New Set Of Samples Research Articles

Northern African strains of human T-lymphotropic virus type 1 arose from a recombination event

Although recombination is a major source of genetic variability in retroviruses, no recombinant strain had been observed for HTLV-1, the first isolated human-pathogenic retrovirus. Different genotypes exist for HTLV-1: Genotypes b and d to g are restricted to central Africa, while genotype c is only endemic in Australo-Melanesia. In contrast, the cosmopolitan genotype A is widely distributed. We applied a combination of phylogenetics and recombination analysis approaches to a set of new HTLV-1 sequences, including the complete LTR and a 522-bp fragment of the env gene, which we collected from 19 countries throughout North, West and Central Africa, the continent where the virus has the largest endemic presence. The samples were obtained from 41 HTLV-1 infected individuals with different clinical statuses including ATL, TSP/HAM and asymptomatic carriers. The recombinant search and breakpoint detection were performed by boot scanning in Simplot to compare inferred clusters of sequences to each other. Finally, molecular clock analyses were performed to date the recombinant event observed. This led us to demonstrate the presence of recombinants in HTLV-1. Indeed, the HTLV-1 strains currently present in North Africa have originated from a recombinant event between strains from Senegal and West Africa. This recombination is estimated to have occurred around 4,0 years ago. This recombination seems to have been generated during reverse transcription. In conclusion, we demonstrate that, albeit rare, recombination can occur in HTLV-1 and may play a role in the evolution of this retrovirus (Desrames et al., J. Virology, 88, 2014). In order to precise the geographical distribution of this recombinant within the African Continent, we studied a new set of samples from HTLV-1 infected patients of diverse African origin. The data on this on-going study will be presented.

Detection of DNA sequences refractory to PCR amplification using a biophysical SERRS assay (Surface Enhanced Resonant Raman Spectroscopy).

The analysis of ancient or processed DNA samples is often a great challenge, because traditional Polymerase Chain Reaction – based amplification is impeded by DNA damage. Blocking lesions such as abasic sites are known to block the bypass of DNA polymerases, thus stopping primer elongation. In the present work, we applied the SERRS-hybridization assay, a fully non-enzymatic method, to the detection of DNA refractory to PCR amplification. This method combines specific hybridization with detection by Surface Enhanced Resonant Raman Scattering (SERRS). It allows the detection of a series of double-stranded DNA molecules containing a varying number of abasic sites on both strands, when PCR failed to detect the most degraded sequences. Our SERRS approach can quickly detect DNA molecules without any need for DNA repair. This assay could be applied as a pre-requisite analysis prior to enzymatic reparation or amplification. A whole new set of samples, both forensic and archaeological, could then deliver information that was not yet available due to a high degree of DNA damage.

Sources of local and regional variability in the MBT′/CBT paleotemperature proxy: Insights from a modern elevation transect across the Eastern Cordillera of Colombia

Distributions of brGDGTs (branched glycerol dialkyl glycerol tetraethers) in soils have been utilized in the literature as a proxy for temperature and pH via the MBT′ and CBT indices (methylation of branched tetraethers and cyclization of branched tetraethers, respectively). However, there is substantial scatter in the empirical relationships between the global MBT′/CBT index and modern temperature, resulting in uncertainty as large as±5.0°C in reconstructed paleotemperature. In this study, we sought to determine the magnitude of several sources of calibration error using a new set of samples spanning a large gradient in elevation (ca. 3000m) and temperature (ca. 16°C) across an Andean transect in the Eastern Cordillera of Colombia. Using in situ temperature monitoring, this field study of an equatorial montane location provided an opportunity to investigate several potential confounding factors affecting the MBT′/CBT paleothermometer, including the mismatch between air temperature and actual soil temperature, and the effect of soil moisture on brGDGT production. In the well-constrained environment of our study, we determined the RMSE (root mean squared-error) for a local calibration of the MBT′/CBT proxy to be 3.0°C, in contrast to the 5.0°C value reported in the most recent global calibration. A comparison between in situ soil temperature measurements at our soil sampling locations and interpolated weather station temperature data indicates that errors in interpolation schemes are not likely to be a significant contributor to the observed scatter in the MBT′/CBT-temperature relationship. Rather, we conclude that the majority of the 3°C scatter in this calibration for the northern Andes arises from transient, site specific variation in factors such as soil moisture and nutrient availability, with several cases showing a difference of up to 7.8°C between closely spaced sites (<600m in distance and<50m in elevation apart). In addition, we compared our dataset with five published regional soil elevation transects and found that that the MBT′ index correlated strongly with temperature at sites with high precipitation, such as Colombia (R2 0.67, 0.47), but correlated weakly with temperature at arid sites (R2 0.01, 0.04). Instead, the arid sites showed a strong relationship among MBT′, CBT and pH that was absent from the higher precipitation transects. This bolsters previous findings that the relationship between brGDGT distributions and temperature may change at sites with low soil moisture. This heterogeneous response in brGDGT distributions to temperature and pH may be largely responsible for the significant scatter in the global calibration dataset. We therefore conclude that the RMSE of 3°C in our local calibration may represent a lower boundary on the error in MBT′/CBT-based temperature reconstruction in moist regions, but further work is needed to reliably identify suitable conditions for the application of this proxy to ancient samples.

