Identification of limiting climatic and geographical variables for the distribution of the tortoise Chelonoidis chilensis (Testudinidae): a baseline for conservation actions
Background. Just as for most other tortoise species, the once common Chaco tortoise, Chelonoidis chilensis (Testudinidae), is under constant threat across it distribution in Argentina, Bolivia and Paraguay. Despite initial qualitative description of the species distribution and further individual reports of new locations for the species, there is no description of the species distribution in probabilistic terms. With this work we aim to produce an updated predictive distribution map for C. chilensis to serve as a baseline management tool for directed strategic conservation planning. Methods. We fitted a spatially expanded logistic regression model within the Bayesian framework that accounts for uncertainty on presence-only and generated pseudo-absence data into the parameter estimates. We contrast the results with reported data for the national networks of protected areas to assess the inclusion of the species in area-based conservation strategies. Results. We obtained maps with predictions of the occurrence of the species and reported the model’s uncertainty spatially. The model suggests that potential suitable habitats for the species are continuous across Argentina, West Paraguay and South Bolivia, considering the variables, the scale and the resolution used. The main limiting variables were temperature-related variables, and precipitation in the reproductive period. Discussion. Given the alarming low density and coverage of protected areas over the distribution area of C. chilensis, the map produced provides a baseline to identify areas where directed strategic conservation management actions would be more efficient for this and other associated species.
Ruete et al. (2015) Identification of limiting climatic and geographical variables for the distribution of the tortoise Chelonoidis chilensis (Testudinidae): a baseline for conservation actions. PeerJ 3:e1298 https://doi.org/10.7717/peerj.1298
Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair
The hair is a filamentous biomaterial consisting of the cuticle, the cortex and the medulla, all held together by the cell membrane complex. The cortex mostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3–90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of the α-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers.
Zhang et al. (2015) Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair. PeerJ 3:e1296 https://doi.org/10.7717/peerj.1296
Metapopulation dynamics are jointly regulated by local and spatial factors. These factors may affect the dynamics of local populations and of the entire metapopulation differently. Previous studies have shown that dispersal can stabilize local populations; however, as dispersal also tends to increase spatial synchrony, its net effect on metapopulation stability has been controversial. Here we present a simple metapopulation model to study how dispersal, in interaction with other spatial and local processes, affects the temporal variability of metapopulations in a stochastic environment. Our results show that in homogeneous metapopulations, the local stabilizing and spatial synchronizing effects of dispersal cancel each other out, such that dispersal has no effect on metapopulation variability. This result is robust to moderate heterogeneities in local and spatial parameters. When local and spatial dynamics exhibit high heterogeneities, however, dispersal can either stabilize or destabilize metapopulation dynamics through various mechanisms. Our findings have important theoretical and practical implications. We show that dispersal functions as a form of spatial intraspecific mutualism in metapopulation dynamics and that its effect on metapopulation stability is opposite to that of interspecific competition on local community stability. Our results also suggest that conservation corridors should be designed with appreciation of spatial heterogeneities in population dynamics in order to maximize metapopulation stability.
