented toward the lumen of the ER, a topology making CYP2W1 available to the ER glycosylation machinery. Immunofluorescence microscopy and cell surface biotinylation experiments revealed approximately 8% of the CYP2W1 on the cell surface. Despite the reverse orientation of CYP2W1 in the ER membrane, apparently making functional interactions with NADPH-cytochrome P450 reductase impossible, CYP2W1 in HEK 293 cells was active in the metabolism of indoline substrates and was able to activate aflatoxin B1 into cytotoxic products. The study identifies for the first time a cytochrome P450 enzyme with a luminal ER orientation and still retaining catalytic activity. Together, these results suggest the possibility of using CYP2W1 as a drug target in the treatment of colon cancer using antibodies and/or specific CYP2W1 activated prodrugs.
The Origin of Nonthermal X-Ray Filaments and TeV Emission in Young Supernova Remnants

At the early, ejecta-dominated stage of supernova remnant (SNR) expansion, a fraction of the swept-up circumstellar magnetic field is dynamically compressed to approximate equipartition at the contact discontinuity separating the SN progenitor's wind (or the interstellar medium) and the ejecta. We propose that the thin nonthermal X-ray filaments observed by the Chandra satellite in several young SNRs are associated with such "pile-up" of the magnetic field. We use a one-dimensional diffusion-convection transport equation to describe the propagation of nonthermal electrons near the contact discontinuity of a young SNR and to calculate spatially resolved emission spectra in the X-ray and TeV bands. The results suggest that the high-energy electrons are possibly accelerated at the forward shock and emit efficiently only when they diffuse into regions of high magnetic field near the contact discontinuity. Much more likely, though, is that they are locally accelerated at the contact discontinuity, in which case the acceleration cannot be related to Fermi-type processes and should occur because of other plasma mechanisms. As a consequence, the forward shock in young SNRs is inconspicuous and often unobservable, similar to that in the Crab Nebula.
Multi-User Resource Allocation for a Distributed Multi-Carrier DS-CDMA Network

This paper addresses an adaptive multi-user resource allocation for a distributed multi-carrier direct sequence-code division multiple access (MC DS-CDMA) network. The packet throughput, which turns out to be nonconvex and nondifferentiable, is considered to measure the system performance. A sub-optimal non-cooperative power control game is proposed to adaptively allocate the transmit power, available subchannels and alphabet size by minimizing the transmit power with a transmit power constraint and a packet throughput requirement. Also, the paper investigates the effect of channel estimation error on the adaptive resource allocation in a distributed MC DS-CDMA network, and shows that using the Gaussian approximation for the signal-dependent noise can lead to a nontrivial discrepancy in system performance.
Roary: rapid large-scale prokaryote pan genome analysis

Summary A typical prokaryote population sequencing study can now consist of hundreds or thousands of isolates. Interrogating these datasets can provide detailed insights into the genetic structure of of prokaryotic genomes. We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying the core and dispensable accessory genes. Roary makes construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results. Using a single CPU Roary can produce a pan genome consisting of 1000 isolates in 4.5 hours using 13 GB of RAM, with further speedups possible using multiple processors. Availability and implementation Roary is implemented in Perl and is freely available under an open source GPLv3 license from http://sanger-pathogens.github. io/Roary Contact roary@sanger.ac. uk Supplementary information Supplementary data are available at Bioinformatics online.
Henoch-Schönlein purpura in north-eastern Turkey

Abstract Aim: To evaluate the epidemiological and clinical findings in children with Henoch-Schönlein purpura (HSP) admitted during a 10-year period, 1995 to 2004, and to compare them with series from other parts of the world. Methods: The medical records of all children aged 17 years or less admitted with a diagnosis of HSP to the Department of Pediatrics of Karadeniz Technical University were evaluated retrospectively for epidemiological and clinical features. Results: Of 116 children, 73 (63%) were boys. The mean (SD) age at presentation was 8.9 (3.7) years and one-third of them were older than 10 years of age. Over half the cases presented between September and January. All patients had the typical skin rash. Gastro-intestinal manifestations were seen in 64 (55.1%) and joint manifestations, common during the early course of the disease, in 73 (62.9%). Two patients required laparatomy, one for acute abdomen and the other for bowel resection owing to intussusception. Renal manifestations were observed in 36 (31%), all within 3 months of initial symptoms, and one patient (0.8%) with nephritic syndrome progressed to end-stage renal disease. Five patients had hypertension without urinary findings. Symptoms recurred in eight patients (6.9%) over a period ranging from 2 to 5 months after complete resolution of symptoms. There was a history of a preceding upper respiratory tract infection in 16 (13.7%) and a streptococcal infection was confirmed by throat culture in 12 of the 42 (28.5%) children at presentation. Conclusion: HSP is generally benign and self-limiting. Hypertension may be seen during the course of the disease without urinary findings. In this area, it seems to affect older children and there is a relatively lower incidence of renal manifestations.
The Adultification of Refugee Children

Abstract This paper presents the findings of a study that examines the social and emotional adjustment of adultified Cuban refugee children from the 1994-1995 Guantanamo wave. It also discusses how changes in family roles affect intergenerational relations and family well-being, and how the migration and resettlement experience affects parent/child roles and disrupts the refugee family.