iNetModels 2.0: an interactive visualization and database of multi-omics data

It is essential to reveal the associations between various omics data for a comprehensive understanding of the altered biological process in human wellness and disease. To date, very few studies have focused on collecting and exhibiting multi-omics associations in a single database. Here, we present iNetModels, an interactive database and visualization platform of Multi-Omics Biological Networks (MOBNs). This platform describes the associations between the clinical chemistry, anthropometric parameters, plasma proteomics, plasma metabolomics, as well as metagenomics for oral and gut microbiome obtained from the same individuals. Moreover, iNetModels includes tissue- and cancer-specific Gene Co-expression Networks (GCNs) for exploring the connections between the specific genes. This platform allows the user to interactively explore a single feature's association with other omics data and customize its particular context (e.g. male/female specific). The users can also register their data for sharing and visualization of the MOBNs and GCNs. Moreover, iNetModels allows users who do not have a bioinformatics background to facilitate human wellness and disease research. iNetModels can be accessed freely at https://inetmodels.com without any limitation.

iNetModels 2.0: an interactive visualization and database of multi-omics data

It is essential to reveal the associations between various omics data for a comprehensive understanding of the altered biological process in human wellness and disease. To date, very few studies have focused on collecting and exhibiting multi-omics associations in a single database. Here, we present iNetModels, an interactive database and visualization platform of Multi-Omics Biological Networks (MOBNs). This platform describes the associations between the clinical chemistry, anthropometric parameters, plasma proteomics, plasma metabolomics, as well as metagenomics for oral and gut microbiome obtained from the same individuals. Moreover, iNetModels includes tissue- and cancer-specific Gene Co-expression Networks (GCNs) for exploring the connections between the specific genes. This platform allows the user to interactively explore a single feature's association with other omics data and customize its particular context (e.g. male/female specific). The users can also register their data for sharing and visualization of the MOBNs and GCNs. Moreover, iNetModels allows users who do not have a bioinformatics background to facilitate human wellness and disease research. iNetModels can be accessed freely at https://inetmodels.com without any limitation.

Pancreatic cancer

In recent years, it has become clear that the current standard therapeutic options for pancreatic cancer are not adequate and still do not meet the criteria to cure patients suffering from this lethal disease. Although research over the past decade has shown very interesting and promising new therapeutic options for these patients, only minor clinical success was achieved. Therefore, there is still an urgent need for new approaches that deal with early detection and new therapeutic options in pancreatic cancer. To provide optimal care for patients with pancreatic cancer, we need to understand better its complex molecular biology and thus to identify new target molecules that promote the proliferation and resistance to chemotherapy of pancreatic cancer cells. In spite of significant progress in curing cancers with chemotherapy, pancreatic cancer remains one of the most resistant solid tumour cancers and many studies suggest that drug-resistant cancer cells are the most aggressive with the highest relapse and metastatic rates. In this context, activated Notch signalling is strongly linked with chemoresistance and therefore reflects a rational new target to circumvent resistance to chemotherapy in pancreatic cancer. Here, we have focused our discussion on the latest research, current therapy options and recently identified target molecules such as Notch-2 and the heparin-binding growth factor midkine, which exhibit a wide range of cancer-relevant functions and therefore provide attractive new therapeutic target molecules, in terms of pancreatic cancer and other cancers also.

LINKED ARTICLES

This article is part of a themed section on Midkine. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2014.171.issue-4.

VEGFR-2, CXCR-2 and PAR-1 germline polymorphisms as predictors of survival in pancreatic carcinoma

BACKGROUND

Hypoxic environment of pancreatic cancer (PC) implicates high vascular in-growth, which may be influenced by angiogenesis-related germline polymorphisms. Our purpose was to evaluate polymorphisms of vascular endothelial growth factor receptor 2 (VEGFR-2), CXC chemokine receptor 2 (CXCR-2), proteinase-activated receptor 1 (PAR-1) and endostatin (ES) as prognostic markers for disease-free (DFS) and overall survival (OS) in PC.

PATIENTS AND METHODS

Genotyping of 173 patients, surgically treated for PC between 2004 and 2011, was carried out by TaqMan(®) genotyping assays or polymerase chain reaction. Chi-square test, Kaplan-Meier estimator and Cox regression hazard model were used to assess the prognostic value of selected polymorphisms.

RESULTS

VEGFR-2 -906 T/T and PAR-1 -506 Del/Del genotypes predicted longer DFS (P = 0.003, P = 0.014) and OS (VEGFR-2 -906, P = 0.011). CXCR-2 +1208 T/T genotype was a negative predictor for DFS (P < 0.0001). Combined analysis for DFS and OS indicated that patients with the fewest number of favorable genotypes simultaneously present (VEGFR-2 -906 T/T, CXCR-2 +1208 C/T or C/C and PAR-1 -506 Del/Del) were at the highest risk for recurrence or death (P < 0.0001).

CONCLUSION

VEGFR-2 -906 C>T, CXCR-2 +1208 C>T and PAR-1 -506 Ins/Del polymorphisms are potential predictors for survival in PC.

