Sports training enhances visuo-spatial cognition regardless of open-closed typology
The aim of this study was to investigate the effects of open and closed sport participation on visuo-spatial attention and memory performance among young adults. Forty-eight young adults—16 open-skill athletes, 16 closed-skill athletes, and 16 non-athletes controls—were recruited for the study. Both behavioral performance and event-related potential (ERP) measurement were assessed when participants performed non-delayed and delayed match-to-sample task that tested visuo-spatial attention and memory processing. Results demonstrated that regardless of training typology, the athlete groups exhibited shorter reaction times in both the visuo-spatial attention and memory conditions than the control group with no existence of speed-accuracy trade-off. Similarly, a larger P3 amplitudes were observed in both athlete groups than in the control group for the visuo-spatial memory condition. These findings suggest that sports training, regardless of typology, are associated with superior visuo-spatial attention and memory performance, and more efficient neural resource allocation in memory processing.
Chueh et al. (2017) Sports training enhances visuo-spatial cognition regardless of open-closed typology. PeerJ 5:e3336 https://doi.org/10.7717/peerj.3336
pathVar: a new method for pathway-based interpretation of gene expression variability
Identifying the pathways that control a cellular phenotype is the first step to building a mechanistic model. Recent examples in developmental biology, cancer genomics, and neurological disease have demonstrated how changes in the variability of gene expression can highlight important genes that are under different degrees of regulatory control. Simple statistical tests exist to identify differentially-variable genes; however, methods for investigating how changes in gene expression variability in the context of pathways and gene sets are under-explored. Here we present pathVar, a new method that provides functional interpretation of gene expression variability changes at the level of pathways and gene sets. pathVar is based on a multinomial exact test, or an asymptotic Chi-squared test as a more computationally-efficient alternative. The method can be used for gene expression studies from any technology platform in all biological settings either with a single phenotypic group, or two-group comparisons. To demonstrate its utility, we applied the method to a diverse set of diseases, species and samples. Results from pathVar are benchmarked against analyses based on average expression and two methods of GSEA, and demonstrate that analyses using both statistics are useful for understanding transcriptional regulation. We also provide recommendations for the choice of variability statistic that have been informed through analyses on simulations and real data. Based on the datasets selected, we show how pathVar can be used to gain insight into expression variability of single cell versus bulk samples, different stem cell populations, and cancer versus normal tissue comparisons.
de Torrente et al. (2017) pathVar: a new method for pathway-based interpretation of gene expression variability. PeerJ 5:e3334 https://doi.org/10.7717/peerj.3334
Comparison in antioxidant and antitumor activities of pine polyphenols and its seven biotransformation extracts by fungi
Microbial transformation can strengthen the antioxidant and antitumor activities of polyphenols. Polyphenols contents, antioxidant and antitumor activities of pine polyphenols and its biotransformation extracts by Aspergillus niger, Aspergillus oryzae, Aspergillus carbonarius, Aspergillus candidus, Trichodermas viride, Mucor wutungkiao and Rhizopus sp were studied. Significant differences were noted in antioxidant and antitumor activities. The highest antioxidant activities in Trolox equivalent antioxidant capacity (TEAC), DPPH radical scavenging activity, superoxide anion radical scavenging activity, hydroxyl radical scavenging activity, reducing power assay and antitumor activity against LoVo cells were biotransformation extract of Aspergillus carbonarius (BAC), biotransformation extract of Mucor wutungkiao (BMW), biotransformation extract of Aspergillus carbonarius (BAC), biotransformation extract of Aspergillus niger (BAN), biotransformation extract of Aspergillus oryzae (BAO) and BMW, respectively. Correlation analysis found that antioxidant and antitumor activities were associated with polyphenols contents and types of free radicals and tumors. A. carbonarius can make polyphenol oxidation, hydroxylation and methylation, and form new polyphenols. In conclusion, A. carbonarius, A. niger and M. wutungkiao are valuable microorganisms used for polyphenols biotransformation and enhance the antioxidant and antitumor activities of polyphenols.
