Biomarker Research Papers - Academia.edu (original) (raw)

Alzheimer's disease (AD) pathology is estimated to develop many years before detectable cognitive decline. Fluid and imaging biomarkers may identify people in early symptomatic and even preclinical stages, possibly when potential treatments can best preserve cognitive function. We previously reported that cerebrospinal fluid (CSF) levels of amyloid-b 42 (Ab 42 ) serve as an excellent marker for brain amyloid as detected by the amyloid tracer, Pittsburgh compound B (PIB). Using data from 189 cognitively normal participants, we now report a positive linear relationship between CSF tau/ptau 181 (primary constituents of neurofibrillary tangles) with the amount of cortical amyloid. We observe a strong inverse relationship of cortical PIB binding with CSF Ab 42 but not for plasma Ab species. Some individuals have low CSF Ab 42 but no cortical PIB binding. Together, these data suggest that changes in brain Ab 42 metabolism and amyloid formation are early pathogenic events in AD, and that significant disruptions in CSF tau metabolism likely occur after Ab 42 initially aggregates and increases as amyloid accumulates. These findings have important implications for preclinical AD diagnosis and treatment.

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- Clinical Trial, Positron Emission Tomography, Amyloid, Biological Sciences
- by Rene Gagnon
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- Molecular Genetics, Adolescent, Child, Young Adult

Carnosinases are Xaa-His dipeptidases that play diverse functions throughout all kingdoms of life. Human isoforms of carnosinase (CN1 and CN2) under appropriate conditions catalyze the hydrolysis of the dipeptides carnosine (β-alanyl-L-histidine) and homocarnosine (γ-aminobutyryl-L-histidine). Alterations of serum carnosinase (CN1) activity has been associated with several pathological conditions, such as neurological disorders, chronic diseases and cancer. For this reason the use of carnosinase levels as a biomarker in cerebrospinal fluid (CSF) has been questioned. The hydrolysis of imidazolerelated dipeptides in prokaryotes and eukaryotes is also catalyzed by aminoacyl-histidine dipeptidases like PepD (EC 3.4.13.3), PepV (EC 3.4.13.19) and anserinase (EC 3.4.13.5). The review deals with the structure and function of this class of enzymes in physiological and pathological conditions. The main substrates of these enzymes, i.e., carnosine, homocarnosine and anserine (β-alanyl-3-methyl-L-histidine) will also be described.

- by Graziella Vecchio
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- Organic Chemistry, Molecules, Biomarker, Substrate Specificity

Variations in extended hopane distributions are now routinely applied in assessing anoxia in ancient marine sediments and for oil-source correlation studies. Current parameters based on the extended hopanes focus on the predominance of the C~S 17a homologues (22s + R isomers), and thus reveal little information on the overall distribution. We present here a new method of characterising extended hopane distributions, using a combination of a CX:C&X ternary diagram, and a hopane odd/even predominance parameter (HOEP). This allows the distinction of virtually all extended hopane distributions.

- by Paul Farrimond
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- Earth Sciences, Organic Geochemistry, Carbon, Biomarkers

Matrix metalloproteinases (MMPs) play an important role in the degradation of extracellular matrix components crucial for tumor growth, invasion and metastasis. MMPs are controlled by natural inhibitors called tissue inhibitors of metalloproteinases (TIMPs). We and others have demonstrated that MMPs and TIMPs are especially important in the process of tumor invasion, progression and the metastasis of colorectal cancer (CRC). It has been proposed that MMPs and TIMPs might play a part not only in tumor invasion and initiation of metastasis but also in carcinogenesis from colorectal adenomas. Several recent studies demonstrated that high preoperative serum or plasma MMP-2, MMP-9 and TIMP-1 antigen levels are strong predictive factors for poor prognosis in patients with CRC and their determination might be useful for identification of patients with higher risk for cancer recurrence. MMP-9 and TIMP-1 have significant potential tumor marker impact in CRC. Their diagnostic sensitivity is consistently higher than those of conventional biomarkers. The pharmacological targeting of CRC by the development of a new generation of selective inhibitors of MMPs, that is highly specific for certain MMPs, is a promising and challenging area for the future.

- by Gábor Lakatos
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- Genetics, Sciences, Extracellular Matrix, Molecular

Analysis of diseases integrating multi-factors increases the complexity of the problem and therefore, development of frameworks for the analysis of diseases is an issue that is currently a topic of intense research. Due to the inter-dependence of the various parameters, the use of traditional methodologies has not been very effective. Consequently, newer methodologies are being sought to deal with the problem. Supervised Learning Algorithms are commonly used for performing the prediction on previously unseen data. These algorithms are commonly used for applications in fields ranging from image analysis to protein structure and function prediction and they get trained using a known dataset to come up with a predictor model that generates reasonable predictions for the response to new data. Gene expression profiles generated by DNA analysis experiments can be quite complex since these experiments can involve hypotheses involving entire genomes. The application of well-known machine le...

- by Sagri Sharma
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- Artificial Intelligence, Machine Learning, Support vector machine, Biomarker
- by YT Szeto
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- Nutrition, Cardiovascular, Oxidative Stress, Antioxidants

Background Early preeclampsia (PE) prediction has been shown to improve the maternal and fetal outcomes in pregnancy. We aimed to evaluate the PE prediction values of a series of serum biomarkers. Methods The singleton pregnant women with PE-related clinical and/or laboratory presentations were recruited and had the blood drawn at their first visits. The prospective cohort was further divided into the PE-positive and PE-negative groups based on the follow-up results. The following markers were tested with the collected serum samples: sFlt-1, PlGF, M, tPAI-C, compliment factors C1q, B, H, BUN, GlyFn, PAPP-A2, BUN, Cre, UA and Cysc. Results Totally 196 women suspected for PE were recruited with follow-up medical records. Twenty-five percent of the recruited subjects developed PE before delivery and 75% remained PE-negative. The serum levels of sFlt-1, BUN, Cre, UA, Cysc and PAPP-A2 were significantly elevated and the PlGF was significantly decreased in the PE-positive patients. The AU...