Scolicidal agents in hydatid cyst surgery

Injecting scolicidal solutions into the hydatid cyst and packing the operative field with sponges soaked in scolicidal agents have been used to avoid dissemination of the parasite during surgery. In the first part of this invitro study, we tried to determine the scolicidal property of various agents in different concentrations and exposure times. In the second part, we tested whether sponges soaked in different type and concentrations of scolicidal agents have any role beyond being a mechanical barrier. 20% saline, 3% hydrogen peroxide, 1.5% cetrimide-0.15% chlorhexidine (10% Savlon), 95% ethyl alcohol, 10% polyvinylpirrolidone-iodine (Betadine) and their further dilutions were used in this study. Protoscoleces were obtained from the cyst containing livers of the sheep and viability was determined with dye-uptake (0.1% Eosin) and flame cell activity. Savlon was found to be the least concentration dependent scolicidal agent among those studied. Scoleces sprayed on sponges soaked in 20% saline, 95% ethyl alcohol, Betadine and 3% hydrogen peroxide were killed after 15 minutes. 3% and 10% saline and normal saline were ineffective. Sponges work not only as a mechanical barrier but also as a chemical one if the agent is chosen correctly. In purely cystic hydatid liver disease, the risk of dissemination of the cyst contents can be avoided by injection of a potent scolicidal agent such as Savlon.

Surgical treatment of hepatic hydatidosis combined with perioperative treatment with albendazole

OBJECTIVE

To evaluate the effect of albendazole combined with surgery on the incidence of recurrent hydatid disease.

DESIGN

Prospective open study.

SETTING

Teaching hospital, Turkey.

SUBJECTS

25 patients who presented with hepatic hydatid disease between December 1992 and October 1995.

INTERVENTIONS

Albendazole 10 mg/kg/day for a month before ultrasonography and then excision, and then albendazole for a further two months.

RESULTS

2 patients were excluded because the albendazole caused disturbance of liver enzyme activities. Of the remaining 23 patients only 7 had viable cysts on ultrasonography. In 15 patients (65%) the germinal layer was partially or totally destroyed, and in 15 the fluid was either cloudy or stained with bile. During a mean follow up period of 29 months only one patient developed recurrent disease.

CONCLUSION

Perioperative treatment with albendazole resulted in fewer recurrences than expected. A longer preoperative period of treatment may increase the success rate; this requires further study.

Unguarded tricuspid orifice: a rare malformation of tricuspid valve diagnosed by echocardiography. Report of two cases and review of the literature

In this report we present two cases with unguarded tricuspid orifice, and review the literature. The complete absence of tricuspid valvular structures is a very rare anomaly coexisting with pulmonary atresia and intact ventricular septum, and is termed unguarded tricuspid orifice. Double tricuspid orifices and isolated dextrocardia were distinguishing features of our first case. The second patient of this report, a 5-year-old boy, is the first case in the literature with this malformation of the tricuspid valve as an isolated anomaly, in addition to being the first surviving case in the literature.

Infantile spasms as the initial symptom of biotinidase deficiency

Two patients with biotinidase deficiency had diagnoses of infantile spasms made at 1 month of age. Biotinidase deficiency may be seen early in the neonatal period without the characteristic findings such as alopecia and seborrheic dermatitis. This diagnosis should be considered in patients with infantile spasms.

[Value of hypertonic media for the isolation of aberrant forms of Candida albicans from women with lower genital tract infections]

Women presenting symptoms and/or signs of lower genital tract infection were examined mycologically and to increase the sensitivity of the culture methods and to estimate the aberrant forms of fungi, hypertonic media was used. 47 yeast species were isolated from 86 patients. On the other hand 8 Candida albicans strains were isolated by using hypertonic culture media in which no growth was observed in any of the media used for routine culture. In relation with this study 8 cases were evaluated and the culture methods that have been used were discussed.

[Prevalence of G. vaginalis, Mycoplasma, Ureaplasma, T. vaginalis, yeast, N. gonorrhoeae and other bacteria in women with vaginal discharge]

Vaginal discharge of 118 women attended to outdoor clinics of obstetrics and gynaecology at Medical Faculty of Ankara University (A.U.T.F.), have been examined. Direct microscopy has been made by means of wet mount, Gram and Giemsa staining. Vaginal pH has been measured, by 10% KOH the presence of "fishy odor" has been investigated. For culturing vaginal secretions in Amies transport medium have been brought to Microbiology Department of Ankara University, Faculty of Medicine Inoculations have been made on to Blood agar, MacConkey agar, Sabouraud Dextrose agar, New York City. Medium, % 5 Human blood bilayer Tween 80 Medium (HBT), Vivey Trichomonas Agar Medium and into M-broth and U9 broth. In this study, we have isolated 9 (7.62%) Gardnerella vaginalis, 41 (33.89%) Ureaplasma, 13 (11.01%) Mycoplasma, 25 (21.18%) yeasts, 4 (3.38%) Trichomonas vaginalis and 43 (36.46%) various bacteria, 26 cases were found to have polymicrobial etiology.