An Updated Overview of Existing Cancer Databases and Identified Needs.

Our search of existing cancer databases aimed to assess the current landscape and identify key needs. We analyzed 71 databases, focusing on genomics, proteomics, lipidomics, and glycomics. We found a lack of cancer-related lipidomic and glycomic databases, indicating a need for further development in these areas. Proteomic databases dedicated to cancer research were also limited. To assess overall progress, we included human non-cancer databases in proteomics, lipidomics, and glycomics for comparison. This provided insights into advancements in these fields over the past eight years. We also analyzed other types of cancer databases, such as clinical trial databases and web servers. Evaluating user-friendliness, we used the FAIRness principle to assess findability, accessibility, interoperability, and reusability. This ensured databases were easily accessible and usable. Our search summary highlights significant growth in cancer databases while identifying gaps and needs. These insights are valuable for researchers, clinicians, and database developers, guiding efforts to enhance accessibility, integration, and usability. Addressing these needs will support advancements in cancer research and benefit the wider cancer community.

Comprehensive and User-Analytics-Friendly Cancer Patient Database for Physicians and Researchers.

Nuanced cancer patient care is needed, as the development and clinical course of cancer is multifactorial with influences from the general health status of the patient, germline and neoplastic mutations, co-morbidities, and environment. To effectively tailor an individualized treatment to each patient, such multifactorial data must be presented to providers in an easy-to-access and easy-to-analyze fashion. To address the need, a relational database has been developed integrating status of cancer-critical gene mutations, serum galectin profiles, serum and tumor glycomic profiles, with clinical, demographic, and lifestyle data points of individual cancer patients. The database, as a backend, provides physicians and researchers with a single, easily accessible repository of cancer profiling data to aid-in and enhance individualized treatment. Our interactive database allows care providers to amalgamate cohorts from these groups to find correlations between different data types with the possibility of finding "molecular signatures" based upon a combination of genetic mutations, galectin serum levels, glycan compositions, and patient clinical data and lifestyle choices. Our project provides a framework for an integrated, interactive, and growing database to analyze molecular and clinical patterns across cancer stages and subtypes and provides opportunities for increased diagnostic and prognostic power.

Malachite Green, the hazardous materials that can bind to Apo-transferrin and change the iron transfer.

Different groups of synthetic dyes might lead to environmental pollution. The binding affinity among hazardous materials with biomolecules necessitates a detailed understanding of their binding properties. Malachite Green might induce a change in the iron transfer by Apo-transferrin. Spectroscopic studies showed malachite green oxalate (MGO) could form the apo-transferrin-MGO complex and change the Accessible Surface Area (ASA) of the key amino acids for iron transfer. According to the ASA results the accessible surface area of Tyrosine, Aspartate, and Histidine of apo-transferrin significantly were changed, which can be considered as a convincing reason for changing the iron transfer. Moreover, based on the fluorescence data MGO could quench the fluorescence intensity of apo-transferrin in a static quenching mechanism. The experimental and Molecular Dynamic simulation results represented that the binding process led to micro environmental changes, around tryptophan residues and altered the tertiary structure of apo-transferrin. The Circular Dichroism (CD) spectra result represented a decrease in the amount of the α-Helix, as well as, increase in the ß-sheet volumes of the apo-transferrin structure. Moreover, FTIR spectroscopy results showed a hypochromic shift in the peaks of amide I and II. Molecular docking and MD simulation confirmed all the computational findings.

Development of a highly sensitive and selective mercury optical sensor based on immobilization of bis(thiophenal)-4,4'-methylenedianiline on a PVC membrane.

A reversible optical sensor was fabricated for highly sensitive and selective determination of Hg(II) ions. The optode was prepared using a newly synthesized ionophore, bis(thiophenal)-4,4'-methylenedianiline, and ETH-5294 as a lipophilic H(+)-selective indicator in a plasticized PVC membrane. Different variables affect the optical signal such as pH and compositions of the membrane components were optimized. The spectrophotometric method (λmax 662 nm) was used for the determination of Hg(II). Under the optimum conditions, the optode has a wide linear dynamic range of 2.51×10(-13) to 1.02×10(-5) mol L(-1) Hg(II) with a detection limit as low as 3.43×10(-14) mol L(-1) and a response time of 90 s (for a highly diluted solution). The influence of potential interference ions on the Hg(II) determination was studied. The results showed that the prepared optical sensor was highly selective to Hg(II) ions so that it had no significant response to a wide variety of common metal ions. The response of the optode to Hg(II) is completely reversible and was lucratively applied for the determination of Hg(II) in different real samples.