- by Junhui Zhong
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- Medicine, Biomarker

The suitability of using helminth communities as bioindicators of environmental quality of the Yucatan coastal lagoons status was tested on the checkered puffer (Spheroides testudineus) in four coastal lagoons along the Yucatan coast. The concentration of chemical pollutants in sediments, water quality parameters, helminth infracommunity characteristics, as well as fish physiological biomarkers, including EROD (7-ethoxyresorufin-O-deethylase) and catalase activities, were measured. Results from sediment analyses demonstrated the presence of hydrocarbons, organochlorine pesticides and polychlorinated biphenyls at varying concentrations, some of which exceeded the Probability Effect Level (PEL). Significant negative associations among organochlorine pesticides, infracommunity characteristics and fish physiological responses were observed in most of the lagoons. Results suggest that EROD activity and parasite infracommunity characteristics could be useful tools to evaluate the effects of chemical pollutants on the fish host and in the environment. Importantly, certain parasites appear to influence biomarker measurements, indicating that parasites should be considered in ecotoxicological studies.

- by Ma Leopoldina Aguirre-Macedo
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- Water, Water quality, Environmental Monitoring, Water Pollution
- by Kim Dowling
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- Geology, Geochemistry, Geophysics, Neutron Activation Analysis
- by Balraj Mittal
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- Cancer, Biomarkers, Environmental Biotechnology, Risk factors

The impact of an extraterrestrial body 65.5 Ma caused the so-called Cretaceous/Paleogene (K/Pg) event that resulted in a mass extinction and rapid changes in the surface environment on Earth. Here we report changes in land vegetation and oceanic redox across the K/Pg boundary at Caravaca, southeastern Spain, using biomarkers. The results reveal that the basal 3-mm-thick layer of the K/Pg boundary clay is marked by a rapid increase in the concentration of terrestrial long-chain n-alkanes and dibenzofuran, indicating the destruction of land vegetation and an increase in the supply of terrestrial organic matter into the marine environment during the deposition of the K/Pg boundary clay. This layer also records a rapid increase in the concentration of dibenzothiophenes, which indicates a change in redox conditions from oxic to anoxic/euxinic conditions in the intermediate water over the seafloor. The low-oxygen conditions could have been caused by an increase in the influx of terrestrial organic matter into the ocean. A rapid increase in the concentration of retene and retene/ cadalene occurred during the deposition of the upper part of the boundary clay 10 kyr after the mass extinction, indicating the recovery of conifers, which greatly decreased at the K/Pg boundary.

- by Kunio Kaiho
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- Evolutionary Biology, Geology, Ecology, Plant

Aquatic insects obtain oxygen either from air dissolved in water or directly from air via surfacing. Diving beetles (Coleoptera: Dytiscidae) rely on a subelytral air store, which has to be renewed periodically at the water's surface. [Correction added after publication 28 July 2007: in the preceding sentence 'Diving beetles Ilybius montanus (Coleoptera: Dytiscidae)' was corrected to 'Diving beetles (Coleoptera: Dytiscidae)']. The way in which diving behaviour responds to changes in the insect's environment has not been previously explored, however. Here, we investigate the diving behaviour of the widespread European species Ilybius montanus (Stephens). We go on to examine how different aspects of the diving behaviour of individual insects change with temperature and water acidity, using both hydrochloric and sulphuric acids. Individual surfacing frequency was significantly higher at 20.5 1C than at 14.5 1C, which resulted from a shortening of the mean dive duration at higher temperatures, no associated change being seen in mean time spent exchanging at the surface. The observed reductions in dive duration may have resulted from increased metabolic rate at higher temperatures, while the constancy of surface time suggests that this represents a trade-off between gas exchange demands and selection to minimize time spent at the surface, perhaps to avoid predation. Although acidity did not affect surfacing frequency or the mean duration of individual dive parameters, it resulted in a breakdown of an individual's ability to regulate diving behaviour with temperature. This effect was most pronounced when experimental water was acidified using sulphuric acid, indicating that anion, as well as acidity itself, is of importance. As the dive response could be broken down into readily quantifiable components, and this behaviour showed marked responses to the factors considered here, we propose that diving activity could serve as an integrative organismal biomarker in these and other surface-exchanging aquatic insects.

