Nobiletin alleviates methotrexate-induced hepatorenal toxicity in rats

We investigated the possible ameliorative effects of nobiletin (NBL) against methotrexate (MTX)-induced hepatorenal toxicity in rats. Twenty-eight Wistar albino rats were randomly divided into four groups, namely: Control; MTX (administered 20 mg/kg MTX); MTX+NBL (administered 20 mg/kg MTX and 10 mg/kg NBL per day); and NBL (administered 10 mg/kg/day NBL). Histopathological, immunohistochemical and biochemical analyses were performed on the kidney and liver tissues of rats at the end of the study. MTX caused renal toxicity, as indicated by increases in malondialdehyde (MDA) and caspase-3, as well as decreases in reduced glutathione (GSH), glucose-6-phosphate dehydrogenase (G6PD), glutathione peroxidase (GPx), catalase (CAT) and B-cell lymphoma-2 (Bcl-2). MTX also caused hepatotoxicity, as indicated by increases in 8-hydroxy-2'-deoxyguanosine (8-OHdG), tumor necrosis factor alpha (TNF-α), MDA and caspase-3 and decrease in interleukin 10 (IL-10), GSH, total antioxidant capacity, GPx, G6PD, CAT and Bcl-2. MTX caused histopathological changes in kidney and liver tissues indicating tissue and cellular damage. Administration of NBL concurrently with methotrexate reduced oxidative stress, inflammatory and apoptotic signs, and prevented kidney and liver damage caused by methotrexate. We consider NBL has attenuating and ameliorating effects on methotrexate-induced hepatorenal toxicity.

The effect of tyrosol on diclofenac sodium-induced acute nephrotoxicity in rats

Although diclofenac (DCF) is a nonsteroidal anti-inflammatory drug that is considered safe, its chronic use and overdose may show some toxic effects. The protective effect of tyrosol (Tyr) pretreatment against DCF-induced renal damage was investigated in this study. The 32 rats used in the study were randomly divided into four groups of eight rats each. According to the data obtained, it was determined that creatinine, urea, and blood urea nitrogen (BUN) levels increased in serum samples of the DCF group. Besides, the levels of reduced glutathione (GSH) and glutathione peroxidase (GPx) activity decreased and the malondialdehyde (MDA) level increased in the kidney tissue. However, no change was observed in catalase (CAT) activity. Cyclooxygenase-2 (COX-2), nuclear factor kappa B (NF-κB), and tumor necrosis factor-alpha (Tnf-α) levels increased and nuclear factor erythroid 2-related factor 2 (Nrf-2) levels decreased. No change was detected in the level of interleukin 1 beta (IL-1β). When the DCF+Tyr group and the DCF group were compared, it was assessed that Tyr had a curative effect on all biochemical parameters. Also, kidney damages, such as degeneration and necrosis of tubular epithelium and congestion of veins, were obviated by treatment with tyrosol in histopathological examinations. It was determined that Tyr pretreatment provided a protective effect against nephrotoxicity induced by DCF with its anti-inflammatory and antioxidant properties.

Carvacrol showed a curative effect on reproductive toxicity caused by Bisphenol AF via antioxidant, anti-inflammatory and anti-apoptotic properties

Bisphenol AF (BPAF) is an endocrine disruptor, and human exposure to these chemicals is growing in industrialized nations. BPAF has been demonstrated in studies to have toxic effects on reproductive health. This study examined the effects of oral exposure to BPAF on the reproductive system and the protective effects of carvacrol in rats. From 32 Wistar albino rats, four separate groups were set up for this purpose. Carvacrol 75 mg/kg and BPAF 200 mg/kg were administered by oral gavage method. Rat sperm parameters and serum testosterone levels were measured after 28 days of administration. The study looked at the MDA in the testis tissues, as well as CAT, GPx, and GSH as antioxidants parameters, NF-κB and TNF-α as inflammatory markers, caspase-3 and Bcl-2 as apoptosis parameters, and PCNA as cell proliferation markers. In addition, testis tissues underwent histological evaluation. As a result, in rats exposed to only BPAF, sperm counts declined, testosterone levels reduced, oxidative stress, inflammation, and apoptosis increased, and cell proliferation decreased. Furthermore, severe disruptions in tissue architecture and decreased spermatogenesis were reported. In contrast, sperm parameters improved, testosterone levels increased, oxidative stress and inflammation decreased, and apoptosis was prevented in the carvacrol-treated group compared to the BPAF-only group. It was also found that spermatogenesis was maintained, and structural abnormalities in testicular tissue were mostly avoided with an increase in PCNA expression. According to the findings, despite BPAF-induced testicular and reproductive toxicity, carvacrol had therapeutic potential due to its anti-inflammatory, antioxidant, cell proliferation-increasing, and anti-apoptotic activities.

Inhibitory effect of stinging nettle (Urtica dioica L.) extract on body weight gain in rats on a high-fat diet

Introduction

The leaves and seeds of Urtica dioica (UD) are used in folk treatments for many diseases. Anticarcinogenic, anti-inflammatory, antioxidant, and antiallergenic properties of UD have been reported.

Aim

To uncover the effects of nettle seed (Urtica dioica; UD) extract on body weight gain in rats on a high-fat diet (HFD).

Material and methods

Male Wistar albino rats (n = 32) were divided into 4 groups, comprising a control group, a group that received a HFD (HFD group), a group that received UD extracts (UD group), and a group that received a HFD as well as UD extracts (HFD + UD group). UD extracts were given a daily dose of 300 mg/kg of body weight orally for 75 days.

