Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of chameleon sequences and their implications in biological processes

Chameleon sequences have been implicated in amyloid related diseases. Here we report an analysis of two types of chameleon sequences, chameleon‐HS (Helix vs. Strand) and chameleon‐HE (Helix vs. Sheet), based on known structures in Protein Data Bank. Our survey shows that the longest chameleon‐HS is eight residues while the longest chameleon‐HE is seven residues. We have done a detailed analysis on the local and global environment that might contribute to the unique conformation of a chameleon sequence. We found that the existence of chameleon sequences does not present a problem for secondary structure prediction programs, including the first generation prediction programs, such as Chou–Fasman algorithm, and the third generation prediction programs that utilize evolution information. We have also investigated the possible implication of chameleon sequences in structural conservation and functional diversity of alternatively spliced protein isoforms. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Left cytoarchitectonic BA 44 processes syntactic gender violations in determiner phrases

Recent neuroimaging studies make contradictory predictions about the involvement of left Brodmann's area (BA) 44 in processing local syntactic violations in determiner phrases (DPs). Some studies suggest a role for BA 44 in detecting local syntactic violations, whereas others attribute this function to the left premotor cortex. Therefore, the present event‐related functional magnetic resonance imaging (fMRI) study investigated whether left‐cytoarchitectonic BA 44 was activated when German DPs involving syntactic gender violations were compared with correct DPs (correct: ‘der Baum’—the[masculine] tree[masculine]; violated: ‘das Baum’—the[neuter] tree[masculine]). Grammaticality judgements were made for both visual and auditory DPs to be able to generalize the results across modalities. Grammaticality judgements involved, among others, left BA 44 and left BA 6 in the premotor cortex for visual and auditory stimuli. Most importantly, activation in left BA 44 was consistently higher for violated than for correct DPs. This finding was behaviourally corroborated by longer reaction times for violated versus correct DPs. Additional brain regions, showing the same effect, included left premotor cortex, supplementary motor area, right middle and superior frontal cortex, and left cerebellum. Based on earlier findings from the literature, the results indicate the involvement of left BA 44 in processing local syntactic violations when these include morphological features, whereas left premotor cortex seems crucial for the detection of local word category violations. Hum Brain Mapp, 2010. © 2010 Wiley‐Liss, Inc.
Notice of RetractionStructural Change and Spatial Pattern of Urbanization in Xinjiang

Xinjiang has experienced considerable urban growth in the past sixty years, especially since the implementation of socio-economic reforms in 1978. When Xinjiang was founded as a Uygur Autonomous Region in 1955, there were only three cities with an urban population of 870 thousand, while in 2008 it had 21 cities with a total urban population with 8.45 million. Such an urban growth is attributed to the boost in the number of cities and the urban population. Urban expansion enhanced geographic inequality between the two major regions in Xinjiang. Compared to the Northern part, Southern Xinjiang only has 33.3% of the total cities and 35% of the urban population. Using Geographic Information System (GIS) and statistical analyses, this study aims at explaining the structure and spatial development of urban growth, and highlighting the current issues of urban inequality in Xinjiang during the past three decades. The conclusions are the following: 1. During the last three decades, extra large cities, medium cities and towns have a tendency to increase their importance in the proportion of the urban population, while the large and small cities begun to lose their importance in Xinjiang; 2. Urban growth disparities between North and South have become increasingly obvious, but seem to be evolving slowly after 2000; 3. According to our study, there are a variety of factors that we feel are important in explaining the urbanization pattern in Xinjiang. Some of them are geographical factors such as topography and water system; some are institutional factors such as urban policy, some are economic factors such as per capita GDP, some are social factors such as education level of population and migration.
Replicative senescence in the immune system: impact of the Hayflick limit on T-cell function in the elderly.