- by Piero Calosi
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- Zoology, Biological Sciences, Environmental Sciences, Temperature
- by Raja Rajeswari
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- Biochemistry, Toxicology, Biomarker

Cancer initiation and progression is controlled by both genetic and epigenetic events. Epigenetics refers to the study of mechanisms that alter gene expression without permanently altering the DNA sequence. Epigenetic alterations are reversible and heritable, and include changes in histone modifications, DNA methylation, and non-coding RNA-mediated gene silencing. Disruption of epigenetic processes can lead to altered gene function and malignant cellular transformation. Aberrant epigenetic modifications occur at the earliest stages of neoplastic transformation and are now believed to be essential players in cancer initiation and progression. Recent advances in epigenetics have not only offered a deeper understanding of the underlying mechanism(s) of carcinogenesis, but have also allowed identification of clinically relevant putative biomarkers for the early detection, disease monitoring, prognosis and risk assessment of cancer patients. At this moment, DNA methylation and non-coding RNA including with microRNAs (miR-NAs) and long non-coding RNAs (lncRNAs) represent the largest body of available literature on epigenetic biomarkers with the highest potential for cancer diagnosis. Following identification of cell-free nucleic acids in systematic circulation, increasing evidence has demonstrated the potential of cell-free epigenetic biomarkers in the blood or other body fluids for cancer detection. In this article, we summarize the current state of knowledge on epigenetic biomarkers -primarily DNA methylation and non-coding RNAsas potential substrates for cancer detection in gastric and colorectal cancer, the two most frequent cancers within the gastrointestinal tract. We also discuss the obstacles that have limited the routine use of epigenetic biomarkers in the clinical settings and provide our perspective on approaches that might help overcome these hurdles, so that these biomarkers can be readily developed for clinical management of cancer patients.

- by Yoshinaga Okugawa
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- MicroRNA, Methylation, DNA methylation, microRNAs
- by yannick nuapia
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- Toxicology, Nmr, Proteins, Biomarker

The N-methyl-D-aspartate (NMDA) receptor antagonist ketamine has rapid antidepressant effects in treatment-resistant major depressive disorder (MDD). In rats, ketamine selectively increased electroencephalogram (EEG) slow wave activity (SWA) during non-rapid eye movement (REM) sleep and altered central brain-derived neurotrophic factor (BDNF) expression. Taken together, these findings suggest that higher SWA and BDNF levels may respectively represent electrophysiological and molecular correlates of mood improvement following ketamine treatment. This study investigated the acute effects of a single ketamine infusion on depressive symptoms, EEG SWA, individual slow wave parameters (surrogate markers of central synaptic plasticity) and plasma BDNF (a peripheral marker of plasticity) in 30 patients with treatment-resistant MDD. Montgomery-Å sberg Depression Rating Scale scores rapidly decreased following ketamine. Compared to baseline, BDNF levels and early sleep SWA (during the first non-REM episode) increased after ketamine. The occurrence of high amplitude waves increased during early sleep, accompanied by an increase in slow wave slope, consistent with increased synaptic strength. Changes in BDNF levels were proportional to changes in EEG parameters. Intriguingly, this link was present only in patients who responded to ketamine treatment, suggesting that enhanced synaptic plasticity -as reflected by increased SWA, individual slow wave parameters and plasma BDNF -is part of the physiological mechanism underlying the rapid antidepressant effects of NMDA antagonists. Further studies are required to confirm the link found here between behavioural and synaptic changes, as well as to test the reliability of these central and peripheral biomarkers of rapid antidepressant response.

- by Fabio Ferrarelli
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- Electroencephalography, Major Depressive Disorder, Ketamine, Brain Waves

The immunohistochemistry technique is used in the search for cell or tissue antigens that range from amino acids and proteins to infectious agents and specific cellular populations. The technique comprises two phases: (1) slides preparation and stages involved for the reaction; (2) interpretation and quantification of the obtained expression. Immunohistochemistry is an important tool for scientific research and also a complementary technique for the elucidation of differential diagnoses which are not determinable by conventional analysis with hematoxylin and eosin. In the last couple of decades there has been an exponential increase in publications on immunohistochemistry and immunocytochemistry techniques. This review covers the immunohistochemistry technique; its history, applications, importance, limitations, difficulties, problems and some aspects related to results interpretation and quantification. Future developments on the immunohistochemistry technique and its expression quantification should not be disseminated in two languages-that of the pathologist and another of clinician or surgeon. The scientific, diagnostic and prognostic applications of this methodology must be explored in a bid to benefit of patient. In order to achieve this goal a collaboration and pooling of knowledge from both of these valuable medical areas is vital

- by Maria Pinhal
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- Immunohistochemistry, Clinical Practice, Biomarker, Scientific Research

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

- by Junhui Zhong
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- Immunology, Medicine, Preeclampsia, Biomarker

Chronic venous disease represents a healthcare problem due to high prevalence and recurrence rates. Studies on chronic venous ulcer wound fluid (CVUWF) have demonstrated increased inflammation and proteolysis which can cause tissue destruction and delayed healing. This review discusses: nearly all known metabolites discovered in the past 25 years in CVUWF studies; the omics approaches characterizing the microenvironment of human venous leg ulcers; and the use of biocompounds as prognostic biomarkers and as possible targets for therapeutic approaches. A biomarker is a biological compound that can be functional or non-functional, specific or non-specific in the diagnosis/prognosis to a disease state and may be quantified to determine progression or regression of disease. Omics studies in CVUWF provide the impetus for future identification of biomarkers within the intricate network in chronic venous disease and set the basis for determining the appropriate combination of molecules that are expressed with the healing status of venous leg ulcers.

- by Ferdinando Mannello
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- Genomics, Metabolomics, Wound Healing, Proteomics

Late Albian deep-water sediments of the Black Flysch Group in the Basque-Cantabrian Basin (western Pyrenees) preserve a fossil pockmark field including methane seep carbonates and associated macrofauna. The geometry of the pockmarks is reconstructed from repeated lens-shaped turbidite deposits with centrally located carbonate bodies. Early diagenetic carbonate phases such as clotted micrite and yellow calcite with δ 13 C values as low as −41.6‰, and hydrocarbon biomarkers (e.g. 2,6,10,15,19-pentamethylicosane) with strong depletions in 13 C indicate that the carbonates precipitated due to anaerobic oxidation of methane. The pockmarks probably formed due to subsidence induced by dewatering and degassing of the gas-charged seabed perhaps enhanced by the weight of the carbonate bodies. The macrofauna resembles that of other late Mesozoic deep-water methane-seeps world-wide, and is dominated by large lucinid and Caspiconcha bivalves, and hokkaidoconchid gastropods. During late diagenesis the carbonate δ 18 O values were reset to a narrow range of −12 to −10‰, the remaining pore spaces and fissures were filled with pyrobitumen, and additional carbonate phases precipitated, potentially due to thermochemical sulfate reduction processes.