Results

The HFD led to weight gain that was partially moderated by the UD extract. Histopathological findings in the HFD + UD group were uniformly significantly lower than those in the HFD group. Serum alanine transaminase, alanine aminotransferase, triglyceride, and low-density lipoprotein levels were significantly higher in the HFD group than in the HFD + UD group, and the HDL levels were lower in the HFD group than in the control group and the HFD + UD group.

Conclusions

The cholesterol levels were discovered to be highest in the HFD + UD group. Therefore, it was concluded that the UD extract did not completely protect the rats against body weight gain.

Exploring of the ameliorative effects of Nerium (Nerium oleander L.) ethanolic flower extract in streptozotocin induced diabetic rats via biochemical, histological and molecular aspects

BACKGROUND

Nerium oleander L. is ethnopharmacologically used for diabetes. Our aim was to investigate the ameliorative effects of ethanolic Nerium flower extract (NFE) in STZ-induced diabetic rats.

METHODS

Seven random groups including control group, NFE group (50 mg/kg), diabetic group, glibenclamide group and NFE treated groups (25 mg/kg, 75 mg/kg, and 225 mg/kg) were composed of forty-nine rats. Blood glucose level, glycated hemoglobin (HbA1c), insulin level, liver damage parameters and lipid profile parameters were investigated. Antioxidant defense system enzyme activities and reduced glutathione (GSH) and malondialdehyde (MDA) contents and immunotoxic and neurotoxic parameters were determined in liver tissue. Additionally, the ameliorative effects of NFE were histopathologically examined in liver. mRNA levels of SLC2A2 gene encoding glucose transporter 2 protein were measured by quantitative real time PCR.

RESULTS

NFE caused decrease in glucose level and HbA1c and increase in insulin and C-peptide levels. Additionally, NFE improved liver damage biomarkers and lipid profile parameters in serum. Moreover, lipid peroxidation was prevented and antioxidant enzyme activities in liver were regulated by NFE treatment. Furthermore, anti-immunotoxic and anti-neurotoxic effects of NFE were determined in liver tissue of diabetic rats. Histopathogically, significant liver damages were observed in the diabetic rats. Histopathological changes were decreased partially in the 225 mg/kg NFE treated group. SLC2A2 gene expression in liver of diabetic rats significantly reduced compared to healthy rats and NFE treatment (25 mg/kg) caused increase in gene expression.

CONCLUSION

Flower extract of Nerium plant may have an antidiabetic potential due to its high phytochemical content.

Inula viscosa ameliorates acetic acid induced ulcerative colitis in rats

Increased pro-inflammatory cytokines and oxidative stress contribute to the pathophysiology of ulcerative colitis (UC). Inula viscosa is a plant with antioxidant and anti-inflammatory properties. We investigated the effect of an ethanolic extract of I. viscosa on an experimental UC model created using acetic acid. Rats were divided into four groups of eight: group 1, control; group 2, 3% acetic acid group; group 3, 100 mg/kg sulfasalazine + 3% acetic acid group; group 4, 400 mg/kg I. viscosa + 3% acetic acid. I. viscosa and sulfasalazine were administered by oral gavage and 3% acetic acid was administered per rectum. We found that I. viscosa treatment decreased colon malondialdehyde, tumor necrosis factor-α, interleukin-1 beta and nuclear factor kappa B levels; it increased reduced glutathione, nuclear factor erythroid 2-related factor 2, heme oxygenase-1 and kelch-like ECH-associated protein 1 levels and glutathione peroxidase enzyme activity. Group 1 colon exhibited normal histological structure. Slight inflammatory cell infiltration and edema and insignificant slight erosion in crypts were detected in colon tissues of group 4. We found that I. viscosa reduced oxidative stress and inflammation, which was protective against UC by inducing the Nrf-2/Keap-1/HO-1 pathway in the colon.

The protective effect of arbutin against potassium bromate-induced oxidative damage in the rat brain

This study aimed to investigate the protective effects of arbutin (ARB) against brain injury induced in rats with potassium bromate (KBrO₃ ). The rats were divided into four groups as Group 1: Control (0.9% NaCl ml/kg/day p.), Group 2: KBrO₃ (100 mg/kg (gavage), Group 3: ARB (50 mg/kg/day p.), and Group 4: KBrO₃  + ARB (100 mg/kg (gavage) + 50 mg/kg/day p.). At the end of the fifth day of the study, the rats in all groups were killed, and their brain tissues were collected. In the collected brain tissues, malondialdehyde (MDA), superoxide dismutase (SOD), and catalase (CAT) levels were measured, and routine histopathological examinations were made. The MDA levels in the group that was exposed to KBrO₃ were significantly higher than those in the control group (p ˂ 0.001). In comparison to the KBrO₃ group, the MDA levels in the KBrO₃  + ARB group were significantly lower (p ˂ 0.001). It was observed that SOD and CAT enzyme activity levels were significantly lower in the KBrO₃ group compared to the control group (p ˂ 0.001), while these levels were significantly higher in the KBrO₃  + ARB group than in the KBrO₃ group (p ˂ 0.001). Additionally, the group that was subjected to KBrO₃ toxicity, as well as ARB administration, had much lower levels of histopathologic signs than the group that was subjected to KBrO₃ toxicity only. Consequently, it was found that KBrO₃ exposure led to injury in the brain tissues of the rats, and using ARB was effective in preventing this injury.

