Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution of a TRIM5-CypA Splice Isoform in Old World Monkeys

The TRIM family proteins share a conserved arrangement of three adjacent domains, an N-terminal RING domain, followed by one or two B-boxes and a coiled-coil, which constitutes the tripartite-motif for which the family is named. However, the C-termini of TRIM proteins vary, and include at least nine evolutionarily distinct, unrelated protein domains. Antiviral restriction factor TRIM5α has a C-terminal B30.2/SPRY domain, which is the major determinant of viral target specificity. Here, we describe the evolution of a cyclophilin-A encoding exon downstream of the TRIM5 locus of Asian macaques. Alternative splicing gives rise to chimeric transcripts encoding the TRIM motif fused to a C-terminal CypA domain (TRIM5-CypA). We detected TRIM5-CypA chimeric transcripts in primary lymphocytes from two macaque species. These were derived in part from a CypA pseudogene in the TRIM5 locus, which is distinct from the previously described CypA insertion in TRIM5 of owl monkeys. The CypA insertion is linked to a mutation in the 3′ splice site upstream of exon 7, which may prevent or reduce expression of the α-isoform. All pig-tailed macaques (M. nemestrina) screened were homozygous for the CypA insertion. In contrast, the CypA-containing allele was present in 17% (17/101) of rhesus macaques (M. mulatta). The block to HIV-1 infection in lymphocytes from animals bearing the TRIM5-CypA allele was weaker than that in cells from wild type animals. HIV-1 infectivity remained significantly lower than SIV infectivity, but was not rescued by treatment with cyclosporine A. Thus, unlike owl monkey TRIMCyp, expression of the macaque TRIM5-CypA isoform does not result in increased restriction of HIV-1. Despite its distinct evolutionary origin, Macaca TRIM5-CypA has a similar domain arrangement and shares ∼80% amino-acid identity with the TRIMCyp protein of owl monkeys. The independent appearance of TRIM5-CypA chimeras in two primate lineages constitutes a remarkable example of convergent evolution. Based on the presence of the CypA insertion in separate macaque lineages, and its absence from sooty mangabeys, we estimate that the Macaca TRIM5-CypA variant appeared 5–10 million years ago in a common ancestor of the Asian macaques. Whether the formation of novel genes through alternative splicing has played a wider role in the evolution of the TRIM family remains to be investigated.
Measuring Bite Force in Small Mammals with a Piezo-resistive Sensor

Abstract We tested the use of piezo-resistive force sensors to measure bite force in small mammals. These force sensors are thin (less than 1 mm) and can be used to measure forces up to 4,500 N. A battery-operated unit, ideal for field research, can be built easily and inexpensively. We tested this sensor in the laboratory and in the field on a variety of small mammals. Although our results indicate that the sensor is somewhat less accurate (coefficient of variation = 4%) than a conventional load cell, the small size and ease of use of the piezo-resistive detector is highly desirable. We also investigated the problem of performance and physiological condition of animals. We found the problem of lack of effort by test animals can enter a significant bias into estimates of maximal bite force.
Detection of biomarkers using recombinant antibodies coupled to nanostructured platforms

The utility of biomarker detection in tomorrow's personalized health care field will mean early and accurate diagnosis of many types of human physiological conditions and diseases. Michael Kierny and Thomas Cunningham contributed equally In the search for biomarkers, recombinant affinity reagents can be generated to candidate proteins or post-translational modifications that differ qualitatively or quantitatively between normal and diseased tissues. The use of display technologies, such as phage-display, allows for manageable selection and optimization of affinity reagents for use in biomarker detection. Here we review the use of recombinant antibody fragments, such as scFvs and Fabs, which can be affinity-selected from phage-display libraries, to bind with both high specificity and affinity to biomarkers of cancer, such as Human Epidermal growth factor Receptor 2 (HER2) and Carcinoembryonic antigen (CEA). We discuss how these recombinant antibodies can be fabricated into nanostructures, such as carbon nanotubes, nanowires, and quantum dots, for the purpose of enhancing detection of biomarkers at low concentrations (pg/mL) within complex mixtures such as serum or tissue extracts. Other sensing technologies, which take advantage of ‘Surface Enhanced Raman Scattering’ (gold nanoshells), frequency changes in piezoelectric crystals (quartz crystal microbalance), or electrical current generation and sensing during electrochemical reactions (electrochemical detection), can effectively provide multiplexed platforms for detection of cancer and injury biomarkers. Such devices may soon replace the traditional time consuming ELISAs and Western blots, and deliver rapid, point-of-care diagnostics to market.
Reliability and validity of the child version of the Eating Disorder Examination: a preliminary investigation.