- by Luis M. Agirrezabala
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- Evolutionary Biology, Geology, Ecology, Biomarker

This paper reviews the experimental procedures of the Gas Chromatography-Mass Spectrometry (GC-MS) technique. The objectives of this study are to present a step-by-step procedure involved in the GC-MS analysis and interpretations of the resulting data both qualitatively and quantitatively, and to identify the possible sources of analytical errors that may be encountered by young inexperienced organic geochemists. The overall process encompasses ultrasonic solvent extraction, fractionation and GC-MS analysis itself. The qualitative and quantitative information obtained from the GC-MS interpretations when integrated together is capable of giving us an insight into the source or origin, depositional environment and level thermal maturity of the analysed sample. The possible sources of analytical errors may include contamination, measurement errors, mechanical/instrumental errors, fractionation errors, and loading errors on the GC. Analytical geochemists must therefore be aware of these errors among others in order to minimise them to the reasonable level. It is recommended that, if weak signals result from the GC-MS analysis of a fraction, such a fraction should be prepared in higher concentration and re-run using selected ion monitoring (SIM) mode so as to enhance signal to noise ratio, and that the GC-MS data should always be interpreted with GC-MS softwares with biomarkers definitions in order to obtain more reliable and robust interpretations.

- by Waheed Akande
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- Earth Sciences, Biomarker, Bitumen, Fractionation
- by Freya J Saykin
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- Genetics, Neuroimaging, Clinical Trial, Mild Cognitive Impairment

Flow cytometry-based assays serve as valuable tools for various aspects of the drug development process ranging from target discovery and characterization to evaluation of responses in a clinical setting. The integrity of the samples and the appropriate selection and characterization of the reagents used in these assays are in themselves challenging. These concerns taken together with the flow-based technology makes the validation of flow cytometry assays a challenging effort. Therefore, apart from summarizing the role of flow cytometry technology in various stages of drug development, this manuscript focuses on recommendations for the validation of methods applying flow cytometry. Information is also provided on the relevant validation parameters for different types of flow cytometry assays to guide the users of this platform. Together, the recommendations and the information on regulatory guidelines provided in this manuscript represent the consensus of all the authors and can assist the flow cytometry user in implementing the appropriate method validation strategies.

- by Jennifer Stewart
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- Immunology, Flow Cytometry, Drug Discovery, Drug development

Beberapa tahun terakhir ini, telah terjadi degradasi lingkungan yang serius terhadap ekosistem perairan, terutama karena polusi manusia. Konsentrasi polutan yang tinggi, baik dari pertanian dan limbah polutan ¬¬¬¬menyebabkan gangguan terhadap ekosistem perairan dan menjadi risiko bagi organisme yang bergantung pada sumber daya air dan juga untuk kesehatan manusia. Studi ini meneliti, berdasarkan pengamatan eksperimen, menggunakan biomarker untuk melakukan penilaian resiko dari limbah polutan terhadap ekosistem perairan Oleh karena itu, Jurnal ini mengidentifikasi penilaian biomarker untuk monitoring polusi manusia pada ekosistem perairan.
Kata Kunci : Degradasi Lingkungan, Penilaian Resiko,Biomarker, Polusi Manusia,Ekosistem Perairan.

- by Paulina Tetjuari
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- Marine Biology, Biomarkers, Biomarker
- by Lesa Mitchell
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- Business, Personalized Medicine, Health, Medicine

Human papillomavirus (HPV) infection is associated with a wide spectrum of disease that ranges from self-limited skin warts to life-threatening cancers. Since HPV plays a necessary etiological role in cervical cancer, it is logical to use HPV as a marker for early detection of cervical cancer and precancer. Recent advances in technology enable the development of high-throughput HPV assays of different formats, including DNA-based, mRNA-based, high-risk group-specific and type-specific methods. The ultimate goal of these assays is to improve the accuracy and costeffectiveness of cervical screening programs. HPV testing has several potential advantages compared to cytologybased screening. However, since the cancer to transient infection ratio is always low in the general population, HPV test results are bound to have a low positive predictive value that may subject women to unnecessary follow-up investigations. The wide-spread administration of prophylactic HPV vaccine will substantially decrease the incidence of cancer and precancer. This poses a number of challenges to cytology-based screening, and the role of HPV testing is expected to increase. Finally, apart from technical and cost-effectiveness considerations, one should also keep in mind the psycho-social impact of using sexually-transmitted agents as a marker for cancer screening.