A subvulvar leiomyosarcoma in a Simmental cow - a case report

In this case, a mass located subcutaneously in the perineal subvulvar region of a six-year-old Simmental cow was examined clinically, pathomorphologically and immunohistochemically. Macroscopically, the solitary, whitishyellow-tumor mass was 19x15x6 cm in size, weighed 1610 grams, and had a lobular structure with a few small cystic formations in the section. Histopathological examination revealed that the tumor parenchyma had smooth muscle-like cells with abundant cytoplasm, pleomorphic cells with blunt-ended or cigar-shaped nuclei, anisocytosis, anisokaryosis and karyomegaly. Immunohistochemically, strong positive expression for α-SMA, vimentin, Ki67 and slight positive for desmin were found, while immulolabeling for pancytokeratin (AE1/AE3), S-100, CD31 and CD34 were negative. In conclusion, on the basis of these findings, the tumor was diagnosed as leiomyosarcoma.

HPTMT Parallel Operators for High Performance Data Science and Data Engineering

Data-intensive applications are becoming commonplace in all science disciplines. They are comprised of a rich set of sub-domains such as data engineering, deep learning, and machine learning. These applications are built around efficient data abstractions and operators that suit the applications of different domains. Often lack of a clear definition of data structures and operators in the field has led to other implementations that do not work well together. The HPTMT architecture that we proposed recently, identifies a set of data structures, operators, and an execution model for creating rich data applications that links all aspects of data engineering and data science together efficiently. This paper elaborates and illustrates this architecture using an end-to-end application with deep learning and data engineering parts working together. Our analysis show that the proposed system architecture is better suited for high performance computing environments compared to the current big data processing systems. Furthermore our proposed system emphasizes the importance of efficient compact data structures such as Apache Arrow tabular data representation defined for high performance. Thus the system integration we proposed scales a sequential computation to a distributed computation retaining optimum performance along with highly usable application programming interface.

Ameliorative Effects of Oleuropein on Lipopolysaccharide-Induced Acute Lung Injury Model in Rats

Acute lung injury (ALI) is one of the most common causes of death in diseases with septic shock. Oleuropein, one of the important components of olive leaf, has antioxidant and anti-inflammatory effects. The objective of this study was to investigate the effects of oleuropein on lipopolysaccharide (LPS)-induced ALI in rats. Oleuropein was administered to rats at a dose of 200 mg/kg for 20 days and LPS was given through intratracheal administration to induce ALI. The study was terminated after 12 h. The results showed that in the group treated with oleuropein, inflammatory cytokines and oxidative stress decreased in serum, bronchoalveolar lavage fluid (BALF), and lung tissue, and there were significant improvements in the picture of acute interstitial pneumonia (AIP) caused by LPS in histopathological examination. Based on the findings of the present study, oleuropein showed protective effects against LPS-induced ALI.

Tyrosol improves ovalbumin (OVA)-induced asthma in rat model through prevention of airway inflammation

Asthma is an inflammatory disease that affects many people around the world, especially persons at paediatric age group. The effectiveness of tyrosol, a natural phenolic compound, was examined in the asthma model induced by ovalbumin (OVA). For this purpose, four groups, each consisting of eight rats, were arranged. For 21 days, physiological saline solution was treated to the control group and OVA was treated to the groups of OVA, OVA + dexamethasone (Dexa) and OVA + tyrosol groups, intraperitoneally and through inhalation. Additionally, 0.25 mg/kg Dexa was treated to the OVA + Dexa group and 20 mg/kg tyrosol to the OVA + tyrosol group by oral gavage. Serum, blood, bronchoalveolar lavage fluid (BALF) and lung tissues of the rats were examined. It was observed that MDA level decreased, GSH level and GPx activity increased, and there was no change in CAT activity in lung tissues of the tyrosol treatment groups. It was also observed that NF-κB, TNF-α, IL-4, IL-5, IL-13, IFN-γ and IgE levels decreased compared to the OVA group in lung tissue and serum samples except for serum NF-κB and IL-4. However, no effect on IL-1 β level was observed. In addition, it was determined that tyrosol treatment increased the IL-10 level on both tissue samples. The results of the histopathological investigation of lung tissue showed that tyrosol significantly ameliorated OVA-induced histopathological lesions. Additionally, PAS staining showed that mucus hypersecretion was significantly reduced with the use of tyrosol. In addition, it was determined that the number of eosinophils decreased significantly in blood and BALF samples. The obtained results showed that tyrosol possessed antioxidant and anti-inflammatory features on OVA-induced rats and preserved tissue architecture.

The protective effects of the Lactarius deliciosus and Agrocybe cylindracea mushrooms on histopathology of carbon tetrachloride induced oxidative stress in rats

We investigated the protective effects of L. deliciosus and A. cylindracea supplementation against carbon tetrachloride (CCI₄) induced oxidative stress by measuring levels of adenosine deaminase (ADA) and myeloperoxidase (MPO), and by observing histopathological changes in liver and kidney tissues of rats. We divided 36 rats into six groups: control, CCl₄, L. deliciosus, A. cylindracea, CCl₄ + L. deliciosus, and CCl₄ + A. cylindracea. We found that administration of CCI₄, A. cylindracea, and CCl₄ + A. cylindracea increased MPO and ADA levels. We observed severe hepato-renal degenerative and necrotic lesions in the CCI₄, A. cylindracea and CCl₄ + A. cylindracea groups. Severe lesions of the liver and kidney were not observed with A. cylindracea administration. CCI₄ induced hepato-renal lesions were ameliorated by L. deliciosus extract supplementation. L. deliciosus could be an important dietary antioxidant for preventing histologic lesions in liver and kidney due to CCI₄ induced oxidative stress in rats.