OBJECTIVE The Eating Disorder Examination (EDE) is a reliable and valid semistructured interview that measures the specific psychopathology of anorexia nervosa (AN) and bulimia nervosa. The current study aims to investigate the psychometric properties of the child adaptation of the EDE (ChEDE 12.0). METHOD The ChEDE was administered to 15 children with AN, 15 children with other clinical eating disturbances, and two groups of 15 age-matched controls. The groups were compared using a two-sample matched groups design. RESULTS Alpha coefficients for each of the ChEDE subscales indicated a high degree of internal consistency, and interrater reliability was found to be high (r = .91 to r = 1.00). The subscale scores of the AN group were significantly higher than those of the other groups, whereas the other eating disturbance group did not differ from its control group. DISCUSSION The ChEDE differentiates children with AN from children with other forms of clinical eating disturbance and control children.
Extrapolating PPPs and comparing ICP benchmark results

Since the 2005 ICP results have been published, various institutions and agencies have extrapolated the results for each of the years up to 2010. They include the World Bank (the World Development Indicators, or WDI), the University of Pennsylvania (Penn World Tables, PWT) and the OECD. It is inevitable that the results from the 2011 ICP will differ significantly from those in the WDI and the PWT, particularly given that the global financial crisis in 2008 and 2009 affected different countries to very different extents. The Global Office is also going to face some presentational problems when the 2011 ICP results become available because analysts will want to compare them with those from the 2005 round. There is no simple way of presenting the two sets of results on a comparable basis so the TAG has been asked to advise the Global Office on the best way to proceed. PPP-based comparisons of activity levels between countries are an important use of national accounts. Despite the conceptual and empirical difficulties, PPP-based volumes provide a much firmer basis for international comparisons than the commonly used alternative of converting national accounts aggregates to a common currency using exchange rates.
Recombinant antigen-based enzyme immunoassay for screening of Treponema pallidum antibodies in blood bank routine

This work reports a comparison of an enzyme immunoassay (EIA) using two major Treponema pallidum recombinant antigens with a T. pallidum hemagglutination (TPHA) assay and a nontreponemal Venereal Disease Reference Laboratory (VDRL) test. A total of 1,822 normal donor serum samples was tested for cardiolipin and T. pallidum antibodies, respectively, by the VDRL assay and EIA. Among these samples, 440 were further tested by TPHA technology. Four samples were found positive by EIA, while all were reported to be negative by both TPHA and VDRL routine assays. Subsequent testing of EIA-positive samples confirmed 100% (four of four samples) and 25% (one of four samples) positive results, respectively, by immunofluorescence assay and a Western blot (immunoblot) syphilis kit. The sensitivity of the recombinant EIA was estimated at virtually 100% with a reference panel of 50 syphilitic samples. According to this study, the newly developed EIA kit shows 100% sensitivity combined to a specificity greater than 99.8% for detecting treponemal immunoglobulin G antibodies in blood bank syphilis screening.
On the Efficient Classification of Data Structures by Neural Networks

In the last few years it has been shown that recurrent neural networks are adequate for processing general data structures like trees and graphs, which opens the doors to a number of new interesting applications previously unexplored. In this paper, we analyze the efficiency of learning the membership of DO AGs (Directed Ordered Acyclic Graphs) in terms of local minima of the error surface by relying on the principle that their absence is a guarantee of efficient learning. We give sufficient conditions under which the error surface is local minima free. Specifically, we define a topological index associated wi th a collection of DOAGs that makes it possible to design the architecture so as to avoid local minima.
LARGE-SCALE NEURAL SYNCHRONY ASSOCIATED WITH TOP-DOWN SELECTIVE ATTENTIONAL MODULATION OF NECKER CUBE PERCEPTION

We investigated top-down selective attentional modulation of bistable perception. Sixteen healthy human observers were presented with the Necker cube on a black background. Observers reported perceptual switches between two possible interpretations by pressing one of two keys. Observers were instructed either to passively view the Necker cube or to try to attend to one of the two possible interpretations. Observers showed strong selective attentional modulation of dominance durations. We measured brain electrical activity by 62ch EEG and used phase locking value to evaluate large-scale phase synchrony between pairs of EEG signals. We observed stronger long-lasting large-scale synchrony at 3-4 Hz among the frontal, parietal and occipital areas associated with perceptual switches in the attentional control condition than in the passive view condition. These results suggest that top-down selective attentional modulation of Necker cube perception is mediated by frontal- parietal-occipital synchrony networks in the theta frequency range.
An investigation of mental health and personality in Swedish social work students upon entry to university training