Li et al. (2017) Comparison in antioxidant and antitumor activities of pine polyphenols and its seven biotransformation extracts by fungi. PeerJ 5:e3264 https://doi.org/10.7717/peerj.3264
A mixed methods study of multiple health behaviors among individuals with stroke
Background Individuals with stroke often have multiple cardiovascular risk factors that necessitate promoting engagement in multiple health behaviors. However, observational studies of individuals with stroke have typically focused on promoting a single health behavior. Thus, there is a poor understanding of linkages between healthy behaviors and the circumstances in which factors, such as stroke impairments, may influence a single or multiple health behaviors. Methods We conducted a mixed methods convergent parallel study of 25 individuals with stroke to examine the relationships between stroke impairments and physical activity, sleep, and nutrition. Our goal was to gain further insight into possible strategies to promote multiple health behaviors among individuals with stroke. This study focused on physical activity, sleep, and nutrition because of their importance in achieving energy balance, maintaining a healthy weight, and reducing cardiovascular risks. Qualitative and quantitative data were collected concurrently, with the former being prioritized over the latter. Qualitative data was prioritized in order to develop a conceptual model of engagement in multiple health behaviors among individuals with stroke. Qualitative and quantitative data were analyzed independently and then were integrated during the inference stage to develop meta-inferences. The 25 individuals with stroke completed closed-ended questionnaires on healthy behaviors and physical function. They also participated in face-to-face focus groups and one-to-one phone interviews. Results We found statistically significant and moderate correlations between hand function and healthy eating habits (r = 0.45), sleep disturbances and limitations in activities of daily living (r = − 0.55), BMI and limitations in activities of daily living (r = − 0.49), physical activity and limitations in activities of daily living (r = 0.41), mobility impairments and BMI (r = − 0.41), sleep disturbances and physical activity (r = − 0.48), sleep disturbances and BMI (r = 0.48), and physical activity and BMI (r = − 0.45). We identified five qualitative themes: (1) Impairments: reduced autonomy, (2) Environmental forces: caregivers and information, (3) Re-evaluation: priorities and attributions, (4) Resiliency: finding motivation and solutions, and (5) Negative affectivity: stress and self-consciousness. Three meta-inferences and a conceptual model described circumstances in which factors could influence single or multiple health behaviors. Discussion This is the first mixed methods study of individuals with stroke to elaborate on relationships between multiple health behaviors, BMI, and physical function. A conceptual model illustrates addressing sleep disturbances, activity limitations, self-image, and emotions to promote multiple health behaviors. We discuss the relevance of the meta-inferences in designing multiple behavior change interventions for individuals with stroke.
Plow et al. (2017) A mixed methods study of multiple health behaviors among individuals with stroke. PeerJ 5:e3210 https://doi.org/10.7717/peerj.3210
A comparison of freezing-damage during isochoric and isobaric freezing of the potato
Background Freezing is commonly used for food preservation. It is usually done under constant atmospheric pressure (isobaric). While extending the life of the produce, isobaric freezing has detrimental effects. It causes loss of food weight and changes in food quality. Using thermodynamic analysis, we have developed a theoretical model of the process of freezing in a constant volume system (isochoric). The mathematical model suggests that the detrimental effects associated with isobaric freezing may be reduced in an isochoric freezing system. To explore this hypothesis, we performed a preliminary study on the isochoric freezing of a produce with which our group has experience, the potato. Method Experiments were performed in an isochoric freezing device we designed. The device is robust and has no moving parts. For comparison, we used a geometrically identical isobaric freezing device. Following freezing and thawing, the samples were weighed, examined with colorimetry, and examined with microscopy. Results It was found that potatoes frozen to −5 °C in an isochoric system experienced no weight loss and limited enzymatic browning. In contrast the −5 °C isobaric frozen potato experienced substantial weight loss and substantial enzymatic browning. Microscopic analysis shows that the structural integrity of the potato is maintained after freezing in the isochoric system and impaired after freezing in the isobaric system. Discussion Tissue damage during isobaric freezing is caused by the increase in extracellular osmolality and the mechanical damage by ice crystals. Our thermodynamic analysis predicts that during isochoric freezing the intracellular osmolality remains comparable to the extracellular osmolality and that isochoric systems can be designed to eliminate the mechanical damage by ice. The results of this preliminary study seem to confirm the theoretical predictions. Conclusion This is a preliminary exploratory study on isochoric freezing of food. We have shown that the quality of a food product preserved by isochoric freezing is better than the quality of food preserved to the same temperature in isobaric conditions. Obviously, more extensive research remains to be done to extend this study to lower freezing temperatures and other food items.
Lyu et al. (2017) A comparison of freezing-damage during isochoric and isobaric freezing of the potato. PeerJ 5:e3322 https://doi.org/10.7717/peerj.3322
StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees
Background Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide trees. Results A tool named StrainSeeker was developed that constructs a list of specific k-mers for each node of any given Newick-format tree and enables the identification of bacterial isolates in 1–2 min. It uses a novel algorithm, which analyses the observed and expected fractions of node-specific k-mers to test the presence of each node in the sample. This allows StrainSeeker to determine where the isolate branches off the guide tree and assign it to a clade whereas other tools assign each read to a reference genome. Using a dataset of 100 Escherichia coli isolates, we demonstrate that StrainSeeker can predict the clades of E. coli with 92% accuracy and correct tree branch assignment with 98% accuracy. Twenty-five thousand Illumina HiSeq reads are sufficient for identification of the strain. Conclusion StrainSeeker is a software program that identifies bacterial isolates by assigning them to nodes or leaves of a custom-made guide tree. StrainSeeker’s web interface and pre-computed guide trees are available at http://bioinfo.ut.ee/strainseeker. Source code is stored at GitHub: https://github.com/bioinfo-ut/StrainSeeker.