The Protective Role of Urtica dioica Seed Extract Against Azoxymethane-Induced Colon Carcinogenesis in Rats

The aim of this study was to investigate the protective role of Urtica dioica seed (UDS) extract against azoxymethane (AOM)-induced colon carcinogenesis in rats. Thirty-two male Wistar albino rats were divided into four groups: Control, AOM, AOM + UDS, and UDS. The AOM and AOM + UDS groups were induced by AOM (15 mg/kg body weight) subcutaneously once a week for 10 weeks. AOM + UDS and UDS groups additionally received fed with pellets included 30 ml/kg UDS extract. At the end of the trial, blood and colon tissue samples were taken from the rats following necropsy. The gross and histopathological findings revealed that the administration of UDS extract significantly decreased lesions including aberrant cript foci, adenoma, and adenocarcinoma formation both numerically and dimensionally. Immunohistochemically, slight CEA and COX-2, strong Caspase-3 immune-expressions were detected in the group AOM + UDS compared to AOM group. Biochemical examinations indicated that a markedly increase in the malondialdehyde and fluctuated antioxidant defense system constituents levels such as reduced glutathione, glutathione s-transferase, glutathione peroxidase, superoxide dismutase were restored in AOM + UDS group. These results reveal that the UDS may act as a chemopreventive dietary agent, inducing apoptosis, resulting in a significant reduction of colon carcinogenesis.

The protective effect of esculetin against aluminium chloride-induced reproductive toxicity in rats

One of the prominent health problems caused by Aluminium was the decrease in male fertility rates. In the study, the protective effect of Esculetin (ESC) against the reproductive toxicity induced by Aluminium chloride (AlCl₃ ) was investigated. For this purpose, AlCl₃ was administrated to Wistar Albino rats at a dose of 34 mg/kg and ESC was administrated at a dose of 50 mg/kg for 70 days. It was determined that AlCl₃ treatment reduced sperm motility and concentration, increased dead/live rate and abnormal sperm rate. It decreased serum testosterone level, and co-treatment of ESC significantly regulated these values. In the AlCl₃ -treated group, MDA level increased and GSH level, GPx and CAT activities decreased compared with those of the control group. However, co-treatment of ESC showed an amelioratory effect on the values except for CAT activity. It was observed that the expression level of NRF-2 increased in the ESC and AlCl₃  + ESC groups, and NF-κB increased in the AlCl₃ group with the control group. It was determined that Caspase-3 expression decreased, and Bcl-2 expression increased in AlCl₃  + ESC group compared to AlCl₃ group. It was also determined that AlCl₃ -induced tissue injury was significantly prevented by ESC co-treatment.

Biomedical effects of Laurus nobilis L. leaf extract on vital organs in streptozotocin-induced diabetic rats: Experimental research

Diabetes mellitus (DM) has been treated with herbs for centuries and many herbs reported to exert antidiabetic activity. Laurus nobilis is an aromatic herb belonging to the Lauraceae family, commonly known as bay. This study aimed to investigate the activity of Laurus nobilis leave extracts on histopathological and biochemical changes in β-cells of streptozotocin (STZ)-induced diabetic rats. Thirty healthy adult male albino rats were included in the study and divided equally into 5 groups for 4 weeks as follow; control group (C), diabetic group (D), diabetic Laurus nobilis extract group (DLN), Laurus nobilis extract group (LN) and diabetic acarbose (DA) group. Histopathologically, D group rats exhibited various degenerative and necrotic changes in their liver, pancreas and kidney, whereas the DLN rats had nearly normal histology. Insulin immunostaining in the pancreatic beta cells was decreased in the D group compared to the C group, whereas the DLN group was similar to the C group. The glucose concentration decreased significantly in both diabetic rats treated with L. nobilis and acarbose (p < 0.05). Additionally, the levels of aspartate aminotransferase (AST), gamma-glutamyltransferase (GGT) and alanine aminotransferase (ALT) enzyme were significantly decreased in both diabetic rats treated with L. nobilis and acarbose, compared to the D group (p ˃ 0.05). Outcomes of this study said that leave extracts of L. nobilis has valuable effect on blood glucose level and ameliorative effect on regeneration of pancreatic islets, it also restored the altered liver enzymes, urea, creatine kinase, total protein levels, calcium and ferritin to near normal.

•

Diabetes mellitus has been treated with herbs for centuries and many herbs reported to exert antidiabetic activity.

•

Historically, traditional herbal treatments have been shown to possess successful pharmacological activity, such as in the case with metformin, isolated from Galega officinalis.

•

Laurus nobilis has a valuable effect on blood glucose level and ameliorative effect on regeneration of pancreatic islets.

•

Laurus nobilis have also been shown to display insulin-enhancing activity in vitro.

•

Laurus nobilis also restored the altered liver enzymes, urea, creatine kinase, total protein levels, calcium and ferritin to near normal.

Nobiletin Protects from Renal Ischemia-Reperfusion Injury in Rats by Suppressing Inflammatory Cytokines and Regulating iNOS-eNOS Expressions

Ischemia-reperfusion injury is an organ failure caused by hypoxia and reperfusion, which is closely associated with oxidative stress and inflammation. In this study, we investigated whether nobiletin had protective effects on inflammatory parameters, oxidative damage, iNOS-eNOS expressions, and histopathological structure of renal tissue in rats with renal ischemia-reperfusion injury. For this purpose, 24 rats were divided into 4 groups: group 1 (Control), group 2 (Ischemia-Reperfusion-IR), group 3 (Nobiletin-10 mg/kg p.o.), group 4 (Nobiletin + IR). The study was continued for 7 days. At the end of the study, urea (p < 0.05), creatine (p < 0.05), MDA (p < 0.001), TNF-alpha (p < 0.001), IL-1 beta (p < 0.05), and IL-6 (p < 0.001) levels increased in the IR group; however, a significant decrease occurred in group 4 (Nobiletin + IR) and it reached the control group levels. In the IR group, GSH (p < 0.01) levels, and GSH.Px (p < 0.01) and CAT (p < 0.05) activities decreased whereas they increased significantly in group 4 (Nobiletin + IR) and reached the same levels as the control group. In histopathological analyses, destruction and increased iNOS-eNOS expressions in the IR group showed a significant decrease in group 4 (Nobiletin + IR). As a result, the application of nobiletin has shown that it has protective effects by reducing kidney damage caused by IR injury.