Wang et al. (2015) Dispersal and metapopulation stability. PeerJ 3:e1295 https://doi.org/10.7717/peerj.1295
Investigation into the effects of antioxidant-rich extract of Tamarindus indica leaf on antioxidant enzyme activities, oxidative stress and gene expression profiles in HepG2 cells
The leaf extract of Tamarindus indica L. (T. indica) had been reported to possess high phenolic content and showed high antioxidant activities. In this study, the effects of the antioxidant-rich leaf extract of the T. indica on lipid peroxidation, antioxidant enzyme activities, H2O2-induced ROS production and gene expression patterns were investigated in liver HepG2 cells. Lipid peroxidation and ROS production were inhibited and the activity of antioxidant enzymes superoxide dismutase, catalase and glutathione peroxidase was enhanced when the cells were treated with the antioxidant-rich leaf extract. cDNA microarray analysis revealed that 207 genes were significantly regulated by at least 1.5-fold (p < 0.05) in cells treated with the antioxidant-rich leaf extract. The expression of KNG1, SERPINC1, SERPIND1, SERPINE1, FGG, FGA, MVK, DHCR24, CYP24A1, ALDH6A1, EPHX1 and LEAP2 were amongst the highly regulated. When the significantly regulated genes were analyzed using Ingenuity Pathway Analysis software, “Lipid Metabolism, Small Molecule Biochemistry, Hematological Disease” was the top biological network affected by the leaf extract, with a score of 36. The top predicted canonical pathway affected by the leaf extract was the coagulation system (P < 2.80 × 10−6) followed by the superpathway of cholesterol biosynthesis (P < 2.17 × 10−4), intrinsic prothrombin pathway (P < 2.92 × 10−4), Immune Protection/Antimicrobial Response (P < 2.28 × 10−3) and xenobiotic metabolism signaling (P < 2.41 × 10−3). The antioxidant-rich leaf extract of T. indica also altered the expression of proteins that are involved in the Coagulation System and the Intrinsic Prothrombin Activation Pathway (KNG1, SERPINE1, FGG), Superpathway of Cholesterol Biosynthesis (MVK), Immune protection/antimicrobial response (IFNGR1, LEAP2, ANXA3 and MX1) and Xenobiotic Metabolism Signaling (ALDH6A1, ADH6). In conclusion, the antioxidant-rich leaf extract of T. indica inhibited lipid peroxidation and ROS production, enhanced antioxidant enzyme activities and significantly regulated the expression of genes and proteins involved with consequential impact on the coagulation system, cholesterol biosynthesis, xenobiotic metabolism signaling and antimicrobial response.
Razali et al. (2015) Investigation into the effects of antioxidant-rich extract of Tamarindus indica leaf on antioxidant enzyme activities, oxidative stress and gene expression profiles in HepG2 cells. PeerJ 3:e1292 https://doi.org/10.7717/peerj.1292
Association among smoking, depression, and anxiety: findings from a representative sample of Korean adolescents
This study investigated the relationship between smoking and depression and anxiety using data from a nationwide survey representing Korean adolescents. Subjects were 6,489 adolescents in middle and high school (age 13–18) who had participated in the 2011 Korean Study of Promotion Policies on Children and Adolescents—Mental Health (KSPCAM). Daily smoking number of times for current smokers was classified as 1–2 times, 2–4 times and over 5 times. The odds ratio for the statistical test was presented using hierarchical logistic regression. When adjusted for covariates (gender, age, household economy, type of residing city, type of school, school record, satisfaction with school life, subjective health status, satisfaction with relationship with parents, and drinking experience), smokers more significantly likely to have depression (OR = 1.27, 95% CI [1.02–1.57]), and anxiety (OR = 1.49, 95% CI [1.14–1.96]) than non-smokers (p < 0.05). In addition, adolescents who smoke more than 5 cigarettes a day were 1.5 times more likely to have depression (OR = 1.48, 95% CI [1.13–1.92]) and anxiety (OR = 1.49, 95% CI [1.07–2.08]) than those who do not smoke. Smoking in adolescence was found to be significantly related with depression and anxiety. To promote the mental health of adolescents, effective smoking cessation programs are required.
Byeon (2015) Association among smoking, depression, and anxiety: findings from a representative sample of Korean adolescents. PeerJ 3:e1288 https://doi.org/10.7717/peerj.1288
Nodes with high centrality in protein interaction networks are responsible for driving signaling pathways in diabetic nephropathy
In spite of huge efforts, chronic diseases remain an unresolved problem in medicine. Systems biology could assist to develop more efficient therapies through providing quantitative holistic sights to these complex disorders. In this study, we have re-analyzed a microarray dataset to identify critical signaling pathways related to diabetic nephropathy. GSE1009 dataset was downloaded from Gene Expression Omnibus database and the gene expression profile of glomeruli from diabetic nephropathy patients and those from healthy individuals were compared. The protein-protein interaction network for differentially expressed genes was constructed and enriched. In addition, topology of the network was analyzed to identify the genes with high centrality parameters and then pathway enrichment analysis was performed. We found 49 genes to be variably expressed between the two groups. The network of these genes had few interactions so it was enriched and a network with 137 nodes was constructed. Based on different parameters, 34 nodes were considered to have high centrality in this network. Pathway enrichment analysis with these central genes identified 62 inter-connected signaling pathways related to diabetic nephropathy. Interestingly, the central nodes were more informative for pathway enrichment analysis compared to all network nodes and also 49 differentially expressed genes. In conclusion, we here show that central nodes in protein interaction networks tend to be present in pathways that co-occur in a biological state. Also, this study suggests a computational method for inferring underlying mechanisms of complex disorders from raw high-throughput data.