Roosaare et al. (2017) StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees. PeerJ 5:e3353 https://doi.org/10.7717/peerj.3353
Exoskeleton may influence the internal body temperatures of Neotropical dung beetles (Col. Scarabaeinae)
The insect exoskeleton is a multifunctional coat with a continuum of mechanical and structural properties constituting the barrier between electromagnetic waves and the internal body parts. This paper examines the ability of beetle exoskeleton to regulate internal body temperature considering its thermal permeability or isolation to simulated solar irradiance and infrared radiation. Seven Neotropical species of dung beetles (Coleoptera, Scarabaeinae) differing in colour, surface sculptures, size, sexual dimorphism, period of activity, guild category and altitudinal distribution were studied. Specimens were repeatedly subjected to heating trials under simulated solar irradiance and infrared radiation using a halogen neodymium bulb light with a balanced daylight spectrum and a ceramic infrared heat emitter. The volume of exoskeleton and its weight per volume unit were significantly more important for the heating rate at the beginning of the heating process than for the asymptotic maximum temperature reached at the end of the trials: larger beetles with relatively thicker exoskeletons heated more slowly. The source of radiation greatly influences the asymptotic temperature reached, but has a negligible effect in determining the rate of heat gain by beetles: they reached higher temperatures under artificial sunlight than under infrared radiation. Interspecific differences were negligible in the heating rate but had a large magnitude effect on the asymptotic temperature, only detectable under simulated sun irradiance. The fact that sun irradiance is differentially absorbed dorsally and transformed into heat among species opens the possibility that differences in dorsal exoskeleton would facilitate the heat gain under restrictive environmental temperatures below the preferred ones. The findings provided by this study support the important role played by the exoskeleton in the heating process of beetles, a cuticle able to act passively in the thermal control of body temperature without implying energetic costs and metabolic changes.
Amore et al. (2017) Exoskeleton may influence the internal body temperatures of Neotropical dung beetles (Col. Scarabaeinae). PeerJ 5:e3349 https://doi.org/10.7717/peerj.3349
Atorvastatin alters the expression of genes related to bile acid metabolism and circadian clock in livers of mice
Aim Atorvastatin is a HMG-CoA reductase inhibitor used for hyperlipidemia. Atorvastatin is generally safe but may induce cholestasis. The present study aimed to examine the effects of atorvastatin on hepatic gene expression related to bile acid metabolism and homeostasis, as well as the expression of circadian clock genes in livers of mice. Methods Adult male mice were given atorvastatin (10, 30, and 100 mg/kg, po) daily for 30 days, and blood biochemistry, histopathology, and gene expression were examined. Results Repeated administration of atorvastatin did not affect animal body weight gain or liver weights. Serum enzyme activities were in the normal range. Histologically, the high dose of atorvastatin produced scattered swollen hepatocytes, foci of feathery-like degeneration, together with increased expression of Egr-1 and metallothionein-1. Atorvastatin increased the expression of Cyp7a1 in the liver, along with FXR and SHP. In contract, atorvastatin decreased the expression of bile acid transporters Ntcp, Bsep, Ostα, and Ostβ. The most dramatic change was the 30-fold induction of Cyp7a1. Because Cyp7a1 is a circadian clock-controlled gene, we further examined the effect of atorvastatin on clock gene expression. Atorvastatin increased the expression of clock core master genes Bmal1 and Npas2, decreased the expression of clock feedback genes Per2, Per3, and the clock targeted genes Dbp and Tef, whereas it had no effect on Cry1 and Nr1d1 expression. Conclusion Repeated administration of atorvastatin affects bile acid metabolism and markedly increases the expression of the bile acid synthesis rate-limiting enzyme gene Cyp7a1, together with alterations in the expression of circadian clock genes.