Zingerone protects liver and kidney tissues by preventing oxidative stress, inflammation, and apoptosis in methotrexate-treated rats

The clinical use of drugs used in the treatment of diseases is limited due to the toxic side effects, and many studies have been conducted to benefit from herbal adjuvant therapies recently to eliminate these effects. In this study, the protective effect of zingerone against liver and kidney damage generated in rats through methotrexate (MTX). Histopathological investigations were performed to determine tissue damage caused by MTX and the healing effect of zingone and liver function markers such as serum alanine transaminase (ALT), aspartate transaminase (AST), alkaline phosphatase (ALP), and renal function markers such as urea, creatine, and aquaporin-1 (AQP-1) were measured. The effects of MTX and protective properties of zingerone on oxidative stress were investigated through the measurement of malondialdehyde and reduced glutathione (GSH) levels, catalase (CAT), and glutathione peroxidase (GPx) enzyme activities. The anti-inflammatory effect of zingerone was determined by measuring the cytokine levels causing inflammation such as nuclear factor-kappa B (NF-κB), tumor necrosis factor-α (TNF-α), and interleukin-1β (IL-1β), and its effects on apoptosis were determined by immunohistochemical analysis of caspase-3 and B-cell lymphoma-2 (Bcl-2) expression levels. According to the results obtained within the scope of the study, it was determined that zingerone treatment prevented the increase in MTX-induced liver and kidney function markers, showed healing effects on antioxidant parameters degraded in both tissues, and decreased the inflammation parameters. It was determined that it also prevented apoptosis and possessed a protective effect on disrupted tissue architecture by decreasing the increased caspase-3 expression and increasing the decreased Bcl-2 level.

Reduction of hepatorenal and pancreatic damage by Ferula elaeochytris extract in STZ induced diabetic rats

The therapeutic potential and antioxidant capacity of Ferula elaeochytris extract (FE) in the liver, kidney and pancreas of rats with diabetes induced by streptozotocin (STZ) was assessed using biochemistry, histopathology and immunohistochemistry. Forty adult Wistar albino male rats were divided randomly into five groups of eight rats each. The normal control (NC) group was untreated. The diabetes control (DC) group was treated with STZ to induce diabetes. The diabetes + acarbose group (DAC) was treated with STZ, then with acarbose daily for 28 days. The diabetes + FE (DFE) group was treated with STZ, then FE daily for 28 days. DC rats had inflammatory cell infiltration, hydropic degeneration and necrosis, whereas the DFE rats exhibited nearly normal histology. Insulin immunostaining in the pancreatic beta cells was decreased in the DC group compared to the NC group, whereas the DFE group was similar to the NC group. Many serum biomarkers of damage to liver, kidneys or pancreas were elevated in the DC group compared to the NC group; these biomarkers were decreased in the DFE group. The DC group exhibited increased malondialdehyde levels and decreased levels of the antioxidant defense system constituents compared to the NC group. The level of biomarkers the DFE group was close to the NC group. FE exhibited a protective effect against tissue damage owing to its antioxidant activities and to its ability to effect regeneration of β-cells in STZ induced diabetic rats.

Use of an antiarrhythmic drug against acute selenium toxicity

OBJECTIVE

Selenium is an essential trace element. But, selenium may have toxic effects in high doses. There are no proven antidotes or curative treatments for acut selenium toxicity. Treatment involves stopping the exposure and providing supportive care for symptoms. Therefore, it is necessary to find more effective substances in the treatment of selenium toxicity. The aim of this study was to increase the survival rate of animals by supporting the heart with amiodarone and to determine the effect of amiodarone on the pathological, hematological and biochemical parameters in acute selenium intoxication.

METHODS

64 Wistar-Albino rats were divided into four groups. Group I was given only distilled water, Group II was given 18 mg/kg dose of amiodarone, Group III was given 18 mg/kg amiodarone and 10 mg/kg sodium selenite and Group IV was given sodium selenite 10 mg/kg (LD₅₀ dose)orally.

RESULTS

11 of the 16 animals in Group IV died within the first 48 h of drug administration. However, no deaths were observed in the rats in Group III. No hematological changes were observed. Biochemically, CK, CK-MB and LDH levels of Group IV were higher than the other groups on both the 2nd and 10th days. In Groups II and III, this serum level decreased, and vitamin B12 levels increased. In macroscopic inspections of the organs of Groups III and IV, slight paleness was detected. Histopathologically, degenerative changes in tissue were observed, especially in Group IV.

CONCLUSION

This study shows that amiodarone application has a reducing effect on selenium toxicity. This was because amiodarone protected the heart by reducing CK and CK-MB levels and increased vitamin B12 levels, which play a role in the synthesis of S-adenosyl methionine that converts selenium into a nontoxic form.