Development of a specific and highly sensitive optical chemical sensor for determination of Hg(II) based on a new synthesized ionophore.

A novel optode for determination of Hg(II) ions is developed based on immobilization of a recently synthesized ionophore, 7-(1H-imidazol-1-ylmethyl)-5,6,7,8,9,10-hexahydro-2H-1,13,4,7,10 benzodioxatriaza cyclopentadecine-3,11(4H,12H)-dione, in a PVC membrane. Dioctyl sebacate was used as a plasticizer, sodium tetraphenylborate as an anionic additive and ETH5294 as a chromoionophore. The response of the optode was based on the complexation of Hg(II) with the ionophore in the membrane phase, resulting an ion exchange process between Hg(II) in the sample solution and H(+) in the membrane. The effects of pH and amounts of the ionophore, chromoionophore, ionic additive and type of plasticizer on the optode response were investigated. The selectivity of the optode was studied in the present of several cations. The optode has a linear response to Hg(II) in the range of 7.2×10(-13)-4.7×10(-4) mol L(-1) with detection limit of 0.18 pmol L(-1). The optode was successfully applied to the determination of Hg(II) in real samples.

A highly sensitive and selective bulk optode based on benzimidazol derivative as an ionophore and ETH5294 for the determination of ultra trace amount of silver ions.

A novel optical chemical sensor (optode) was fabricated for the determination of silver ions. The optical sensor was prepared by incorporating recently synthesized ionophore, 7-(1H-benzimidazol-1-ylmethyl)-5,6,7,8,9,10-hexahydro-2H-1,13,4,7,10-benzodioxatriaza cyclopentadecine-3,11(4H,12H)-dione, sodium tetraphenyl borate (NaTPB) as an anionic additive, 3-octadecanoylimino-7-(diethylamino)-1,2-benzophenoxazine (ETH5294) as a chromoionophore, and dioctyl phthalate (DOP) as a plasticizer in a poly(vinyl chloride) membrane. The effect of several parameters in determining Ag(+) was studied and optimized. The spectrophotometric method (λ(max) of 660 nm) was used for the determination of Ag(+). Under the optimum conditions, the optical sensor has a wide dynamic range of 1.02×10(-11) to 8.94×10(-5) mol L(-1) Ag(+) with the detection limit as low as 2.8×10(-12) mol L(-1). The response time of the sensor was ~150 s, with a RSD% of 0.4% (for 1.0×10(-6) mol L(-1), n=7). The optode could be regenerated by 0.2 mol L(-1) HCl solution. The interferences of potential interfering ions were studied. It was shown that the new optode was very selective to silver ions and had no significant response to common ions such as Mn(2+), Cd(2+), Ni(2+), Hg(2+), and Co(2+). It can be claimed that the sensor can specifically detect silver ions. The sensor was successfully applied for the determination of silver ions in different real samples.

An optical chemical sensor for mercury ion based on 2-mercaptopyrimidine in PVC membrane.

An optical chemical sensor based on 2-mercaptopyrimidine (2-MP) in plasticized poly(vinyl chloride) (PVC) membrane incorporating (N,N-diethyl-5-(octadecanoylimino)-5H benzo[a]phenoxazine-9-amine (ETH 5294) and sodium tetraphenyl borate (NaTPB) for batch and flow-through determination of mercury ion is described. The response of the sensor is based on selective complexation of Hg(2+) with 2-MP in the membrane phase, resulting in an ion exchange process between H(+) in the membrane and Hg(2+) in the sample solution. The influences of several experimental parameters, such as membrane composition, pH, and type and concentration of the regenerating reagent, were investigated. The sensor has a response range of 2.0 x 10(-9) to 2.0 x 10(-5) mol L(-1) Hg(2+) with a detection limit of 4.0 x 10(-10) mol L(-1) and a response time of < or = 45 s at optimum pH of 6.5 with high measurement repeatability and sensor-to-sensor reproducibility. It shows high selectivity for Hg(2+) over several transition metal ions, including Ag(+), Cd(2+), Co(2+), Cr(3+), Cu(2+), Fe(3+), Mn(2+), Ni(2+), and common alkali and alkaline earth ions such as Na(+), K(+), Mg(2+), Ca(2+), and Pb(2+). The sensor membrane can be easily regenerated with dilute acid solutions. The sensor has been used for the determination of mercury ion concentration in water samples.