- by Lucia Giovannelli and +1
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- Biomarker

Despite several decades of intensive effort to improve the imaging techniques for lung cancer diagnosis and treatment, primary lung cancer is still the number one cause of cancer death in the United States and worldwide. The major causes of this high mortality rate are distant metastasis evident at diagnosis and ineffective treatment for locally advanced disease. Indeed, approximately forty percent of newly diagnosed lung cancer patients have distant metastasis. Currently, the only potential curative therapy is surgical resection of early stage lung cancer. Therefore, early detection of lung cancer could potentially increase the chance of cure by surgery and underlines the importance of screening and detection of lung cancer. In the past fifty years, screening of lung cancer by chest X-Ray (CXR), sputum cytology, computed tomography (CT), fluorescence endoscopy and low-dose spiral CT (LDCT) has not improved survival except for the recent report in 2010 by the National Lung Screening Trial (NLST), which showed a 20 percent mortality reduction in high risk participants screened with LDCT compared to those screened with CXRs. Furthermore, serum biomarkers for detection of lung cancer using free circulating DNA and RNA, exosomal microRNA, circulating tumor cells and various lung cancer specific antigens have been studied extensively and novel screening methods are being developed with encouraging results. The history of lung cancer screening trials using CXR, sputum cytology and LDCT, as well as results of trials involving various serum biomarkers, are reviewed herein.

- by Carl Freter
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- Bioinformatics, Life Sciences, Biomedical Research, Biomarker

In this study, organic matter content, type and maturity as well as some petrographic and physical characteristics of the Jurassic coals exposed in the eastern Taurus were investigated and their depositional environments were interpreted.The total organic carbon (TOC) contents of coals in the Feke–Akkaya, Kozan–Gedikli and Kozan–Kizilinc areas are 24.54, 66.78 and 49.15%, respectively. The Feke–Akkaya and Kozan–Kizilinc coals have low Hydrogen Index (HI) values while the Kozan–Gedikli coals show moderate HI values. All coal samples display very low Oxygen Index (OI) values. The Kozan–Gedikli coals contain Type II organic matter (OM), the Feke–Akkaya coals contain a mixture of type II and type III OM; and the Kozan–Kizilinc coals are composed of Type III OM. Sterane distribution was calculated as C27 > C29 > C28 from the m/z 217 mass chromatogram for all coal samples.Tmax values for the Feke–Akkaya, Kozan–Gedikli and Kozan–Kizilinc coals are 439, 412 and 427 °C. Vitrinite reflectance values (%Ro) for the Feke–Akkaya and Kozan–Kizilinc coal samples were measured as 0.65 and 0.51 and these values reveal that the Feke–Akkaya and Kozan–Kizilinc coals are at subbituminous A or high volatile C bituminous coal stage. On the basis of biomarker maturity parameters, these coals have a low maturity.The pristane/phytane (Pr/Ph) ratios for the Feke–Akkaya, Kozan–Gedikli and Kozan–Kizilinc coals are 1.53, 1.13 and 1.25, respectively. In addition, all coals show a homohopane distribution which is dominated by low carbon numbers, and C35 homohopane index is very low for all coal samples. All these features may indicate that these coals were deposited in a suboxic environment.The high sterane/hopane ratios with high concentrations of steranes, low Pr/Ph ratios and C25/C26 tricyclic ratios > 1 may indicate that these coals formed in a swamp environment were temporarily influenced by marine conditions.

- by Serdar Kozan
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- Mechanical Engineering, Chemical Engineering, Earth Sciences, Geology

A combination of bioenergetics and biochemical biomarkers in mussels was applied to assess possible pollution impacts in a protected semi-enclosed estuary (Amvrakikos Gulf, NW Greece) that receives pesticide discharges through riverine transport. Scope for growth, a physiological condition index representing the energy budget of the organism, was applied to detect general stress effects on the health status of mussels. The low energy budgets of mussels revealed stress conditions and provided early warning signals of possible consequences at higher levels of biological organization. Biochemical markers of exposure confirmed a risk of pesticide contamination. Decreased acetylcholinesterase activities indicated exposure to organophosphate and carbamate pesticides. Responses of the antioxidant enzyme glutathione peroxidase suggested the presence of contaminants capable of reactive oxygen species production that could be related to organochlorine pesticide contamination in the area. On the other hand, metallothionein levels implied low metal contamination.

- by Efthimia Cotou
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- Environmental Monitoring, Public Health, Water Pollution, Pesticide Residues

It is easier to demonstrate the consistent effects of foods on satiety than on cognitive performance. This is understandable since the satiety system incorporates physiological signalling systems that mediate the effects of foods on function. Specific manipulations of proteins, carbohydrates and fats have the potential to act as functional foods for appetite control. Because of the importance of the optimal functioning of cognitions for survival, these functions are quite strongly protected against short-term dietary and physiological perturbances. Therefore, food manipulations may be better detected through the degree of effort exerted to maintain performance rather than via changes in the actual performance itself. This procedure has not been widely used hitherto. The concept of biomarkers may have to be interpreted differently from research on physiological systems or clinical endpoints. For satiety, adjustments in the profile of hunger could serve as a biomarker or surrogate endpoint. For cognitions, correlated physiological variables may be more difficult to measure than the functional endpoint itself. Changes related to unitary functions (such as tracking) could serve as biomarkers for more complex, integrated skills (such as car driving). Since food manipulations may affect multiple functions, the challenge is to design foods with good satiety control that do not impair mental performance; or alternatively to engineer foods that optimise cognitive performance without compromising satiety. This rapidly developing field has great potential for close collaboration between academia and industry in the production of commercially successful products that show clear improvements in human functioning with the capacity to protect against disease or impairment.