Protective Effects of Tyrosol Against DSS-Induced Ulcerative Colitis in Rats

In this study, the effects of tyrosol were investigated in DSS-induced experimental ulcerative colitis model. For this purpose, rats were divided into five groups of seven rats in each: control group, colitis group (DSS-4%), tyrosol group (tyrosol 20 mg/kg), sulfasalazine (sulfasalazine+DSS 100 mg/kg), and treatment group (tyrosol+DSS 20 mg/kg). In the study, the active substances were administered to all animals for a period of 21 days. At the end of the study, malondialdehyde (MDA) levels increased (p < 0.001); GSH level (p < 0.05) along with GSH.Px (p < 0.01) and CAT (p < 0.001) activities decreased in the DSS-induced colitis group. However, with the administration of tyrosol, MDA and GSH levels along with GSH.Px and CAT activities came to the same levels as the control group. In the colitis group, an increase occurred in IL-6, COX-2, and NF-κB parameters, which created a significant difference compared to the control group (p < 0.001). Similarly, TNF-α levels also significantly increased with the administration of DSS (p < 0.05) which created a significant difference compared to the control group, while there was no difference among the other groups. As for the Nrf-2 data, it decreased with the administration of DSS which created a significant difference compared to the control group (p < 0.05), while there was no difference in other groups. In the colitis-induced group, IL-6, COX-2, and NF-κB gene expression levels also similarly increased but returned to the normal levels with the administration of tyrosol. In the histopathological scoring, the negativity that increased with the administration of DSS returned to the normal levels with the administration of tyrosol+DSS. In conclusion, according to the data obtained, tyrosol fixed the destruction picture in the DSS-induced colitis model, giving rise to thought that it has a protective effect.

A histopathological, immunohistochemical and biochemical investigation of the antidiabetic effects of the Pistacia terebinthus in diabetic rats

We investigated the antidiabetic activity of Pistacia terebinthus (PT) extracts in streptozotocin (STZ) induced diabetic rats. We used 40 Wistar albino male rats divided into five groups: control (C), diabetes (DM), diabetes + acarbose (DM + AC), diabetes + PT (DM + PT) and PT. DM was established by intraperitoneal injection of STZ. Immunohistochemistry revealed that STZ reduced insulin immunoreactivity in the pancreas of the diabetic rats. To the contrary, insulin immunoreactivity in the pancreatic β cells of PT treated diabetic rats was increased significantly. Decreased levels of blood glucose, aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), lactate dehydrogenase (LDH), glucose, total triglyceride (TG), total cholesterol (TC), high density lipoprotein (HDL) and low density lipoprotein (LDL) were found in the PT supplemented diabetic group. Also, malondialdehyde (MDA) and antioxidant defense system enzyme levels were normalized in the DM + PT group. PT exhibited a protective effect on liver, kidney and pancreas that had been damaged by STZ induced DM.

Tyrosol prevents AlCl3 induced male reproductive damage by suppressing apoptosis and activating the Nrf-2/HO-1 pathway

Aluminium is a ubiquitous element that occurs naturally in the soil making human exposure to it is unavoidable. Tyrosol is present in olive oil and is known to have antioxidant effects. Therefore, the present study explores the toxic effects of aluminium chloride (AlCl₃ ) and evaluates the possible protection by tyrosol in male rats. Testicular injury was induced by the administration of AlCl₃ (34 mg kg^-1  day^-1 ). Rats were treated with either tyrosol (20 mg kg^-1 day^-1 ) or AlCl3 (34 mg kg^-1 day^-1 ). The experiment lasted for 10 weeks. Biochemical, histopathological and protein expression profiles were determined to decipher the role of tyrosol in protecting the cellular damage. Further, histomorphometric analyses of testes showed deranged architecture along with other noted abnormalities. AlCl₃ group rats' testes showed decreased GSH levels, CAT activities, Nrf-2, HO-1, bcl-2 expressions and sperm motility whereas increased caspase-3 expressions, MDA levels, abnormal and dead/live sperm ratio. However, tyrosol treatment attenuated these changes. The present results demonstrate the beneficial role of tyrosol treatment in AlCl₃ induced testicular toxicity alterations of rat.

Chemopreventive efficacy of juniper berry oil (Juniperus communis L.) on azoxymethane-induced colon carcinogenesis in rat

The aim of this study was to investigate the chemopreventive effects of juniper berry (JB) oil on azoxymethane (AOM)-induced colon cancer in rats. Thirty-two male Wistar albino rats were allocated into four groups: Control, AOM, AOM + JB, and JB groups. Whereas the control group was fed with standard pellet feed, the AOM and AOM + JB groups were administered of AOM (15 mg/kg body weight) subcutaneously once every 2 weeks for 10 weeks. AOM + JB and JB groups additionally received JB oil (100 µl/kg) orally. At the end of the 16-week experimental period, blood and tissue samples were obtained from the rats following necropsy. The macroscopic findings showed that the application of JB oil significantly decreased adenoma and adenocarcinoma formation both numerically and dimensionally. Immunohistochemically, CEA, COX-2, and Ki-67 immune-expressions decreased, and the immune-expression of caspase-3 increased in AOM + JB treated rats. Additionally, JB oil supplementation ameliorated antioxidant defense systems and lipid peroxidation within the colon tissue of AOM + JB treated rats. These results reveal that the JB oil acted as a chemopreventive dietary agent, inhibiting cell proliferation and COX-2 expression and inducing apoptosis, resulting in a significant reduction in colon tumor formation.

Correction to: Protective Effects of Tyrosol Against DSS-Induced Ulcerative Colitis in Rats

The Funding Information is missing in the original article.

Congenital extraneural hemangioblastoma in a lamb

A 1-mo-old Ivesi male lamb was presented with 2 large red masses on the skin of the left ear. The tumors were removed using gentle dissection and submitted for histologic evaluation. The tumors consisted of numerous thin-walled capillaries lined by endothelial cells and nests of stromal cells. Immunohistochemically, the endothelial cells were positive for CD45, and the stromal cells were positive for neuron-specific enolase. GFAP-positive cells were occasionally present within the tumor. Endothelial and stromal cells were negative for S100, CD34, CD31, and factor VIII-related antigen. The tumor had strong gross, microscopic, and immunohistochemical similarities with human extraneural hemangioblastoma.