Abedi et al. (2015) Nodes with high centrality in protein interaction networks are responsible for driving signaling pathways in diabetic nephropathy. PeerJ 3:e1284 https://doi.org/10.7717/peerj.1284
Risk factors and prognosis of hypoalbuminemia in surgical septic patients
The aim of this study was to investigate the risk factors of hypoalbuminemia and effects of different albumin levels on the prognosis of surgical septic patients. We preformed a retrospective clinical study including 135 adult patients from September 2011 to June 2014. The albumin levels and severity markers were recorded during the first 48 h after enrollment, and logistic regression analyses were used to determine the risk factors. The outcomes of patients with different albumin levels were also compared. The acute physiology and chronic health evaluation II (APACHE II) score (OR 1.786, 95% CI [1.379–2.314], P < 0.001), C-reactive protein (CRP) (OR 1.016, 95% CI [1.005–1.027], P = 0.005), and blood lactate (OR 1.764, 95% CI [1.141–2.726], P = 0.011) were established as the independent risk factors of hypoalbuminemia in patients with surgical sepsis. The severity markers and outcomes of patients with albumin levels ≤20 g/L were significantly worse than that of 21–25 g/L and ≥26 g/L, whereas the latter two groups had similar prognosis. Every 1 g/L decrease of albumin level below the optimal cut-off (23 g/L) was associated with a 19.4% increase in hospital mortality and a 28.7% increase in the incidence of multiple organ dysfunction syndrome. In conclusion, APACHE II score (≥14.5), CRP (≥34.25 mg/L), and blood lactate (≥.35 mmol/L) were established as the independent risk factors of hypoalbuminemia in the early stage of surgical sepsis. Patients with baseline albumin level ≤20 g/L had worse prognosis than that of albumin level ≥21 g/L. Albumin levels were negatively correlated the prognosis of surgical sepsis when below about 23 g/L.
Sun et al. (2015) Risk factors and prognosis of hypoalbuminemia in surgical septic patients. PeerJ 3:e1267 https://doi.org/10.7717/peerj.1267
Measuring the well-being of health care professionals in the Punjab: a psychometric evaluation of the Warwick–Edinburgh Mental Well-being Scale in a Pakistani population
Background. There is growing awareness of the public health importance of mental well-being both in the general population and in specific groups. The well-being of health professionals is likely to influence the quality of the care they deliver. This study was carried out to examine the well-being of Pakistani healthcare professionals, and to evaluate the psychometric performance of the Warwick–Edinburgh Mental Well-being Scale (WEMWBS) in this population. Methods. A cross-sectional survey was carried out from June, 2013 to December, 2014 among 1,271 Pakistani health care providers (HCPs) working in seven different cities in Punjab province, Pakistan, to examine the acceptability, internal consistency, test-retest reliability and content and construct validity of the English version of the WEMWBS in a Pakistani population sample. All data were analyzed in SPSS v. 21. Results. Our analysis demonstrated unidimensional construct validity, high internal consistency (0.89) and test-retest reliability, good validity and easy readability of WEMWBS in our sample of Pakistani HCPs. The mean WEMWBS score was 48.1 (SD 9.4), which is lower than in the general population in other countries. Male HCPs scored significantly higher on the WEMWBS than their female counterparts (P < 0.05), and older respondents had higher scores. Conclusion. The WEMWBS appears acceptable for use in Pakistani HCPs, and findings from this study verify its validity and internal consistency for this population sample. Our respondents had lower well-being scores than those reported in general population surveys in the UK.
