DeepSS2GO: protein function prediction from secondary structure.

Predicting protein function is crucial for understanding biological life processes, preventing diseases and developing new drug targets. In recent years, methods based on sequence, structure and biological networks for protein function annotation have been extensively researched. Although obtaining a protein in three-dimensional structure through experimental or computational methods enhances the accuracy of function prediction, the sheer volume of proteins sequenced by high-throughput technologies presents a significant challenge. To address this issue, we introduce a deep neural network model DeepSS2GO (Secondary Structure to Gene Ontology). It is a predictor incorporating secondary structure features along with primary sequence and homology information. The algorithm expertly combines the speed of sequence-based information with the accuracy of structure-based features while streamlining the redundant data in primary sequences and bypassing the time-consuming challenges of tertiary structure analysis. The results show that the prediction performance surpasses state-of-the-art algorithms. It has the ability to predict key functions by effectively utilizing secondary structure information, rather than broadly predicting general Gene Ontology terms. Additionally, DeepSS2GO predicts five times faster than advanced algorithms, making it highly applicable to massive sequencing data. The source code and trained models are available at https://github.com/orca233/DeepSS2GO.

Systematic characterisation of the structure and radical scavenging potency of Pu'Er tea () polyphenol theaflavin.

The structure, energetics and radical scavenging potency of theaflavin (TF), a natural polyphenolic antioxidant found in oxidised tea, have been characterised by a series of density functional theory (DFT) determinations. Exploratory conformational searches yielded 153 distinct neutral structures. Results showed TF's structural preferences to be regulated by its unique fused double ring benzotropolone moiety, and its degree of planarity, with structural diversity, principally arising from variations of its nine -OH groups. The distinct 3D conformational 'poses' are shown to be stabilised by a complex network of intra-system interactions, damping overall structural floppiness. This rigidification, together with stability, is shown to be coupled with radical scavenging potency in the TF system. Radical scavenging via hydrogen atom abstraction (HAB) in H2O solution was determined to be spontaneous with very low reaction barriers (ΔGrel ∼ 4 kJ mol-1).

Burden of atrial fibrillation: a retrospective review of patients presenting to acute medical services.

BACKGROUND: Atrial fibrillation (AF) is a major risk factor for stroke and is associated with increased stroke severity and greater morbidity and mortality. Anticoagulation is highly effective for preventing episodes of thromboembolism but remains under-utilised. AIMS: The aim of this review was to estimate the short-term risk of thromboembolic events in patients presenting with an acute medical illness, to assess rates of anticoagulation in eligible patients with AF and to describe physician decisions when prescribing anticoagulation in a hospital setting. METHODS: A retrospective cohort analysis of patients with AF presenting to acute medical services at Wellington Regional Hospital between 1 January 2012 and 31 December 2012 was performed. RESULTS: A total of 751 patient presentations with AF was identified; 613 unique patient encounters were eligible for analysis, and 38.8% of patients with a CHA2 DS2 -VASc score ≥2 were discharged after anticoagulation. The mean CHA2 DS2 -VASc score was 4.03 (SD = 1.94). The CHA2 DS2 -VASc score was not associated with being started on anticoagulation, odds ratio 1.16 (95% confidence interval = 0.83-1.61), P = 0.38, but age by decade older was associated with a reduced likelihood of being started on anticoagulation, odds ratio 0.61 (95% confidence interval = 0.41-0.89), P = 0.01. In untreated patients with a CHA2 DS2 -VASc score ≥2, the most frequently documented reasons not to initiate anticoagulation were decision deferred to the primary care physician, 15.6%; fall risk or frailty, 7.2%; and high bleeding risk, 6.6%. However, no reason was documented in 56.9%. The thromboembolic rate in patients discharged without anticoagulation within 3 months of presentation to acute medical services was 7/330 (2.1%). CONCLUSION: Anticoagulation for stroke prevention in AF remains under-utilised in eligible patients presenting to acute medical services at a tertiary-level hospital.

Racial intermarriage pairings.

Most studies of racial intermarriage rely on the prevalence of intermarriage to measure the strength of group boundaries, without scrutinizing the nature of intermarriage pairings. Examination of intermarried couples' characteristics reveals (1) that intermarriages and endogamous marriages follow different patterns, and (2) that intermarriage pairings for some groups reflect a generalized racial status hierarchy. According to evidence from the 1990 U.S. Census PUMS, patterns in blacks' and Mexican Americans' marriages with whites suggest that a generalized racial status hierarchy disadvantages members of these minority groups. For marriages between Japanese Americans and whites, however, crossing the group boundary does not affect couples' characteristics.

Functional analysis of the trypanosomal AAA protein TbVCP with trans-dominant ATP hydrolysis mutants.