- by John Blundell
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- Nutrition and Dietetics, Cognition, Attention, Animal Production

Organic-rich mudstones with up to 10 wt% TOC from the upper portion of the Belle Fourche Formation and the lower part of the Second White Specks Formation in the Western Canada Sedimentary Basin were evaluated as source rocks. Both geochemistry and organic petrography indicate an open marine paleoenvironment with deposition of Type II kerogen based on the predominance of marine alginite and amorphous organic matter (OM), limited amounts of terrigenous vitrinite and inertinite macerals, the presence of marine fossils, and the low ratio of TOC to total sulfur ($1.26). The prevalence of short-chain n-alkanes (n-C 13 to n-C 19 ), a predominance of C 28 abb(H)-20S steranes, and small concentrations of oleanane confirm the dominantly algal and planktonic origin of OM. Alternating oxic to anoxic paleoenvironmental sedimentary conditions are proposed based on common bioturbation, abundant inoceramid prisms, and good organic richness. Biomarker distributions are consistent with intermittent anoxia, without unequivocal evidence for water column stratification or hypersalinity. The thermal maturity measured in seven sediment cores by different methods consistently indicates a westward increase in maturity according to vitrinite reflectance, T max , and hopane and sterane biomarkers. Two cores are thermally immature ($0.42 %Ro), one is early mature ($0.65 %Ro), and four cores are within the oil window ($0.78 to 0.89 %Ro). All thermally mature cores retain good to very good hydrocarbon potential (248 mg HC/g rock) and are dominantly oil-prone and minor gas-prone based on their maceral compositions. The upper Belle Fourche and lower Second White Specks Formations represent potential targets for unconventional light shale oil production.

The Masila Basin is an important hydrocarbon province in Yemen, but the origin of hydrocarbons and their generation history are not fully understood. In this regard, 10 crude oils from different petroleum reservoir sections in the Masila Basin were characterized by a variety of biomarker and non-biomarker parameters using GC, GC-MS and stable carbon isotope techniques. Oils from the Masila Basin display pristane/phytane (Pr/Ph) ratios ranging from 1.7 to 2.0, low sulfur content, high C 35 homohopane index, relatively high C 27 sterane concentrations and relatively high tricyclic terpanes suggesting a marine clay source rock that was deposited in mildly anoxic to suboxic conditions with dominantly algal organic matter. C 29 20S/(20S + 20R) steranes and bb/(bb + aa) sterane ratios indicate that the Masila oils have reached peak oil window maturity. Another related feature of these oils is the absence of 18a (H)-oleanane, which suggests a source age older than Cretaceous. The carbon isotope compositions are similar to those of the potential source rocks, which range from À25.4‰ to À28.3‰, indicating a marine environment. The new data presented in this paper suggest that the Masila oils constitute one oil family and that the oil originated from the Upper Jurassic Madbi source rock in the basin.

- by Wan Hakimi
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- Earth Sciences, Geology, Geophysics, Sedimentology

- by Simon Brassell
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- Earth Sciences, Organic Geochemistry, Environmental Sciences, CHEMICAL SCIENCES

Availability of genome sequence of human and different pathogens has advanced proteomics research for various clinical applications. One of the prime goals of proteomics is identification and characterization of biomarkers for cancer and other fatal human diseases to aid an early diagnosis and monitor disease progression. However, rapid detection of low abundance biomarkers from the complex biological samples under clinically relevant conditions is extremely difficult, and it requires the development of ultrasensitive, robust and high-throughput technological platform. In order to overcome several technical limitations associated with sensitivity, dynamic range, detection time and multiplexing, proteomics has started integrating several emerging disciplines such as nanotechnology, which has led to the development of a novel analytical platform known as ‘nanoproteomics’. Among the diverse classes of nanomaterials, the quantum dots, gold nanoparticles, carbon nanotubes and silicon nanowires are the most promising candidates for diagnostic applications. Nanoproteomics offers several advantages such as ultralow detection, short assay time, high-throughput capability and low sample consumption. In this article, we have discussed the application of nanoproteomics for biomarker discovery in various diseases with special emphasis on various types of cancer. Furthermore, we have discussed the prospects, merits and limitations of nanoproteomics.► Applications of nanoproteomics in diagnostics have steadily been growing over the years. ► Quantum dots, gold nanoparticles, carbon nanotubes and silicon nanowires are the most promising for diagnostic applications. ► Nanoproteomics allow for real-time, rapid multiplexed analysis, low sample consumption and high sensitivity.

- by Sandipan Ray
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- Biosensors, Cancer, Proteomics, Carbon Nanotubes
- by Filomena D’Amato and +1
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- Long Term Potentiation, Intercellular Communication, Chemical, Neuropeptides

Schizophrenia is a highly heritable, chronic, severe, disabling neurodevelopmental brain disorder with a heterogeneous genetic and neurobiological background, which is still poorly understood. To allow better diagnostic procedures and therapeutic strategies in schizophrenia patients, use of easy accessible biomarkers is suggested. The most frequently used biomarkers in schizophrenia are those associated with the neuroimmune and neuroendocrine system, metabolism, different neurotransmitter systems and neurotrophic factors. However, there are still no validated and reliable biomarkers in clinical use for schizophrenia. This review will address potential biomarkers in schizophrenia. It will discuss biomarkers in schizophrenia and propose the use of specific blood-based panels that will include a set of markers associated with immune processes, metabolic disorders, and neuroendocrine/neurotrophin/neurotransmitter alterations. The combination of different markers, or complex multi-marker panels, might help in the discrimination of patients with different underlying pathologies and in the better classification of the more homogenous groups. Therefore, the development of the diagnostic, prognostic and theranostic biomarkers is an urgent and an unmet need in psychiatry, with the aim of improving diagnosis, therapy monitoring, prediction of treatment outcome and focus on the personal medicine approach in order to improve the quality of life in patients with schizophrenia and decrease health costs worldwide.