Gerontologists, lured by the prospect of understandingthe cellular events that underlie the gross features ofhuman aging, are focusing increasingly on replicative(orcellular) senescence. The term “replicative senescence”describes the irreversible state of growth arrest experi-enced by all mitotically competent cells of human originfollowing a fairly predictable number of cell divisions inculture. First identiﬁed in human fetal ﬁbroblasts byHayﬂick, replicative senescence, or the so-called Hay-ﬂick limit, results from an intrinsic natural barrier tounlimited cell division exhibited by all normal somaticcells.The characteristics of replicative senescencehavebeenexplored in a variety of cell types (reviewed in Smithand Smith 1996; see also Be´rube´ et al. 1998 [in thisissue]), but only recently has this model been applied tothe immune system. Ironically, the Hayﬂick limit maybe particularly deleterious for immune cells, since theability to undergo rapid clonal expansion is absolutelyessential to their function. The decline of T-cell immunefunction during aging suggests that T cells might be anideal system in which to explore the potential role ofreplicative senescence during in vivo aging. Well-char-acterized cell surface markers, signal transduction path-ways, and functional traits further enhance the potentialutility of T cells as a model system, both to elucidatethe process of replicative senescence itself and to assessits physiological consequences.This review will summarize the results of research onT-cell replicative senescence in cell culture and will dem-onstrate that cells from elderly people have undergonechanges in vivo that are similar to those observed in thecell culture model. I will argue that T-cell replicativesenescence contributes to increased morbidity and mor-tality during aging and that the proportion of replica-
Effects of bariatric surgery on hepatic and intestinal lipoprotein particle metabolism

Purpose of review Insulin resistance and type 2 diabetes, driven largely by obesity, are characterized by an increase in triglyceride-rich lipoproteins (TRLs) due to both reduced TRL clearance from the circulation and increased production by the liver (apoB-100 containing VLDLs) and intestine (apoB-48 containing chylomicrons). Bariatric surgery is the only treatment currently that leads to marked, sustained weight loss. Here, we will review the effects of bariatric surgery on circulating triglyceride/TRL and TRL production and clearance. Recent findings Bariatric surgery leads to a marked reduction in fasting and postprandial plasma triglyceride. Only one study to date has assessed TRL kinetics after bariatric surgery and has reported a reduction in TRL apoB-100 concentration (i.e. the number of VLDL particles) due to reduced production and increased clearance and reduced TRL apoB-48 concentration (the number of chylomicron particles) due to reduced production. Some bariatric surgery studies have reported no/weak correlation between weight loss and improvements in triglyceride/TRL, suggesting that as yet unidentified factors beyond weight loss may contribute to the marked changes in TRL that occur postbariatric surgery. Summary Available data suggest that bariatric surgery reduces triglyceride and intestinal and hepatic TRL production with increased clearance of hepatic TRL particles. These effects of bariatric surgery on TRL kinetics need to be confirmed with additional studies. Further studies are also needed to compare the effects of various bariatric surgery procedures on TRL kinetics and to elucidate underlying mechanisms.
ERRATUM Carbon balance and tree growth in a Fagus sylvatica stand

The objectives of this study were 1) to scale photosynthesis from leaf to crown and to tree scale, 2) to determine the proportion of assimilated carbon used for wood construction and whether the fraction of assimilation used for production varies am ong social classes and 3) to validate the approach by comparing assimilation estimates with independent measurements provided by th e eddy covariance technique ( EC). Measurements (growth and gas exchange) were performed in a 30-year-old F gus sylvaticastand during the 1997 growing season on five sample trees of different crown classes (dominant, codominant and intermediate trees). A nonlinear relationship between net CO 2 assimilation and photosynthetically active radiation ( PAR) was found for each sample trees. Canopy net CO2 assimilation was then modelled over a period of non limiting soil water soil water content. Simulated gross assimilation scaled to stand level was in good agreement with stand measurements performed by EC. growth / carbon balance / photosynthesis / crown class / Fagus sylvaticaL Résumé– Bilan de carbone et croissance dans un jeune peuplement de Fagus sylvatica. Les objectifs de cette étude étaient 1) d'estimer la photosynthèse à l'échelle de la couronne, puis à l'échelle de l'arbre à partir de mesures foliaires, 2) de détermi ner la proportion du carbone assimilé utilisée pour la construction de bois et sa variation en fonction du statut social de l'arbre, 3) d e valider l'estimation de l'assimilation en la comparant à une mesure indépendante (technique des corrélations turbulentes, EC). Les mesures (croissance et échanges gazeux) ont été effectuées pendant la saison de végétation 1997 sur cinq hêtres de 30 ans de statuts so ciaux différents (dominant, codominant et dominé). Une relation non linéaire entre l'assimilation nette de CO 2 et le rayonnement photosynthetiquement actif ( PAR) a été établie pour chaque arbre échantillon. L'assimilation nette de CO 2 à l'échelle de la couronne a ensuite été estimée pour une période sans stress hydrique. L'estimation de l'assimilation brute à l'échelle du peuplement à partir de m esures foliaires est en bon accord avec des mesures effectuées à l'échelle du peuplement par EC. croissance / bilan de carbone / photosynthèse / statut social / Fagus sylvaticaL
dnaA protein‐regulated transcription: effects on the in vitro replication of Escherichia coli minichromosomes.

