PROPER: Performance visualization for optimizing and comparing ranking classifiers in MATLAB

Background

One of the recent challenges of computational biology is development of new algorithms, tools and software to facilitate predictive modeling of big data generated by high-throughput technologies in biomedical research.

Results

To meet these demands we developed PROPER - a package for visual evaluation of ranking classifiers for biological big data mining studies in the MATLAB environment.

Conclusion

PROPER is an efficient tool for optimization and comparison of ranking classifiers, providing over 20 different two- and three-dimensional performance curves.

     

Distribution of Metals (Cu,Zn, Pb,and Cd) in Sediments of the Anzali Lagoon,North Iran

Concentrations of four metals (Cu, Zn, Pb, and Cd) in the sediments of the Anzali Lagoon in the northern part of Iran were determined to evaluate the level of contamination and spatial distribution. The sediments were collected from 21 locations in the lagoon. At each lagoon site a core, 60 cm long, was taken. The ranges of the measured concentrations in the sediments are as follows: 17–140 mg kg^?1 for Cu, 20–113 mg kg^?1 for Zn, 1–37 mg kg^?1 for Pb and 0.1–3.5 mg kg^?1 for Cd in surficial (0-20 cm) and 16–87 mg kg^?1 for Cu, 28.5–118 mg kg^?1 for Zn, 3–20 mg kg^?1 for Pb and 0.1–3.5 mg kg^?1 for Cd in deep (40–60 cm) sediments. The results of the geoaccumulation index (I_geo) show that Cd causes moderate to heavy pollution in most of the study area. Environmental risk evaluation showed that the pollution in the Anzali Lagoon is moderate to considerable and the ranking of the contaminants followed the order: Cd > Cu > Pb > Zn. Some locations present severe pollution by metals depending on the sources, of which sewage outlets and phosphate fertilizers are the main sources of contaminants to the area.     

Adverse Outcomes of Anticoagulant Use among Hospitalized Patients with Chronic Kidney Disease: A Comparison of the Rates of Major Bleeding Events between Unfractionated Heparin and Enoxaparin

Background

Anticoagulation therapy is usually required in patients with chronic kidney disease (CKD) for treatment or prevention of thromboembolic diseases. However, this benefit could easily be offset by the risk of bleeding.

Objectives

To determine the incidence of adverse outcomes of anticoagulants in hospitalized patients with CKD, and to compare the rates of major bleeding events between the unfractionated heparin (UFH) and enoxaparin users.

Methods

One year prospective observational study was conducted in patients with CKD stages 3 to 5 (estimated GFR, 10–59 ml/min/1.73 m²) who were admitted to the renal unit of Dubai Hospital. Propensity scores for the use of anticoagulants, estimated for each of the 488 patients, were used to identify a cohort of 117 pairs of patients. Cox regression method was used to estimate association between anticoagulant use and adverse outcomes.

Results

Major bleeding occurred in 1 in 3 patients who received anticoagulation during hospitalization (hazard ratio [HR], 4.61 [95% confidence interval [CI], 2.05–10.35]). Compared with enoxaparin users, patients who received anticoagulation with unfractionated heparin had a lower mean [SD] serum level of platelet counts (139.95 [113]×10³/µL vs 205.56 [123] ×10³/µL; P<0.001), and had a higher risk of major bleeding (HR, 4.79 [95% CI, 1.85–12.36]). Furthermore, compared with those who did not receive anticoagulants, patients who did had a higher in-hospital mortality (HR, 2.54 [95% CI, 1.03–6.25]); longer length of hospitalization (HR, 1.04 [95% CI, 1.01–1.06]); and higher hospital readmission at 30 days (HR, 1.79 [95% CI, 1.10–2.91]).

Conclusions

Anticoagulation among hospitalized patients with CKD was significantly associated with an increased risk of bleeding and in-hospital mortality. Hence, intensive monitoring and preventive measures such as laboratory monitoring and/or dose adjustment are warranted.     

Synthesis,metabolism and in vitro cytotoxicity studies on novel lavendamycin antitumor agents

A series of lavendamycin analogues with two, three or four substituents at the C-6, C-7 N, C-2′, C-3′ and C-11′ positions were synthesized via short and efficient methods and evaluated as potential NAD(P)H:quinone oxidoreductase (NQO1)-directed antitumor agents. The compounds were prepared through Pictet–Spengler condensation of the desired 2-formylquinoline-5,8-diones with the required tryptophans followed by further needed transformations. Metabolism and toxicity studies demonstrated that the best substrates for NQO1 were also the most selectively toxic to NQO1-rich tumor cells compared to NQO1-deficient tumor cells.     

Identification of extremely halophilic archaea associated with adult <Emphasis Type="Italic">Artemia urmiana</Emphasis>

The brine shrimp, Artemia is the dominant macrozooplankton present in many hypersaline environments. Artemia urmiana is the only macroscopic organism in Urmia Salt Lake (Iran), and the high salinity of the lake makes it a suitable environment for halophilic archaea too. Because of common environment for Artemia and extreme halophiles; this investigation is concentrated on studying the relationship between Artemia and halophilic archaea in Urmia Lake. In this study first the procedure of arhaea isolation was done. Then, isolated strains were sub-cultured and DNA was extracted and amplified by PCR using specific primers for amplifying archaeal 16S rRNA. The amplified archeal DNA fragments were purified, and sequenced. 16S rRNA sequences were compared to known sequences using the NCBI BLAST program. Sequences relating to Halorubrum, Haloarcula and Halobacterium species were identified in Urmia Salt Lake water and Artemia adults and the phylogenetic tree of different species was constructed. Only Halorubrum species were present in association with Artemia. They belong to Halobacteriaceae family of archeae which are isolated from different salt lakes in different parts of world and we could show their existence in adult Artemia, another organism living in hypersaline enviroments.     

