Weighted p-value adjustments for animal carcinogenicity trend test

A typical animal carcinogenicity experiment routinely analyzes approximately 10-30 tumor sites. Comparisons of tumor responses between dosed and control groups and dose-related trend tests are often evaluated for each individual tumor site/type separately. p-Value adjustment approaches have been proposed for controlling the overall Type I error rate or familywise error rate (FWE). However, these adjustments often result in reducing the power to detect a dose effect. This paper proposes using weighted adjustments by assuming that each tumor can be classified as either class A or class B based on prior considerations. The tumors in class A, which are considered as more critical endpoints, are given less adjustment. Two weighted methods of adjustments are presented, the weighted p adjustment and weighted alpha adjustment. A Monte Carlo simulation shows that both weighted adjustments control the FWE well. Furthermore, the power increases if a treatment-dependent tumor is analyzed as in class A tumors and the power decreases if it is analyzed as in class B tumors. A data set from a National Toxicology Program (NTP) 2-year animal carcinogenicity experiment with 13 tumor types/sites observed in male mice was analyzed using the proposed methods. The modified poly-3 test was used to test for increased carcinogenicity since it has been adopted by the NTP as a standard test for a dose-related trend. The unweighted adjustment analysis concluded that there was no statistically significant dose-related trend. Using the Food and Drug Administration classification scheme for the weighted adjustment analyses, two rare tumors (with background rates of 1% or less) were analyzed as class A tumors and 11 common tumors (with background rates higher than 1%) as class B. Both weighted analyses showed a significant dose-related trend for one rare tumor.     

Arterial vascularization of the mandible and maxilla of neotropical primates

The objective of the present investigation was to conduct a comparative macroscopic study of the arterial vascularization of the mandible and maxilla of neotropical primates of the genera Cebus, Alouatta, Callithrix, and Leontopithecus. After vinyl was injected into the arterial system of the head of each specimen, the pieces were macerated and corroded. The level of the bifurcation of the common carotid artery into the internal and external carotids varied between the first and third cervical vertebrae. The external carotid artery accounts for most of the vascularization of the facial structures. The actual vessels responsible for the supply of this region are the sublingual, facial, angular, lingual, submandibular, submental, inferior and superior labial, maxillary, inferior alveolar, infraorbital, superior posterior alveolar, palatine major, and sphenopalatine arteries. We conclude that although the arterial vascular pattern was similar in all the genera studied, and resembles the human pattern, there are notable variations in the vasculature of the mandible and maxilla among these four neotropical genera.     

Differential activities of the two closely related withanolides, withaferin a and withanone: bioinformatics and experimental evidences

BACKGROUND AND PURPOSE: Withanolides are naturally occurring chemical compounds. They are secondary metabolites produced via oxidation of steroids and structurally consist of a steroid-backbone bound to a lactone or its derivatives. They are known to protect plants against herbivores and have medicinal value including anti-inflammation, anti-cancer, adaptogenic and anti-oxidant effects. Withaferin A (Wi-A) and Withanone (Wi-N) are two structurally similar withanolides isolated from Withania somnifera, also known as Ashwagandha in Indian Ayurvedic medicine. Ashwagandha alcoholic leaf extract (i-Extract), rich in Wi-N, was shown to kill cancer cells selectively. Furthermore, the two closely related purified phytochemicals, Wi-A and Wi-N, showed differential activity in normal and cancer human cells in vitro and in vivo. We had earlier identified several genes involved in cytotoxicity of i-Extract in human cancer cells by loss-of-function assays using either siRNA or randomized ribozyme library. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, we have employed bioinformatics tools on four genes, i.e., mortalin, p53, p21 and Nrf2, identified by loss-of-function screenings. We examined the docking efficacy of Wi-N and Wi-A to each of the four targets and found that the two closely related phytochemicals have differential binding properties to the selected cellular targets that can potentially instigate differential molecular effects. We validated these findings by undertaking parallel experiments on specific gene responses to either Wi-N or Wi-A in human normal and cancer cells. We demonstrate that Wi-A that binds strongly to the selected targets acts as a strong cytotoxic agent both for normal and cancer cells. Wi-N, on the other hand, has a weak binding to the targets; it showed milder cytotoxicity towards cancer cells and was safe for normal cells. The present molecular docking analyses and experimental evidence revealed important insights to the use of Wi-A and Wi-N for cancer treatment and development of new anti-cancer phytochemical cocktails.     

Assessment of metals in agricultural soil of surrounding areas of Urmia Lake,northwest Iran: A preliminary ecological risk assessment and source identification

The aim of this study was to quantify the levels of toxic heavy metals and sodium in topsoil of farmlands around the Urmia Lake. A total of 96 topsoil samples were collected, pre-treated, and analyzed for metals using ICP-AES.