Both initiation of replication and initiation of transcription are influenced by dnaA protein, when minichromosomes are assayed in vitro for dnaA protein complementation. This dnaA protein effect is seen only if minichromosomes are used containing the 16‐kd promoter, from which transcription is directed into the minimal origin. Determination of the 16‐kd promoter activity both in vivo and in vitro showed that this strong promoter is specifically repressed by dnaA protein. The 16‐kd promoter is thus an integral regulatory region of oriC.
Long-term switching to low-tar low-nicotine cigarettes.

Summary Puffing patterns and blood measures of smoke intake were studied in 12 subjects before and after switching to low-tar (10.9 mg) low-nicotine (0.7 mg) cigarettes for 12 weeks. Puff rate, puff volume, total volume puffed per cigarette and the number of cigarettes smoked were not changed significantly after switching lo the lower yield cigarettes. The reduction in mouth-level nicotine intake (calculated from butt content) was identical to the 47 per cent reduction in the machine-smoked nicotine yields. This is in keeping with the measures of puffing in showing the absence of any tendency to compensate for the reduced yields by increasing the intensity of puffing. In contrast, plasma nicotine and cotinine levels were reduced proportionally less than the nominal yields indicating that the subjects compensated to some extent by increasing inhalation. The average reductions in plasma nicotine and cotinine were identical (30per cent). Plasma thiocyanate and COHb levels were not significantly different after switching to the lower yield cigarettes but the estimated tar intake to the lungs was reduced by about 15per cent. Although the low-yield cigarettes were rated as slightly too weak, there was no significant loss of satisfaction. The fact that subjects tolerated a 30 per cent reduction in plasma nicotine without loss of satisfaction and without puffing more intensively suggests that the increase in inhalation was not determined by a need to maintain nicotine intake. This and the, discrepancies between natural and experimental switching studies are discussed.
Dimensions and Categories: The "Big Five" Factors and the DSM Personality Disorders

The five-factor model of personality, which has been widely studied in personality psychology, has been hypothesized to have specific relevance for DSM-defined personality disorders. To evaluate hypothesized relationships of the five-factor model of personality to personality disorders, 144 patients with personality disorders (diagnosed via a structured interview) completed an inventory to assess the five-factor model. Results indicated that the majority of the personality disorders can be differentiated in theoretically predictable ways using the five-factor model of personality. However, while the personality disorders as a whole appear to be differentiable from normal personality functioning on the five factors, the patterns are quite similar across the disorders, a finding that may provide some insight into the general nature of personality pathology but may also suggest problems with discriminant validity. Third, it does not appear that considering disorders as special combinations of features (as might be expected in some categorical models) is more informative than considering them as the sum of certain features (as might be expected in a dimensional model).
Is improvement possible in the measurement of behaviour disturbance in dementia?

