Assessing the Role of Livestock in Big Cat Prey Choice Using Spatiotemporal Availability Patterns

Livestock is represented in big cat diets throughout the world. Husbandry approaches aim to reduce depredation, which may influence patterns of prey choice, but whether felids have a preference for livestock or not often remains unclear as most studies ignore livestock availability. We assessed prey choice of the endangered Persian leopard (Panthera pardus saxicolor) in Golestan National Park, Iran, where conflict over livestock depredation occurs. We analyzed leopard diet (77 scats) and assessed wild and domestic prey abundance by line transect sampling (186 km), camera-trapping (2777 camera days), double-observer point-counts (64 scans) and questionnaire surveys (136 respondents). Based on interviews with 18 shepherds, we estimated monthly grazing time outside six villages with 96 conflict cases to obtain a small livestock (domestic sheep and goat) availability coefficient. Using this coefficient, which ranged between 0.40 and 0.63 for different villages, we estimated the numbers of sheep and goats available to leopard depredation. Leopard diet consisted mainly of wild boar (Sus scrofa) (50.2% biomass consumed), but bezoar goat (Capra aegagrus) was the most preferred prey species (I_j = 0.73), whereas sheep and goats were avoided (I_j = -0.54). When absolute sheep and goat numbers (~11250) were used instead of the corrected ones (~6392), avoidance of small livestock appeared to be even stronger (I_j = -0.71). We suggest that future assessments of livestock choice by felids should incorporate such case-specific corrections for spatiotemporal patterns of availability, which may vary with husbandry methods. Such an approach increases our understanding of human-felid conflict dynamics and the role of livestock in felid diets.     

Anti-inflammatory effects of resolvins in diabetic nephropathy: Mechanistic pathways

The incidence of diabetes mellitus is growing rapidly. The exact pathophysiology of diabetes is unclear, but there is increasing evidence of the role of the inflammatory response in both developing diabetes as well as its complications. Resolvins are naturally occurring polyunsaturated fatty acids that are found in fish oil and sea food that have been shown to possess anti-inflammatory actions in several tissues including the kidneys. The pathways by which resolvins exert this anti-inflammatory effect are unclear. In this review we discuss the evidence showing that resolvins can suppress inflammatory responses via at least five molecular mechanisms through inhibition of the nucleotide-binding oligomerization domain protein 3 inflammasome, inhibition of nuclear factor κB molecular pathways, improvement of oxidative stress, modulation of nitric oxide synthesis/release and prevention of local and systemic leukocytosis. Complete understanding of these molecular pathways is important as this may lead to the development of new effective therapeutic strategies for diabetes and diabetic nephropathy.     

Potential roles of microRNAs in redox state: An update

Oxidative stress is an important underlying cause of many disease processes and may arise due to either increasing free radical generation or decreasing antioxidant defense systems. MicroRNAs (miRs) are 22-nucleotide non-coding RNAs that may regulate many intracellular processes; and, more recently, they have been implicated in the pathways for free radical generation leading to oxidative stress. However, conversely, there is evidence that miRs may have an antioxidant effect, thus miR expression may be critical for the maintenance of the normal redox state and cell homeostasis. This review addresses these discrepant and opposing miR actions on how they may modify and regulate the oxidative balance.     

Sodium–glucose cotransporter 2 inhibitors and inflammation in chronic kidney disease: Possible molecular pathways

Clinical trials with sodium–glucose cotransporter 2 (SGLT2) inhibitors (empagliflozin, dapagliflozin, and canagliflozin) have shown a decrease in the progression of chronic kidney disease (CKD). SGLT2 inhibitors represent a new category of oral antidiabetic agents that can also reduce systolic and diastolic blood pressure, as well as serum uric acid, and improve the glomerular filtration rate. Apart from affecting renal hemodynamics and glycotoxicity, evidence suggests that SGLT2 inhibitors may be renoprotective due to their effects on inflammation in renal tissues. Inflammatory responses play a prominent role in the pathophysiology of CKD as several structural and functional disorders of renal failure are strongly related to the overproduction of proinflammatory mediators. The present review discusses the anti-inflammatory properties of SGLT2 inhibitors. The different molecular pathways through which SGLT2 inhibitors may affect inflammation in the kidneys are also commented upon.     

Demethoxycurcumin: A naturally occurring curcumin analogue for treating non-cancerous diseases

Turmeric extracts contain three primary compounds, which are commonly referred to as curcuminoids. They are curcumin, demethoxycurcumin (DMC), and bisdemethoxycurcumin. While curcumin has been the most extensively studied of the curcuminoids, it suffers from low overall oral bioavailability due to extremely low absorption as a result of low water solubility and instability at acidic pH, as well as rapid metabolism and clearance from the body. However, DMC, which lacks the methoxy group on the benzene ring of the parent structure, has much greater chemical stability at physiological pH and has been recently reported to exhibit antitumor properties. However, the treatment of noncancerous diseases with DMC has not been comprehensively reviewed. Therefore, here we evaluate published scientific literature on the therapeutic properties of DMC. The beneficial pharmacological actions of DMC include anti-inflammatory, neuroprotective, antihypertensive, antimalarial, antimicrobial, antifungal, and vasodilatory properties. In addition, DMC's ability to ameliorate the effects of free radicals and an environment characterized by oxidative stress caused by the accumulation of advanced glycation end-products associated with diabetic nephropathy, as well as DMC's capacity to inhibit the migration and proliferation of vascular smooth muscle cells following balloon angioplasty are also addressed. This review collates the available literature regarding the therapeutic possibilities of DMC in noncancerous conditions.     