Waqas et al. (2015) Measuring the well-being of health care professionals in the Punjab: a psychometric evaluation of the Warwick–Edinburgh Mental Well-being Scale in a Pakistani population. PeerJ 3:e1264 https://doi.org/10.7717/peerj.1264
The prevalence and anatomical characteristics of the accessory head of the flexor pollicis longus muscle: a meta-analysis
Background and Objectives. The accessory head of the flexor pollicis longus muscle (AHFPL), also known as the Gantzer’s muscle, was first described in 1813. The prevalence rates of an AHFPL significantly vary between studies, and no consensus has been reached on the numerous variations reported in its origin, innervation, and relationships to the Anterior Interosseous Nerve (AIN) and the Median Nerve (MN). The aim of our study was to determine the true prevalence of AHFPL and to study its associated anatomical characteristics. Methods. A search of the major electronic databases PubMed, EMBASE, Scopus, ScienceDirect, and Web of Science was performed to identify all articles reporting data on the prevalence of AHPFL in the population. No date or language restriction was set. Additionally, an extensive search of the references of all relevant articles was performed. Data on the prevalence of the AHFPL in upper limbs and its anatomical characteristics and relationships including origin, insertion, innervation, and position was extracted and pooled into a meta-analysis using MetaXL version 2.0. Results. A total of 24 cadaveric studies (n = 2,358 upper limb) were included in the meta-analysis. The pooled prevalence of an AHFPL was 44.2% (95% CI [0.347–0.540]). An AHFPL was found more commonly in men than in women (41.1% vs. 24.1%), and was slightly more prevalent on the right side than on the left side (52.8% vs. 45.2%). The most common origin of the AHFPL was from the medial epicondyle of the humerus with a pooled prevalence of 43.6% (95% CI [0.166–0.521]). In most cases, the AHFPL inserted into the flexor pollicis longus muscle (94.6%, 95% CI [0.731–1.0]) and was innervated by the AIN (97.3%, 95% CI [0.924–0.993]). Conclusion. The AHFPL should be considered as more a part of normal anatomy than an anatomical variant. The variability in its anatomical characteristics, and its potential to cause compression of the AIN and MN, must be taken into account by physicians to avoid iatrogenic injury during decompression procedures and to aid in the diagnosis and treatment of Anterior Interosseous Nerve Syndrome.
Roy et al. (2015) The prevalence and anatomical characteristics of the accessory head of the flexor pollicis longus muscle: a meta-analysis. PeerJ 3:e1255 https://doi.org/10.7717/peerj.1255
Population subdivision of the surf clam Mactra chinensis in the East China Sea: Changjiang River outflow is not the sole driver
The northwestern Pacific, characterized by unique tectonic and hydrological settings, has greatly intrigued marine phylogeographers. However, current studies mostly focus on the influence of Pleistocene isolation of sea basins in population structure of species in the region, leaving the contribution of other factors (such as freshwater outflow and environmental gradients) largely unexploited. Here we shed light on the question by investigating phylogeography of the surf clam Mactra chinensis in the East China Sea (ECS). Genetic information was acquired from 501 specimens collected from its main distribution in the region, represented by mitochondrial cytochrome oxidase I (COI) and nine polymorphic microsatellite loci. A shallow and star-like phylogeny was revealed for all COI haplotypes, indicating the origin of populations from a single refugium. Although no divergent lineages existed, population subdivision was detected in both data sets. The most striking pattern was the significant differentiation between populations north and south of a biogeographic boundary—the Changjiang Estuary, suggesting a barrier effect of the freshwater outflow to gene flow. For the northern group, substructure was revealed by COI result as one southernmost population was significant different from other ones. Clear latitude gradations in allele frequencies were revealed by microsatellite analyses, likely influenced by environmental gradient factors such as temperature. Our results demonstrate that genetic subdivision can arise for populations within the ECS despite they have a single origin, and multiple mechanisms including Changjiang River outflow, environmental gradient factors and life-history traits may act in combination in the process.
Ni et al. (2015) Population subdivision of the surf clam Mactra chinensis in the East China Sea: Changjiang River outflow is not the sole driver. PeerJ 3:e1240 https://doi.org/10.7717/peerj.1240