The aims were to describe Swedish social work students' personality characteristics upon entry to their training and to analyze relationships between personality traits, mental health, and some sociodemographic variables. One hundred and twenty-one female social work students completed a sociodemographic form, the Temperament and Character Inventory, and the Symptom Checklist. They scored significantly higher on harm avoidance, reward dependence, and self-transcendence and reported more somatization, obsessive compulsive, and phobic-anxious symptoms, and less hostility, than Swedish individuals from the general population of the same age. Personality traits significantly predicted the various mental symptom scores. It is recommended to implement modules or training courses within social work training in Sweden that bring an improvement of self-directedness and cooperativeness character trait into focus.
Perceptual properties of vibrotactile material texture: Effects of amplitude changes and stimuli beneath detection thresholds

We investigate the perceptual properties of vibro-tactile material textures: in particular, the effects of changes in vibrotactile amplitudes and of vibratory stimuli that are beneath detection thresholds. Existing knowledge of the perceptual properties of vibrotactile gratings does not hold for vibrotactile material textures because material textures are composed of many more frequency components than those of grating textures. We experimentally investigate perceptual properties of wood and sandpaper textures through lossy data compression of the textures. Lossy data compression is suitable for manipulating many independent variables of material textures while maintaining their qualities. By quantization of vibratory amplitudes, we find that subjective quality of textures does not change until the number of quantization steps reaches 12. This represents that data sizes of material textures are reduced by up to approximately 75% while maintaining their qualities. By cutting off the frequency components whose amplitudes are beneath the shifted-threshold curve, we find that even subliminal stimuli affect perception. Developers of vibro-tactile material textures should be aware of these perceptual properties.
Detection of prodromal symptoms of relapse in mania & unipolar depression by relatives & patients

Background & objectives: Detection of prodromal symptoms among patients with mania by their immediate relatives has been seldom examined. We carried out this study to examine the ability to detect and report prodromol symptoms of manic relapses by patients themselves and their relatives. Methods: The ability of patients and their relatives to detect prodromal symptoms was examined among 60 remitted patients, 30 each with DSM-IV diagnoses of bipolar disorder and recurrent depressive disorder, with recent manic/depressive relapses, and their 60 immediate relatives, using an instrument composed of items from common symptom-scales, as well as by unstructured interview. Results: Seventy per cent of patients with mania reported prodromes prior to relapse. This was significantly (P<0.01) less than the proportion of their relatives (97%), as well as the proportion of patients with unipolar depression (93%), reporting prodromal symptoms (P<0.05) among patients. Mean duration of the prodromal period reported by patients with mania was about 20 days (median-10 days); relatives reported durations which were longer by about 5 days. Prodromes of unipolar depression (mean 42.7 days; median- 21 days), were significantly longer than of mania, when reported by patients, but not by their relatives. Differences in reporting of prodromes, between relatives and patients seen in mania, were not observed in unipolar depression. The number and type of prodromal symptoms of mania reported was similar among patients and relatives. Interpretation & conclusions: Our findings showed that relatives of patients with mania were better at detecting prodromes of relapse; thus, input from relatives can improve the early detection of prodromal symptoms to prevent relapses of bipolar disorder.
Waves in the Magnetized Solar Atmosphere. II. Waves from Localized Sources in Magnetic Flux Concentrations

Numerical simulations of wave propagation in a two-dimensional stratified magneto-atmosphere are presented for conditions that are representative of the solar photosphere and chromosphere. Both the emergent magnetic flux and the extent of the wave source are spatially localized at the lower photospheric boundary of the simulation. The calculations show that the coupling between the fast and slow magneto-acoustic-gravity (MAG) waves is confined to thin quasi-one-dimensional atmospheric layers where the sound speed and the Alfvén velocity are comparable in magnitude. Away from this wave conversion zone, which we call the magnetic canopy, the two MAG waves are effectively decoupled because either the magnetic pressure (B2/8π) or the plasma pressure (p = NkBT) dominates over the other. The character of the fluctuations observed in the magneto-atmosphere depend sensitively on the relative location and orientation of the magnetic canopy with respect to the wave source and the observation point. Several distinct wave trains may converge on and simultaneously pass through a given location. Their coherent superposition presents a bewildering variety of Doppler and intensity time series because (1) some waves come directly from the source while others emerge from the magnetic canopy following mode conversion, (2) the propagation directions of the individual wave trains are neither co-aligned with each other nor with the observer's line of sight, and (3) the wave trains may be either fast or slow MAG waves that exhibit different characteristics depending on whether they are observed in high-β or low-β plasmas (β ≡ 8πp/B2). Through the analysis of four numerical experiments a coherent and physically intuitive picture emerges of how fast and slow MAG waves interact within two-dimensional magneto-atmospheres.
Testing the starburst/AGN connection with SWIRE X‐ray/70 μm sources