Traditionally, cognitive features of dementia have been emphasized at the expense of non-cognitive features. However, the importance of the latter is being increasingly recognized. Non-cognitive features include disorders of behaviour, personality, mood, thought content and perception, and functional disability (Burns et al., 1990a,b; Allen and Burns, 1995). Behaviour disturbance has been a neglected area of research in the context of dementia (Fairburn and Hope, 1988; Nilsson et al., 1988; Ryden, 1988; Finkel, 1996a,b). Explanations for this neglect include the importance attached to cognition in the diagnosis of dementia (Fairburn and Hope, 1988; Devanand et al., 1992), the assumptions that behavioural changes are secondary to cognitive changes (Fairburn and Hope, 1988; Dian et al., 1990) or an expression of personality change (Rubins et al., 1987b; Fairburn and Hope, 1988; Dian et al., 1990), diculties in accurately de®ning behaviour disturbance (Shah, 1998) and paucity of standardized instruments to measure behaviour disturbance (Shah, 1998). Moreover, many types of behaviour disturbances have predominantly been studied under the broad umbrella of behaviour disturbance (Reisberg et al., 1987; Drachman et al., 1992) and thus individual behaviours have often been measured indirectly and fractionally. There are several forms of behaviour disturbances in dementia (Hope and Patel, 1993): aggressive behaviour including irritability and verbal aggression; activity disturbance including pottering, checking and nocturnal wandering; eating behaviour, changes in food preference and eating inedible foods; disturbances of diurnal rhythm such as sundowning and alterations in sleep±wake cycle; sexual behaviour such as self-exposure and attempted fondling; and other miscellaneous behaviours like screaming or the peculiar behaviour of moving objects from one part of the house to another without good reason. Aggressive behaviour is not uncommonly encountered in caring for individuals with dementia (Shah, 1998). Moreover, both mental health professionals and family carers are poor at predicting aggressive behaviour with accuracy (Shah, 1998). It causes considerable distress to relatives and carers (O'Connor et al., 1990; Everitt et al., 1991). It often results in poor receipt of domiciliary services (Shah, 1993), poor pain relief (Cariaga et al., 1991), referral to specialist services (Margo et al., 1980), long-term hospitalization (Shah, 1992; Eastley and Mian, 1993), nursing home placement (Steele et al., 1990), physical restraint (Guirguis and Durost, 1978) and overmedication (Shah, 1993; Martin et al., 1994). Thus, aggressive behaviour will be considered as a `representative' and issues related to its measurement are discussed in detail; similar arguments can be rehearsed for other forms of behaviour disturbances.
Differential patterning of cGMP in vascular smooth muscle cells revealed by single GFP-linked biosensors

Here, we report the design of unprecedented, non-FRET based cGMP-biosensors, named FlincGs, to assess the dynamics of nitric oxide (NO) and atrial natriuretic peptide (ANP) induced synthesis of intracellular cGMP, [cGMP]i. Regulatory fragments of PKG I α, PKG I β, and an N-terminal deletion mutant of PKG I α were fused to circular permutated EGFP to generate α-, β-, and δ-FlincG, with high dynamic ranges and apparent KD,cGMP values of 35 nM, 1.1 μM, and 170 nM, respectively. All indicators displayed significant selectivity for cGMP over cAMP, and 1.5- to 2.1-fold increases in fluorescence intensity at 510 nm when excited at 480 nm. Surprisingly, FlincGs displayed an additional excitation peak at 410 nm. δ-FlincG permitted ratiometric (480/410 nm) measurements, with a cGMP-specific 3.5-fold ratio change. In addition, δ-FlincG presented cGMP association and dissociation kinetics sufficiently fast to monitor rapid changes of [cGMP]i in intact cells. In unpassaged, adenoviral transfected vascular smooth muscle (VSM) cells, δ-FlincG had an EC50,cGMP of 150 nM, and revealed transient global cGMP elevations to sustained physiological NO (EC50,DEA/NO = 4 nM), and the decay phase depended on the activity of PDE-5. In contrast, ANP elicited sustained submembrane elevations in [cGMP]i, which were converted to global cGMP elevations by inhibition of PDE-5 by sildenafil. These results indicate that FlincG is an innovative tool to elucidate the dynamics of a central biological signal, cGMP, and that NO and natriuretic peptides induce distinct cGMP patterning under the regulation of PDE-5, and therefore likely differentially engage cGMP targets.
Competitive Personality Attitudes and Forgiveness of Others