TbVCP is a member of the AAA (ATPases Associated with a variety of cellular Activities) family of proteins containing two ATPase domains. Southern analysis indicates TbVCP to have a single-locus, two-copy, genomic organization. One copy, but not both, can be disrupted by targeted gene replacement, suggesting that TbVCP is essential for trypanosome viability. Site-directed mutagenesis of the ATP hydrolysis motifs indicates that the second conserved ATPase domain is essential for TbVCP activity. Constitutive overexpression of TbVCP with a single mutation in the second hydrolysis motif or with mutations in both hydrolysis motifs was not possible. Regulated overexpression of these mutants resulted in cell death as a dominant negative phenotype. In each case cell growth arrested at 24-h post-induction and at all stages of the cell cycle as judged by replication of nuclear and kinetoplast genomes. Onset of growth arrest coincided with the development of severe and characteristic morphological alterations for each mutant. Neither constitutive nor regulated overexpression of wild type TbVCP or the single first hydrolysis domain mutant had any overt effect on cell viability or morphology. However, the distinct phenotype of the double mutant indicates that the first hydrolysis domain, although not essential, does modulate overall TbVCP function. Finally, yeast complementation studies demonstrated that TbVCP can functionally replace the yeast homologue Cdc48p, indicating that protein.protein interactions essential to function have been maintained over great phylogenetic distances.

Role of cyclin-dependent kinase inhibitors in the growth arrest at senescence in human prostate epithelial and uroepithelial cells.

Cellular senescence has been proposed to be an in vitro and in vivo block that cells must overcome in order to immortalize and become tumorigenic. To characterize these pathways, we focused on changes in the cyclin-dependent kinase inhibitors and their binding partners that underlie the cell cycle arrest at senescence. As a model, we utilized normal human prostate epithelial cell (HPEC) and human uroepithelial cell (HUC) cultures. After 30-40 population doublings cells became growth-arrested in G0/1 with a threefold decrease in Cdk2-associated activity, a point defined as pre-senescence. Temporally following this growth arrest, the cells develop a senescence morphology and express senescence-associated beta-galactosidase (SA-beta-gal). Levels of p16(INK4a) and p57(KIP2) rise in HUCs during progressive passages, whereas only p16 increases in HPEC cultures. The induced expression of p57, similar to p16, produces a senescent-like phenotype. pRB, cyclin D, p19(INK4d) and p27(KIP1) decrease in both cell types. We find that p53, p21(CIP1) and p15(INK4b) are transiently elevated in HPECs and HUCs at the pre-senescent growth arrest, then return to low proliferating levels at terminal senescence. Analysis of p53, p21(CIP1), p15(INK4b), p16(INK4a), and p57(KIP2) reveals altered expression in immortalized, non-tumorigenic HPV16 E6 and E7 prostate lines and in tumorigenic prostate cancer cells. These results indicate: (i) the existence of a subset of growth inhibiting genes elevated at the onset of the senescence, (ii) a distinct class of genes involved in the maintenance of senescence, and (iii) the frequent inactivation of these pathways during immortalization.

Children's use of inanimate transitional objects in coping with hassles.

This study examined children's use of inanimate transitional objects when coping with daily hassles. Mothers of 50 preschoolers rated their children on frequency of hassles, intensity of reaction to daily hassles, coping effectiveness, and frequency of object use. No significant differences were found between those children with an inanimate transitional object and those without such an object. Among those children with an object, a significant object effect on frequency of hassles (p less than .05) and a significant object effect on coping effectiveness were found. A significant age effect was also found, indicating that older children used their inanimate transitional objects more often than younger children. Among those children with an inanimate transitional object, significant positive relationships were found between frequency of hassles, intensity of reaction to hassles, coping effectiveness, and frequency of object use. The results indicated that children who used their thumb as an inanimate transitional object experienced fewer hassles than children who used a soft object. The results also suggested that an increase in the number of hassles experienced was related to more intense reactions to hassles, less effective coping, and an increase in object use. The nature of the object and the developmental issue of separation-individuation are considered as well.

Self-esteem of adolescent girls as related to weight.

The Rosenberg Self-esteem Scale was administered to 550 14- and 16-yr.-old (+/- 6 mo.) girls. Self-esteem scores were categorized by weight and weight by height. Scores on the Quetelet Index for obesity were correlated with self-esteem scores. Mean self-esteem of the low- and middle-weight by height group was significantly higher than the mean of the high-weight by height group. In analyzing weight alone, the self-esteem of the middle-weight group was significantly higher than the self-esteem of the high-weight group. The correlation of the obesity index and self-esteem indicated that as weight increased self-esteem decreased.

Divergent thinking and hemispheric dominance for language function among preschool children.

An investigation of the relationship of hemispheric dominance (dichotic listening) and divergent thinking (Torrance Tests of Creative Thinking) with 27 preschool children (11 males and 16 females; mean age of 4-8) indicated a positive relationship between right hemispheric dominance and scores on the Product Improvement task. Low intertask correlations suggested that the Unusual Uses and Product Improvement tasks were not measuring the same construct. These findings were discussed with regard to nature of the task (stimulus specificity) and the age of the subjects in this study. The findings show that divergent thinking is associated with right hemispheric dominance in children as young as 4 years.

Preschool children's understanding of children with orthopedic disabilities and their expectations.

The present study investigated whether preschool children (N = 121) had a realistic understanding of the limitations imposed by various orthopedic disabilities. The results have indicated that the preschoolers were aware that orthopedic disabilities may impose some physical limitations. Ss tended to perceive able-bodied children more capable in performing various tasks than disabled children. This evaluative judgment does not necessarily mean that the preschoolers were discriminating against the disabled children, but it may be a reflection of a sense of realism that the able-bodied children have less trouble in doing these tasks than their disabled counterpart. It was suggested that, with increased understanding of the realistic limitations imposed by orthopedic disabilities, children may be come less biased toward their disabled peers. This change in attitude would have significant impact on the self-concepts of disabled children.