We explore the nature of X-ray sources with 70 μm counterparts selected in the Spitzer Wide-Area Infrared Extragalactic Survey (SWIRE) fields: ELAIS-N1, Lockman Hole and Chandra Deep Field South, for which Chandra X-ray data are available. A total of 28 X-ray/70μm sources in the redshift interval 0.5 50 M ⊙ ) yr -1 ) that dominates in the IR. It is found that the X-ray and IR luminosities of the sample sources are broadly correlated, consistent with a link between AGN activity and star formation. Contrary to the predictions of some models for the co-evolution of AGN and galaxies, the X-ray/70 μm sources in the sample are not more obscured at X-ray wavelengths compared to the overall X-ray population. It is also found that the X-ray/70 μm sources have lower specific star formation rates compared to the general 70 μm population, consistent with AGN feedback moderating the star formation in the host galaxies.
How to Build a Domain Theory On the Validity Centered Design of Construct-Linked Scales of Learning and Growth

Measurement experts, and especially those sympathetic to the traditions of these volumes, emphasize the importance of putting forth substantial efforts to build useful scientific variables, instrumented so as to yield measures, not mere scores. Building a domain theory is more than its instruments, but the development of the instrument and the development of the theory are synergistic. A great instrument is inseparable from a great theory. A domain theory gives an account of both sides of the person/item map – the substantive processes employed by the persons, and the construct-relevant sources of task difficulty. This article explains the concept of a domain theory, places it within other types of theory needed in educational research, and shows how it and its validity argument are built by giving attention to the design processes of validity-centered design. The general problem of measuring learning and growth in educational or training domains is the background for the examples and discussion herein. In order to describe how to build a domain theory, with its necessary construct-linked measurement scales, this article is organized under the following four headings:
A Heuristic Approach for Configuration Learning of Supervised Instance Matching

Instance matching is the problem of finding instances that co-describe the same topic. The performance of an instance matching system relies on the specified configuration, which is optimally designed for each particular dataset. We propose cLearn, a heuristic-based algorithm that automatically searches for the most appropriate matching configuration for the given repositories. cLearn is effective when being tested on OAEI benchmarks and outperforms previous supervised systems.
Processing load during listening: The influence of task characteristics on the pupil response

This study examined the magnitude of the pupillary response evoked by a number of tasks varying in the nature and complexity of the auditory and linguistic information provided. The tasks comprised passive listening, anticipation to verbally responding to a prompt signal, auditory detection, and the identification of meaningful words. Performance in the auditory detection and identification tasks was matched at 79% correct. In all, 42 normally hearing adults (aged 18–44 years, mean age 25.5 years) from three different sites (Amsterdam, Cologne, and Warsaw) participated. During each condition, the pupil diameter was measured. A Repeated Measures ANOVA was conducted to examine within and between subject (site) differences in the pupil response over 8 time intervals during the four conditions. The maximum mean pupil dilation was largest in the words-in-noise identification task (0.13 mm) and differed significantly from the maximum mean dilation in the noise-in-noise-detection task. The latter did not differ significantly from the pupil response during passive listening to noise and an answer prompt. No significant differences between sites were observed. Task evoked pupillary responses to theory-based measures of linguistic processing are robust, reliable, and sensitive to differences in task demands. Word-in-noise identification requires more processing load than nonspeech detection. To obtain information about within-subject differences in auditory processing, examination of both processing load and behavioural performance is recommended. Methodological implications are discussed.
A Functional Size Measurement Method for Event-Based Objectoriented Enterprise Models

The effective management of IS-related processes requires measuring the functional size of information systems. Functional size measurement is usually performed using the Function Points Analysis method. Earlier attempts to apply Function Point counting rules to object-oriented systems met with serious problems because the implicit model of functional user requirements in Function Points Analysis is hard to reconcile with the object-oriented paradigm. The emergence of a new generation of functional size measurement methods has changed this picture. The main implementation of this generation, COSMIC Full Function Points, explicitly defines a generic model of functional user requirements onto which artifacts belonging to any IS specification or engineering methodology can be mapped. In this paper we present specific COSMIC-FFP mapping rules for methodologies that take an event-based approach to information system engineering. In particular we show that the event-oriented nature of the COSMIC-FFP measurement rules provides for a natural mapping of concepts. To illustrate the mapping rules we use MERODE, a formal event-based object-oriented methodology for systems development in information processing intensive domains. The mapping rules presented are confined to the enterprise layer in a MERODE IS architecture.