ABSTRACT The authors conducted a survey to determine whether competitive attitudes are differentially associated with forgiveness or lack of forgiveness of others. The results showed that hypercompetitiveness was associated with a lack of forgiveness, whereas personal development competitiveness was associated positively with forgiveness. Discussion centers on the need to discourage socialization practices that foster the adoption of a self-contained individualism that is associated with a maladaptive hypercompetitiveness. Instead, parents should promote an ensembled individualism that is associated with a psychologically healthy personal development competitive orientation.
Attitudes and Beliefs About Hepatitis B Vaccination Among Gay Men: The Birmingham Measurement Study

ABSTRACT This study was designed to develop reliable and valid quantitative measures of the beliefs and attitudes toward hepatitis B virus (HBV) vaccination among gay men, using a community-based participatory research approach. A convenience sample of 358 gay men was recruited in two gay bars. Exploratory factor analysis performed on the first split-half sample was used to assess the factor structure from five scales measuring beliefs about HBV vaccination. The scales were based on constructs from the health belief model and the social cognitive theory. Confirmatory factor analysis was performed on the remaining half-sample using structural equation modeling. Multivariable analysis further validated the scales. These findings propose standardized measures that may be useful in assessing the beliefs and attitudes of gay men toward HBV vaccination to guide intervention design and evaluation.
Molecular characterization of zebrafish embryogenesis via DNA microarrays and multiplatform time course metabolomics studies.

One of the greatest strengths of "-omics" technologies is their ability to capture a molecular snapshot of multiple cellular processes simultaneously. Transcriptomics, proteomics, and metabolomics have, individually, been used in wide-ranging studies involving cell lines, tissues, model organisms, and human subjects. Nonetheless, despite the fact that their power lies in the global acquisition of parallel data streams, these methods continue to be employed separately. We highlight work done to merge transcriptomics and metabolomics technologies to study zebrafish (Danio rerio) embryogenesis. We combine information from three bioanalytical platforms, that is, DNA microarrays, (1)H nuclear magnetic resonance ((1)H NMR), and mass spectrometry (MS)-based metabolomics, to identify and provide insights into the organism's developmental regulators. We apply a customized approach to the analysis of such time-ordered measurements to provide temporal profiles that depict the modulation of metabolites and gene transcription. Initially, the three data sets were analyzed individually but later they were fused to highlight the advantages gained through such an integrated approach. Unique challenges posed by fusion of such data are discussed given differences in the measurement error structures, the wide dynamic range for the molecular species, and the analytical platforms used to measure them (i.e., fluorescence ratios, NMR, and MS intensities). Our data analysis reveals that changes in transcript levels at specific developmental stages correlate with previously published data with over 90% accuracy. In addition, transcript profiles exhibited trends that were similar to the accumulation of metabolites over time. Profiles for metabolites such as choline-like compounds (Trimethylamine-N-oxide, phosphocholine, betaine), creatinine/creatine, and other metabolites involved in energy metabolism exhibited a steady increase from 15 hours post fertilization (hpf) to 48 hpf. Other metabolite and transcript profiles were transiently rising and then falling back to baseline. The "house keeping" metabolites such as branched chain amino acids exhibited a steady presence throughout embryogenesis. Although the transcript profiling corresponds to only 16 384 genes, a subset of the total number of genes in the zebrafish genome, we identified examples where gene transcript and metabolite profiles correlate with one another, reflective of a relationship between gene and metabolite regulation over the course of embryogenesis.
Polyclonal Mycobacterium avium infections in patients with AIDS: variations in antimicrobial susceptibilities of different strains of M. avium isolated from the same patient

Broth microdilution MICs were determined for pairs of strains isolated from five AIDS patients with polyclonal Mycobacterium avium infection. Four (80%) of the five patients were infected simultaneously with strains having different antimicrobial susceptibility patterns. These findings have implications for the interpretation of susceptibility data in M. avium prophylaxis and treatment trials.