Median concentrations of As, Cd, Cu, Ni, Pb, Zn, and Na in sampling sites were 5, 0.26, 30, 40, 13, 84, and 251 mg/kg, respectively. The enrichment factor, geoaccumulation index, and contamination factor of the metals ranked them in the order of: Na > Pb > Cu > As > Cd > Zn > Ni, indicating minor contamination for them except Na and Pb with moderate contamination. Furthermore, the spatial analysis indicated that Cd, Cu, Pb, Ni, and Zn had similar distribution patterns in the north and northwest lands of the lake. Principal component analysis revealed anthropogenic sources for Cd, Cu, Ni, Pb, and Zn in the soil, whereas, sources of As and Na were most likely related to the dust emitting from the dried bed of Urmia Lake and from a cement industry. Potential ecological risk index in 7% of the sampling sites was at serious or considerable pollution level, and Cd and Pb were identified as the main pollutants.     

Age‐specific reference intervals for routine biochemical parameters in healthy neonates,infants, and young children in Iran

Age and sex need to be considered in the establishment of reference intervals (RIs), especially in early life when there are dynamic physiological changes. Since data for important biomarkers in healthy neonates and infants are limited, particularly in Iranian populations, we have determined age‐specific RIs for 7 laboratory biochemical parameters. This cross‐sectional study comprised a total of 344 paediatric participants (males: 158, females: 186) between the ages of 3 days and 30 months (mean age: 12.91 ± 7.15 months). Serum levels of creatinine, urea, uric acid, calcium, phosphate, vitamin D and high‐sensitivity C‐reactive protein (hs‐CRP) were measured using an Alpha classic‐AT plus auto‐analyser. We determined age‐specific RIs using CLSI Ep28‐A3 and C28‐A3 guidelines. No sex partitioning was required for any of the biomarkers. Age partitioning was required for kidney function tests and phosphate. The serum concentration of urea and creatinine increased with age, while phosphate and uric acid decreased with age. Age partitioning was not required for serum calcium, vitamin D, and hs‐CRP, which remained relatively constant throughout the age range. Age‐specific RIs for 7 routine biochemical markers were determined to address critical gaps in RIs in early life to help improve clinical interpretation of blood test results in young children, including neonates. Established age partitions demonstrate the biochemical changes that take place during child growth and development. These novel data will ultimately better disease management in the Iranian paediatric population and can be of value to clinical and hospital laboratories with similar populations.     

Down-regulation of cell surface receptors is modulated by polar residues within the transmembrane domain

How recycling receptors are segregated from down-regulated receptors in the endosome is unknown. In previous studies, we demonstrated that substitutions in the transferrin receptor (TR) transmembrane domain (TM) convert the protein from an efficiently recycling receptor to one that is rapidly down regulated. In this study, we demonstrate that the "signal" within the TM necessary and sufficient for down-regulation is Thr(11)Gln(17)Thr(19) (numbering in TM). Transplantation of these polar residues into the wild-type TR promotes receptor down-regulation that can be demonstrated by changes in protein half-life and in receptor recycling. Surprisingly, this modification dramatically increases the TR internalization rate as well ( approximately 79% increase). Sucrose gradient centrifugation and cross-linking studies reveal that propensity of the receptors to self-associate correlates with down-regulation. Interestingly, a number of cell surface proteins that contain TM polar residues are known to be efficiently down-regulated, whereas recycling receptors for low-density lipoprotein and transferrin conspicuously lack these residues. Our data, therefore, suggest a simple model in which specific residues within the TM sequences dramatically influence the fate of membrane proteins after endocytosis, providing an alternative signal for down-regulation of receptor complexes to the well-characterized cytoplasmic tail targeting signals.     

High-valent iron complexes with tetraamido macrocyclic ligands: structures, Mössbauer spectroscopy, and DFT calculations

Iron complexes of tetraamido macrocyclic ligands (TAML) are unique synthetic oxidation catalysts. In general, the central Fe(III) ion (S=3/2) is surrounded by four, almost planar, deprotonated amide-N sigma-donors although the full suite with new generation systems includes some substitution of amides with related donor functionalities. Oxidation under different conditions affords a variety of high-valent forms of iron-TAMLs. This review provides a summary and discussion of structural and spectroscopic features of complexes oxidized by one equivalent above the ferric state. These comprise Fe(IV)-TAML high spin (S=2) and intermediate spin (S=1) systems, wherein the oxidation equivalent can be taken from the metal (Fe(IV)) or the ligand (TAML radical-cation Fe(III)), and coupled spin (S=0) systems of mu-oxoiron(IV) dimers. The discussion is principally based on data obtained by X-ray crystallography, M?ssbauer spectroscopy, and density functional theory calculations.