Prevalence,pathological mechanisms,and genetic basis of limb-girdle muscular dystrophies: A review

Limb-girdle muscular dystrophies (LGMDs) are a highly heterogeneous group of neuromuscular disorders that are associated with weakness and wasting of muscles in legs and arms. Signs and symptoms may begin at any age and usually worsen by time. LGMDs are autosomal disorders with different types and their prevalence is not the same in different areas. New technologies such as next-generation sequencing can accelerate their diagnosis. Several important pathological mechanisms that are involved in the pathology of the LGMD include abnormalities in dystrophin–glycoprotein complex, the sarcomere, glycosylation of dystroglycan, vesicle and molecular trafficking, signal transduction pathways, and nuclear functions. Here, we provide a comprehensive review that integrates LGMD clinical manifestations, prevalence, and some pathological mechanisms involved in LGMDs.     

Human germline and pan-cancer variomes and their distinct functional profiles

Identification of non-synonymous single nucleotide variations (nsSNVs) has exponentially increased due to advances in Next-Generation Sequencing technologies. The functional impacts of these variations have been difficult to ascertain because the corresponding knowledge about sequence functional sites is quite fragmented. It is clear that mapping of variations to sequence functional features can help us better understand the pathophysiological role of variations. In this study, we investigated the effect of nsSNVs on more than 17 common types of post-translational modification (PTM) sites, active sites and binding sites. Out of 1 705 285 distinct nsSNVs on 259 216 functional sites we identified 38 549 variations that significantly affect 10 major functional sites. Furthermore, we found distinct patterns of site disruptions due to germline and somatic nsSNVs. Pan-cancer analysis across 12 different cancer types led to the identification of 51 genes with 106 nsSNV affected functional sites found in 3 or more cancer types. 13 of the 51 genes overlap with previously identified Significantly Mutated Genes (Nature. 2013 Oct 17;502(7471)). 62 mutations in these 13 genes affecting functional sites such as DNA, ATP binding and various PTM sites occur across several cancers and can be prioritized for additional validation and investigations.     

Census-based rapid and accurate metagenome taxonomic profiling

Background

Understanding the taxonomic composition of a sample, whether from patient, food or environment, is important to several types of studies including pathogen diagnostics, epidemiological studies, biodiversity analysis and food quality regulation. With the decreasing costs of sequencing, metagenomic data is quickly becoming the preferred typed of data for such analysis.

Results

Rapidly defining the taxonomic composition (both taxonomic profile and relative frequency) in a metagenomic sequence dataset is challenging because the task of mapping millions of sequence reads from a metagenomic study to a non-redundant nucleotide database such as the NCBI non-redundant nucleotide database (nt) is a computationally intensive task. We have developed a robust subsampling-based algorithm implemented in a tool called CensuScope meant to take a ‘sneak peak’ into the population distribution and estimate taxonomic composition as if a census was taken of the metagenomic landscape. CensuScope is a rapid and accurate metagenome taxonomic profiling tool that randomly extracts a small number of reads (based on user input) and maps them to NCBI’s nt database. This process is repeated multiple times to ascertain the taxonomic composition that is found in majority of the iterations, thereby providing a robust estimate of the population and measures of the accuracy for the results.

Conclusion

CensuScope can be run on a laptop or on a high-performance computer. Based on our analysis we are able to provide some recommendations in terms of the number of sequence reads to analyze and the number of iterations to use. For example, to quantify taxonomic groups present in the sample at a level of 1% or higher a subsampling size of 250 random reads with 50 iterations yields a statistical power of >99%. Windows and UNIX versions of CensuScope are available for download at https://hive.biochemistry.gwu.edu/dna.cgi?cmd=censuscope. CensuScope is also available through the High-performance Integrated Virtual Environment (HIVE) and can be used in conjunction with other HIVE analysis and visualization tools.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-918) contains supplementary material, which is available to authorized users.     

Air kerma strength characterization of a GZP6 Cobalt-60 brachytherapy source

Background

Task group number 40 (TG-40) of the American Association of Physicists in Medicine (AAPM) has recommended calibration of any brachytherapy source before its clinical use. GZP6 afterloading brachytherapy unit is a ⁶⁰Co high dose rate (HDR) system recently being used in some of the Iranian radiotherapy centers.

Aim

In this study air kerma strength (AKS) of ⁶⁰Co source number three of this unit was estimated by Monte Carlo simulation and in air measurements.

Materials and methods

Simulation was performed by employing the MCNP-4C Monte Carlo code. Self-absorption of the source core and its capsule were taken into account when calculating air kerma strength. In-air measurements were performed according to the multiple distance method; where a specially designed jig and a 0.6 cm³ Farmer type ionization chamber were used for the measurements. Monte Carlo simulation, in air measurement and GZP6 treatment planning results were compared for primary air kerma strength (as for November 8th 2005).

Results

Monte Carlo calculated and in air measured air kerma strength were respectively equal to 17240.01 μGym² h⁻¹ and 16991.83 μGym² h⁻¹. The value provided by the GZP6 treatment planning system (TPS) was “15355 μGym² h⁻¹”.

Conclusion

The calculated and measured AKS values are in good agreement. Calculated-TPS and measured-TPS AKS values are also in agreement within the uncertainties related to our calculation, measurements and those certified by the GZP6 manufacturer. Considering the uncertainties, the TPS value for AKS is validated by our calculations and measurements, however, it is incorporated with a large uncertainty.