Long-Range Changes in Neurolysin Dynamics Upon Inhibitor Binding

Crystal structures of neurolysin, a zinc metallopeptidase, do not show a significant conformational change upon the binding of an allosteric inhibitor. Neurolysin has a deep channel where it hydrolyzes a short neuropeptide neurotensin to create inactive fragments and thus controls its level in the tissue. Neurolysin is of interest as a therapeutic target since changes in neurotensin level have been implicated in cardiovascular disorders, neurological disorders, and cancer, and inhibitors of neurolysin have been developed. An understanding of the dynamical and structural differences between apo and inhibitor-bound neurolysin will aid in further design of potent inhibitors and activators. For this purpose, we performed several molecular dynamics (MD) simulations for both apo and inhibitor-bound neurolysin. A machine learning method (Linear Discriminant Analysis) is applied to reveal differences between the apo and inhibitor-bound ensembles in an automated way, and large differences are observed on residues that are far from both the active site and the inhibitor binding site. The effects of inhibitor binding on the collective motions of neurolysin are extensively analyzed and compared using both Principal Component Analysis and Elastic Network Model calculations. We find that inhibitor binding induces additional low-frequency motions that are not observed in the apo form. ENM also reveals changes in inter- and intradomain communication upon binding. Furthermore, differences are observed in the inhibitor-bound neurolysin contact network that are far from the active site, revealing long-range allosteric behavior. This study also provides insight into the allosteric modulation of other neuropeptidases with similar folds.

Investigating the precision of Web image search engines for popular and less popular entities

Image search is the second most frequently used search service on the Web. However, there are very few studies investigating any aspect of it. In this study, we investigate the precision of Web image search engines of Google and Bing for popular and less popular entities using text-based queries. Furthermore, we investigate four additional aspects of Web image search engines that have not been studied before. We used 60 different queries in total from three different domains for popular and less popular categories. We examined the relevancy of the top 100 images for each query. Our results indicate that image search is a solved problem for popular entities. They deliver 97% precision on the average for popular entities. However, precision values are much lower for less popular entities. For the top 100 results, average precision is 48% for Google and 33% for Bing. The most important problem seems to be the worst cases in which the precision can be less than 10%. The results show that significant improvement is needed to better identify relevant images for less popular entities. One of the main issues is the association problem. When a Web page has query words and multiple images, both Google and Bing are having difficulty determining the relevant images.

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3^rd7 mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLR gene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar

Evaluating search features of Google Knowledge Graph and Bing Satori

Purpose

– The purpose of this paper is to better understand three main aspects of semantic web search engines of Google Knowledge Graph and Bing Satori. The authors investigated: coverage of entity types, the extent of their support for list search services and the capabilities of their natural language query interfaces.

Design/methodology/approach

– The authors manually submitted selected queries to these two semantic web search engines and evaluated the returned results. To test the coverage of entity types, the authors selected the entity types from Freebase database. To test the capabilities of natural language query interfaces, the authors used a manually developed query data set about US geography.

Findings

– The results indicate that both semantic search engines cover only the very common entity types. In addition, the list search service is provided for a small percentage of entity types. Moreover, both search engines support queries with very limited complexity and with limited set of recognised terms.

Research limitations/implications

– Both companies are continually working to improve their semantic web search engines. Therefore, the findings show their capabilities at the time of conducting this research.

Practical implications

– The results show that in the near future the authors can expect both semantic search engines to expand their entity databases and improve their natural language interfaces.

Originality/value

– As far as the authors know, this is the first study evaluating any aspect of newly developing semantic web search engines. It shows the current capabilities and limitations of these semantic web search engines. It provides directions to researchers by pointing out the main problems for semantic web search engines.

Prediction of pregnancy viability in bovine in vitro-produced embryos and recipient plasma with Fourier transform infrared spectroscopy

We analyzed embryo culture medium (CM) and recipient blood plasma using Fourier transform infrared (FTIR) metabolomics to predict pregnancy outcome. Individually cultured, in vitro-produced (IVP) blastocysts were transferred to recipients as fresh and vitrified-warmed. Spent CM and plasma samples were evaluated using FTIR. The discrimination capability of the classifiers was assessed for accuracy, sensitivity (pregnancy), specificity (nonpregnancy), and area under the receiver operator characteristic curve (AUC). Within all IVP fresh embryos (birth rate=52%), high AUC were obtained at birth, especially with expanded blastocysts (CM: 0.80±0.053; plasma: 0.89±0.034). The AUC of vitrified IVP embryos (birth rate = 31%) were 0.607±0.038 (CM, expanded blastocysts) and 0.672±0.023 (plasma, all stages). Recipient plasma generally predicted pregnancy outcome better than did embryo CM. Embryos and recipients with improved pregnancy viability were identified, which could increase the economic benefit to the breeding industry.

The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases

The vibrational dynamics of various type II restriction endonucleases, in complex with cognate/non-cognate DNA and in the apo form, are investigated with the elastic network model in order to reveal common functional mechanisms in this enzyme family. Scissor-like and tong-like motions observed in the slowest modes of all enzymes and their complexes point to common DNA recognition and cleavage mechanisms. Normal mode analysis further points out that the scissor-like motion has an important role in differentiating between cognate and non-cognate sequences at the recognition site, thus implying its catalytic relevance. Flexible regions observed around the DNA-binding site of the enzyme usually concentrate on the highly conserved β-strands, especially after DNA binding. These β-strands may have a structurally stabilizing role in functional dynamics for target site recognition and cleavage. In addition, hot spot residues based on high-frequency modes reveal possible communication pathways between the two distant cleavage sites in the enzyme family. Some of these hot spots also exist on the shortest path between the catalytic sites and are highly conserved.