- by Dubravka Švob Štrac
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- Genetics, Schizophrenia, Biomarkers, Medicine

Nephrin is a 180 KD trans-membrane protein expressed in glomerular podocytes. It was first identified in children with congenital nephrotic syndrome of the Finnish type (NPHS1). Nephrin forms an integral part of podocytes, which-together with endothelial cells and the basement-form the glomerular filtration barrier. Podocytopathies result in the detection of nephrin in the urine. We reviewed the literature to determine if urine nephrin measurements could become useful as a biomarker to detect early podocyte injury. Our search identified a total of 19 studies that have been published to date. The most common clinical conditions for which urine nephrin analyses were carried out included diabetic nephropathy, glomerulonephritis and pre-eclampsia. Nephrin measurement was carried out using commercially available ELISA kits, the messenger ribonucleic acid real-time polymerase chain Reaction, or electrophoresis. Nephrinuria showed positive correlation with proteinuria and severity of podoc...

- by Eugenie Lumbers and +1
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- Biomarker

Alterations of genetic and epigenetic features can provide important insights into the natural history of breast cancer. Although DNA methylation analysis is a rapidly developing field, a reproducible epigenetic blood-based assay for diagnosis and follow-up of breast cancer has yet to be successfully developed into a routine clinical test. The aim of this study was to review multiple serum DNA methylation assays and to highlight the value of those novel biomarkers in diagnosis, prognosis and prediction of therapeutic outcome. Serum is readily accessible for molecular diagnosis in all individuals from a peripheral blood sample. The list of hypermethylated genes in breast cancer is heterogeneous and no single gene is methylated in all breast cancer types. There is increasing evidence that a panel of epigenetic markers is essential to achieve a higher sensitivity and specificity in breast cancer detection. However, the reported percentages of methylation are highly variable, which can be partly explained by the different sensitivities and the different intra-/inter-assay coefficients of variability of the analysis methods. Moreover, there is a striking lack of receiver operating characteristic (ROC) curves of the proposed biomarkers. Another point of criticism is the fact that 'normal' patterns of DNA methylation of some tumor suppressor and other cancer-related genes are influenced by several factors and are often poorly characterized. A relatively frequent methylation of those genes has been observed in high-risk asymptomatic women. Finally, there is a call for larger prospective cohort studies to determine methylation patterns during treatment and follow-up. Identification of patterns specific for a differential response to therapeutic interventions should be useful. Only in this way, it will be possible to evaluate the predictive and prognostic characteristics of those novel promising biomarkers.

- by Joris Delanghe
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- Genetics, Treatment Outcome, Risk assessment, Epigenetics
- by Philip Weinstein
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- Forensic Toxicology, Biomarker, Hydrogen Sulfide

Context: In the Indian traditional system of medicine, Streblus asper Lour (Moraceae) is prescribed for the treatment of diabetes mellitus. Objective: In the present study, α-amyrin acetate isolated from S. asper, and the petroleum ether extract of S. asper stem bark (PESA) was screened for their antidiabetic properties in streptozotocin (STZ)-induced diabetic rats. Materials and methods: Successive Soxhlet extraction of the dried stem bark with petroleum ether and then with ethanol (95%) yielded petroleum ether and ethanol extracts, respectively, which were concentrated under reduced pressure. Hyperglycemia was induced in rats by STZ (50 mg/kg, b.w.). Twenty-four hours after STZ induction, respective groups of diabetic rats received PESA (100, 250 and 500 mg/kg, b.w.) and α-amyrin acetate (25, 50 and 75 mg/kg, b.w.) respectively, orally daily for 15 days. Glibenclamide (0.5 mg/kg, orally) served as a reference. Blood glucose levels were measured on every 5th day during the 15 days of treatment. The serum lipid profiles and biochemical parameters, viz., serum glutamic oxaloacetic transaminase (SGOT), serum glutamic pyruvic transaminase (SGPT), alkaline phosphatase (ALP), insulin and glycosylated hemoglobin level, were measured. Results: PESA significantly (p < 0.01) normalized blood-glucose levels and serum biochemical parameters as compared with those of STZ controls. α-Amyrin acetate (75 mg/kg, b.w.) exhibited maximum glucose lowering effect (71.10%) in diabetic rats compared to the other dose (25, 50 mg/kg) at the end of the study. The protective effect was further confirmed by histopathological examination of the liver. Conclusion: PESA and α-amyrin acetate demonstrated remarkable antidiabetic activity in STZ-induced diabetic rats.

- by Arijit Mondal
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- Plant Biology, Ethnopharmacology, Oxidative Stress, India

Foods and beverages have been at the heart of our society for centuries, sustaining humankindhealth, life, and the pleasures that go with it. The more we grow and develop as a civilization, the more we feel the need to know about the food we eat and beverages we drink. Moreover, with an ever increasing demand for food due to the growing human population food security remains a major concern. Food safety is another growing concern as the consumers prefer varied foods and beverages that are not only traded nationally but also globally. The 21st century science and technology is at a new high, especially in the field of biological sciences. The availability of genome sequences and associated highthroughput sensitive technologies means that foods are being analyzed at various levels.

- by Anna Maria Timperio
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- Proteomics, Nanotechnology, Food Analysis, Beverages

This review summarizes the application of Tetrahymena spp. in ecotoxicology, in order to promote a more integrated, multi-level ecotoxicological assessment approach regarding the effects of chemical stressors on several biological levels (from molecule to ecosystem). Such a multi-level testing approach in one species facilitates the establishment of missing causal relationships between biochemical responses and ecological effects. The review illustrates that Tetrahymena spp. represent excellent ecotoxicological test species due to their important role in the microbial foodweb, wide distribution and abundance, sequenced genome in T. thermophila, large background knowledge and scientific publications in cellular biology, ecology and ecotoxicology. Several bioassays have already been developed on different biological organisation levels, such as enzyme assays (biochemical level), behavioral tests (individual level), population growth tests (population level) and microcosms (community l...