Li et al. (2017) Atorvastatin alters the expression of genes related to bile acid metabolism and circadian clock in livers of mice. PeerJ 5:e3348 https://doi.org/10.7717/peerj.3348
Predictive ability of the Mini Nutritional Assessment Short Form (MNA-SF) in a free-living elderly population: a cross-sectional study
Background Various scales have been used to perform a quick and first level nutritional assessment, and the MNA is one of the most used and recommended by experts in the elderly in all areas. This scale has a short form, the MNA-SF, revised and validated in 2009, which has two versions: the BMI-MNA-SF contains the first six items of the full scale including Body Mass Index while the CC-MNA-SF includes Calf Circumference instead of BMI. Objective To evaluate the predictive ability for nutritional status of the two versions of the MNA-SF against the MNA in free-living elderly in the province of Valencia. Methods Cross-sectional study of 660 free-living elderly in the province of Valencia selected in 12 community centres using stratified sampling by blocks. Inclusion criteria: being aged 65 or over, living at home, having functional autonomy, residing in the province of study for more than one year, regularly attending community centres and voluntarily wanting to take part. Results Of the 660 subjects studied, 319 were men (48.3%) and 341 (51.7%) women with a mean age of 74.3 years (SD = 6.6). In terms of nutritional assessment, using the BMI-MNA-SF and the CC-MNA-SF we found that 26.5% and 26.2% were at risk of malnutrition and 0.9% and 1.5% were malnourished respectively. With the full MNA, 23.3% were at risk of malnutrition. Spearman’s rank correlation coefficients indicate a high association between the full MNA score and the MNA-SFs scores (BMI-MNA-SF: ρ = 0.78p < 0.001; CC-MNA-SF: ρ = 0.78p < 0.001). In addition we obtained a very high correlation between the two MNA-SFs (ρ = 0.96p < 0.001). We evaluated the agreement between the full MNA and the MNA-SFs classification in three nutritional categories (normal nutritional status, risk of malnutrition, malnutrition) with Cohen’s kappa coefficients (BMI-MNA-SF: κ = 0.54p < 0.001; CC-MNA-SF: κ = 0.52p < 0.001). These values indicate moderate agreement with the full MNA. There is very good agreement between the BMI-MNA-SF and CC-MNA-SF (κ = 0.88p < 0.001). In order to determine the ability of both MNA-SFs to identify subjects not requiring any nutritional intervention, we considered the dichotomised categorisation of the full MNA and the MNA-SFs as “normal nutritional status” vs. “malnutrition and risk of malnutrition” Areas under the ROC curves using MNA as the gold standard indicate moderately high prognostic accuracy (BMI-MNA-SF: AUC = 0.88p < 0.001; CC-MNA-SF: AUC = 0.87 p < 0.001). Both versions of the MNA-SF showed similar sensitivity, specificity and diagnostic effectiveness (BMI-MNA-SF: 73.4%, 86.6%, 83.5%; CC-MNA-SF 73.4%, 86.2%, 83.2%). Conclusions In its two versions the MNA-SF presents useful predictive ability against the MNA. The advantage of the CC-MNA-SF is that using it requires fewer resources and less time in primary care, although always the characteristics of the population must take into account to make the right decision based on the MNA-SF scales.
Montejano Lozoya et al. (2017) Predictive ability of the Mini Nutritional Assessment Short Form (MNA-SF) in a free-living elderly population: a cross-sectional study. PeerJ 5:e3345 https://doi.org/10.7717/peerj.3345
Comparative transcriptome analyses of a late-maturing mandarin mutant and its original cultivar reveals gene expression profiling associated with citrus fruit maturation
Characteristics of late maturity in fruit are good agronomic traits for extending the harvest period and marketing time. However, underlying molecular basis of the late-maturing mechanism in fruit is largely unknown. In this study, RNA sequencing (RNA-Seq) technology was used to identify differentially expressed genes (DEGs) related to late-maturing characteristics from a late-maturing mutant ‘Huawan Wuzishatangju’ (HWWZSTJ) (Citrus reticulata Blanco) and its original line ‘Wuzishatangju’ (WZSTJ). A total of approximately 17.0 Gb and 84.2 M paried-end reads were obtained. DEGs were significantly enriched in the pathway of photosynthesis, phenylpropanoid biosynthesis, carotenoid biosynthesis, chlorophyll and abscisic acid (ABA) metabolism. Thirteen candidate transcripts related to chlorophyll metabolism, carotenoid biosynthesis and ABA metabolism were analyzed using real-time quantitative PCR (qPCR) at all fruit maturing stages of HWWZSTJ and WZSTJ. Chlorophyllase (CLH) and divinyl reductase (DVR) from chlorophyll metabolism, phytoene synthase (PSY) and capsanthin/capsorubin synthase (CCS) from carotenoid biosynthesis, and abscisic acid 8′-hydroxylase (AB1) and 9-cis-epoxycarotenoid dioxygenase (NCED1) from ABA metabolism were cloned and analyzed. The expression pattern of NCED1 indicated its role in the late-maturing characteristics of HWWZSTJ. There were 270 consecutive bases missing in HWWZSTJ in comparison with full-length sequences of NCED1 cDNA from WZSTJ. Those results suggested that NCED1 might play an important role in the late maturity of HWWZSTJ. This study provides new information on complex process that results in the late maturity of Citrus fruit at the transcriptional level.
Wang et al. (2017) Comparative transcriptome analyses of a late-maturing mandarin mutant and its original cultivar reveals gene expression profiling associated with citrus fruit maturation. PeerJ 5:e3343 https://doi.org/10.7717/peerj.3343