Google stemming mechanisms

In this study we investigated the stemming mechanisms of Google. We used its web interface and submitted many queries via a program. Stemming is the process of correlating morphologically similar words with one another. Search engines use stemming to match documents having one form of a word with queries having another form of the same word. We investigated the stemming mechanism of Google for three classes of words: singulars/plurals, combined words, and verbs with many postfixes. Our results indicate that Google uses a document-based algorithm for stemming. It evaluates each document separately and makes a decision to index or not for the conflated forms of the words it has. It indexes documents only for word forms that are semantically strongly correlated. While it indexes documents for singulars and plurals frequently, it rarely indexes documents for word forms with the postfixes of -able or -tively.

Investigation of the accuracy of search engine hit counts

This study investigates the accuracy of search engine hit counts for search queries. We investigate the accuracy of hit counts for Google, Yahoo and Microsoft Live Search, and the accuracy of single and multiple term queries. In addition, we investigate the consistency of hit count estimates for 15 days. The results show that all three provide estimates for the number of matching documents and the estimation patterns of their counting algorithms differ greatly. The accuracy of hit counts for multiple word queries has not been studied before. The results of our study show that the number of words in queries affects the accuracy of estimations significantly. The percentages of accurate hit count estimations are reduced almost by half when going from single word to two word query tests in all three search engines. With the increase in the number of query words, the error in estimation increases and the number of accurate estimations decreases.

The effect of 3-in-1 femoral nerve block with ropivacaine 0.375% on postoperative morphine consumption in elderly patients after total knee replacement surgery

Total knee replacement (TKR) is one of the most painful orthopedic surgical procedures. This study was aimed to investigate the effect of a single-shot preoperative 3-in-1 femoral nerve block on postoperative pain by using 0.375% ropivacaine, and on the consumption of morphine by using PCA following the TKR surgery. Side effects were also evaluated in this setting. 34 patients were included in this study. Group R (n=17) received a 3-in-1 femoral nerve block (FNB) with 40 mll of ropivacaine 0.375%. Group S (n=17) received only a 2 mg loading dose of morphine 30 minutes before the end of surgery, and no block was performed. Both groups received general anesthesia and postoperatively had a PCA pump programmed to deliver morphine. VAS scores at rest, morphine consumption and adverse effects were recorded. Two patients were excluded from each group. Pain scores at 0, 1, 2, 3, 4, 6, 8 postoperative hours were significantly lower in group R in resting position (p<0.05). Group R experienced no pain at the recovery room and this state lasted 8 hours after the surgery while group S reached the acceptable score (VAS ? 3) one hour after leaving the recovery room. The morphine requirement was significantly lower in Group R at 12, 18, 24, 48 hr after TKR (p<0.001). Side effects were also lower in this group. Preoperative single-shot 3-in-1 FNB with 40 cc of ropivacaine 0.375% provides better VAS scores, less morphine consumption and fewer side effects in elderly patients when compared to the group with no block.

A methicillin-resistant Staphylococcus aureus outbreak in a new University hospital due to a strain transferred with an infected patient from another city six months previously

Kocaeli University Medical School was established in 1995. The first methicillin resistant Staphylococcus aureus isolate was detected two years later in a patient transferred from a different city. Six months after this, we detected a small MRSA outbreak in the intensive care unit involving four patients, two of whom had bacteremia, and a staff nasal carrier. All isolates, including the first, appeared to be a single outbreak strain, demonstrated by pulsed field gel electrophoresis profiles which different by at most two bands, identical randomly amplified polymorphic DNA profiles, and identical coagulase gene types by PCR. Antibiogram were identical except that one isolate was additionally resistant to cotrimoxazole. These results show that MRSA isolates can spread between hospitals with infected or colonized patients and can apparently persist in the hospital for six months without causing infection. Screening of asymptomatic patients on wards affected by MRSA or transferred from other hospitals may be helpful in controlling these infections.

Laryngopyocele: signs on computed tomography

A laryngocele is an air-filled dilation of the saccule of the larynx. An infected laryngocele is called a laryngopyocele. Our experience with a case of laryngopyocele with signs on computed tomography before and after antibiotic therapy is presented since laryngopyocele is more unusual.

[Epidemiology of rheumatic syndromes in Turkey. III. Incidence of rheumatic sacro-iliitis in men of 20-22 years]

1436 young men were investigated clinically and radiologically for rheumatic sacro iliitis. In two men (1.4%) definite bilateral sacro iliitis was diagnosed. In 18 cases (12.5%) the signs were not sufficient to make a definite diagnosis. They were regarded as suspected iliitis. For comparison the cards of 6138 patients who had called at our outpatient clinic over a 5 years' period were checked. In 40 cases (0.65%) a definite diagnosis of bilateral sacro iliitis was made, in another 45 cases (0.73%) sacro iliitis was suspected, but definite proof was lacking. The group we investigated has two characteristics. As to sex and age our test subjects (recruits) represent a group in which bilateral sacro iliitis appears relatively often. Infections are reported to increase the frequency of bilateral sacro iliitis. Our test subjects were only investigated for tuberculos infection. Active tuberculosis was not found. Also factors which may have a negative influence on the frequency were investigated. First of all the soldiers had been examined by clinical committees before recruitment. Advanced and thus clinically typical cases were eliminated by these committees and the frequency rate in the remaining group thereby decreased. The recruits came from very different parts of the country and various geographic and social factors may influence the morbidity. The frequency rates obtained at the end of the investigation have therefore to be regarded as the result of various factors some with positive and some with negative influence.