A fluorescent aptasensor for sensitive analysis oxytetracycline based on silver nanoclusters

A fluorescent aptasensor for detection of oxytetracycline (OTC) was presented based on fluorescence quenching of DNA aptamer‐templated silver nanoclusters (AgNCs). The specific DNA scaffolds with two different nucleotides fragments were used: one was enriched with a cytosine sequence fragment (C12) that could produce DNA–AgNCs via a chemical reduction method, and another was the OTC aptamer fragment that could selectively bind to the OTC antibiotic. Thus, the as‐prepared AgNCs could exhibit quenched fluorescence after binding to the target OTC. The fluorescence ratio of the DNA–AgNCs was quenched in a linearly proportional manner to the concentration of the target in the range of 0.5 nM to 100 nM with a detection limit of 0.1 nM. This proposed nanobiosensor was demonstrated to be sensitive, selective, and simple, introducing a viable alternative for rapid determination of toxin OTC in honey and water samples. Copyright © 2016 John Wiley & Sons, Ltd.     

Expression of neutrophil gelatinase-associated lipocalin (NGAL) in peripheral nerve repair

Introduction: Trauma is one of the causes of peripheral nerve injuries. Free radicals increase after tissue damage. Free radicals are usually scavenged and detoxi?ed by antioxidants. In this study, we assessed the antioxidative role of the NGAL molecule in sciatic nerve repair in rats. Materials and methods: The sciatic nerves of 40 rats were crushed and the total mRNA of samples from day 1 and 3 and week 1, 3, 5 post injury was extracted. The expression of the NGAL gene was confirmed by RT-PCR. For immunohistochemistry analysis, the samples were ?xed in paraformaldehyde and cut in 20 micrometer slices by cryostat. Results: The expression of NGAL signi?cantly upregulated in day 1, 3 and week 1 following the crushing of sciatic nerves in comparison with the intact nerves. Immunohistochemistry results also confirmed the protein expression of this gene. Discussion: The NGAL molecule showed upregulation in the degeneration process after nerve injury, so it may play an important role in nerve repair.     

Length–weight relationships and condition factors of two fish species from the southern Caspian Sea basin: Alburnoides samiii Mousavi‐Sabet,Vatandoust & Doadrio, 2015 and Ponticola iranicus Vasil′eva,Mousavi‐Sabet & Vasil′ev, 2015

The present study describes the length–weight relationships (LWRs) and condition factors (K) of Alburnoides samiii and Ponticola iranicus in the Sefidroud River from the southern Caspian Sea basin, September 2013 to August 2014. This study presents the first known reference in the FishBase database regarding the LWRs and condition factors for these two indigenous species.     

Therapeutic resistance and cancer recurrence mechanisms: Unfolding the story of tumour coming back

Cancer recurrence is believed to be one of the major reasons for the failure of cancer treatment strategies. This biological phenomenon could arise from the incomplete eradication of tumour cells after chemo- and radiotherapy. Recent developments in the design of models reflecting cancer recurrence and in vivo imaging techniques have led researchers to gain a deeper and more detailed insight into the mechanisms underlying tumour relapse. Here, we provide an overview of three important drivers of recurrence including cancer stem cells (CSCs), neosis, and phoenix rising. The survival of cancer stem cells is well recognized as one of the primary causes of therapeutic resistance in malignant cells. CSCs have a relatively latent metabolism and show resistance to therapeutic agents through a variety of routes. Neosis has proven to be as an important mechanism behind tumour self-proliferation after treatment which gives rise to the expansion of tumour cells in the injured site via production of Raju cells. Phoenix rising is a pro-recurrence pathway through which apoptotic cancer cells send strong signals to the neighbouring diseased cells leading to their multiplication. The mechanisms involved in therapeutic resistance and tumour recurrence have not yet been fully understood and mostly remain unexplained. Without doubt, an improved understanding of the cellular machinery contributing to recurrence will pave the way for the development of novel, sophisticated and effective anti-tumour therapeutic strategies which can eradicate tumour without the threat of relapse.     

Seasonal changes in the testicular activity of the Iranian Mountain Viper,Montivipera albicornuta (Nilson & Andrén, 1985) (Reptilia: Viperidae)

The Iranian Mountain Viper, Montivipera albicornuta, is a venomous snake endemic to Iran. We compared the seasonal cycle of testicular activity of 74 male specimens during a one-year period in two cold mountain climate habitats: Tarom (in Zanjan Province) and Bostanabad (in Eastern Azerbaijan Province) in northwestern Iran. The maximum testicular volume was observed in both habitats during autumn. The diameter of seminiferous tubules reached a maximum length in winter and a minimum in summer. The number of spermatids increased in autumn. Spermiogenesis occurred in spring and the maximum number of spermatozoa was reached then. In M. albicornuta in Iran, the testes were more active in autumn and spring, and spermatogenesis started in autumn and continued until mating in spring.