- by Almut Gerhardt
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- Biology, Risk assessment, Biosensor, Population Growth

CITATIONS 16 READS 162 6 authors, including:

- by Mariano Sanz
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- Dentistry, Biomedical Engineering, Biomarker, Periodontitis

Non-specfic carboxylesterase and glutathione S-transferase activity was measured in the ground beetle, Pterosthicus oblongopunctatus (Coleoptera: Carabidae), from five sites along a gradient of heavy metal pollution. A previous study determined that beetles from the two most polluted sites (site codes OLK2 and OLK3) were more susceptible to additional stressors compared with beetles from the reference site (Stone et al., Environ. Pollut. 113, 239-244 2001), suggesting the possibility of physiological impairment. Metal body burdens in ground beetles from five sites along the gradient ranged from 79 to 201 mgyg Zn, 0.174 to 8.66 mgyg Pb and 1.14 to 10.8 mgyg Cd, whereas Cu seemed to be efficiently regulated regardless of metal levels in the soil. Beetle mid-and hindguts were homogenized and the soluble fraction containing glutathione S-transferase (GST) and carboxylesterase (CaE) was assayed using kinetic analyses. Significantly higher levels of GST were found only in female beetles from the most polluted sites (OLK2 and OLK3; Ps0.049, P-0.001, respectively) compared with the reference site (OLK7). In addition, OLK3 females had significantly higher levels of CaE compared with the reference beetles (Ps0.01). Male beetles did not differ in enzyme activity along the metal gradient. Overall, obvious trends in detoxification enzymes were not detected in ground beetles in association with metal body burdens. ᮊ

- by Paul Jepson
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- Ecotoxicology, Kinetics, Stress, Environmental Pollution

The Maikop Formation, deposited in eastern Azerbaijan during Oligocene and Early Miocene, represents a prolific source unit for the oils found within the southern Gobustan area and the Kura Depression. Based on biomarker characteristics, the oils are believed to have originated from a clastic source rock deposited in an anoxic to suboxic, transitional marine environment with low to moderate input of terrigenous organic matter. However, due to the thermal immaturity of accessible Maikop rocks, oil-source rock correlation based on biomarker fingerprints is hampered.

Multiple anthropogenic activities present along coastal environments may affect the health status of aquatic ecosystems. In this study, specimens of European sea bass (Dicentrarchus labrax) were exposed for 30 days to highly contaminated sediment collected from the industrial area between Augusta and Priolo (Syracuse, Italy), defined as the most mercury polluted site in the Mediterranean. The aim was to evaluate the responses of juvenile D. labrax to highly contaminated sediments, particularly enriched in Hg, in order to enhance the scarce knowledge on the potential compensatory mechanisms developed by organisms under severe stress conditions. Apoptotic and proliferative activities [cell turnover: Proliferating Cell Nuclear Antigen (PCNA) and FAS Ligand (FasL)], onset of hypoxic condition [hypoxia: Hypoxia Inducibile Factor-1α (HIF-1α)], and changes in the neuroendocrine control mechanisms [neurotransmission: Tyrosine Hydroxylase (TH), Choline Acetyltransferase (ChAT), Acetylcholinesterase (AChE), 5-Hydroxytryptamine (5-HT) and 5-Hydroxytryptamine receptor 3 (5-HT3)] were investigated in sea bass gill tissues. In the specimens exposed to the polluted sediment, the occurrence of altered cell turnover may result in impaired gas exchange that leads to a condition of "functional hypoxia". Changes in neurotransmission pathways were also observed, suggesting a remodeling process as an adaptive response to increase the O 2 -carrying capacity and restore the normal physiological conditions of the gills. Overall, these findings demonstrated that although chronic exposure to heavy metal polluted sediments alters the functioning of both the nervous and endocrine systems, as well as plasticity of the gill epithelium, fish are able to trigger a series of physiological adjustments or adaptations interfering with specific neuroendocrine control mechanisms that enable their long-term survival.

- by Vincenzo Parrino and +4
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- Apoptosis, Western blotting, Italy, Heavy metals

Generally physical and chemical methods are use in river water quality monitoring; currently biomarker is developed as alternative biomonitoring method. The aim of this study is to look at the probability using aquatic species in monitoring river water pollutants exposure. This study was done by using Hyposarcus pardalis as biomarker to analyze river water quality in Upstream Citarum River. Hyposarcus pardalis were taken along the river at five sampling point and look at the Cu and Zn concentration. Results from this study show that there was an indication that river water quality has been degrading along the river from upstream to downstream. Zn concentration in Hyposarcus pardalis were increasing as well as Cu concentration. The increase of Zn concentration in Hyposarcus pardalis indicating that the river was polluted by Zn. Secondary data and observation at sampling location shown that textile was the dominant industry which may contribute the Zn concentration in river as they received the effluent. Cu is use in metal coating process, as well as textile industry metal industries were identified at Majalaya, Bantar Panjang, Dayeuh Kolot and Katapang in Bandung-Indonesia. As a receiving water from many activities along the river, upstream Citarum River water quality become degrading as the increasing of heavy metal Zn and Cu concentration in Hyposarcus pardalis.

- by Dwina Roosmini
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- Heavy Metal Pollution, Biomonitoring, Biomarker