An Effective Strategy to Reduce the Labeling Cost in the Definition of Training Sets by Active Learning

This letter proposes a novel strategy for reducing the cost of in situ sample labeling for the definition of training sets by active learning (AL) in the framework of supervised classification of remote sensing images. AL methods define a training set according to an iterative procedure that at each iteration requires the labeling of a set of new samples selected by the classifier. The proposed strategy can be embedded in any AL method to identify the most informative area on the ground where focusing each AL iteration to reduce the overall cost (in terms of time) of labeling. To this end, at each iteration, the most uncertain unlabeled samples are initially identified. Then, the area on the ground (having a size predefined by the user) that has the highest spatial density of informative (i.e., uncertain and diverse) unlabeled samples is selected by the proposed strategy, and the AL technique is applied only to the samples of that area. This results in a decrease of the overall labeling cost with respect to that required by the use of a given technique in a standard way. Experimental results obtained by embedding the presented strategy in different literature active learning methods confirm its effectiveness.

An optimized predictor panel for colorectal cancer diagnosis based on the combination of tumor-associated antigens obtained from protein and phage microarrays

Humoral response in cancer patients appears early in cancer progression and can be used for diagnosis, including early detection. By using human recombinant protein and T7 phage microarrays displaying colorectal cancer (CRC)-specific peptides, we previously selected 6 phages and 6 human recombinant proteins as tumor-associated antigens (TAAs) with high diagnostic value. After completing validation in biological samples, TAAs were classified according to their correlation, redundancy in reactivity patterns and multiplex diagnostic capabilities. For predictor model optimization, TAAs were reanalyzed with a new set of samples. A combination of three phages displaying peptides homologous to GRN, NHSL1 and SREBF2 and four proteins PIM1, MAPKAPK3, FGFR4 and ACVR2B, achieved an area under the curve (AUC) of 94%, with a sensitivity of 89.1% and specificity of 90.0%, to correctly predict the presence of cancer. For early colorectal cancer stages, the AUC was 90%, with a sensitivity of 88.2% and specificity of 82.6%. In summary, we have defined an optimized predictor panel, combining TAAs from different sources, with highly improved accuracy and diagnostic value for colorectal cancer. This article is part of a Special Issue entitled: Translational Proteomics.

New age constraints for hominid footprints found on Jeju Island, South Korea

In 2004 numerous hominid footprints, along with diverse animal footprints, were found in the Late Quaternary strata of Jeju Island, South Korea. However, the age of the sediments in which the footprints were found is still controversial. Previous age estimates included radiocarbon ages of ca. 15,000 yr BP (Late Pleistocene) and quartz optically stimulated luminescence ages of ca. 7000 yr BP (mid-Holocene). In this study we report on 11 AMS 14C dating results from a new set of samples collected from the footprint-bearing strata and from associated sediments. Despite some variations and age reversal, all samples collected from the footprint-bearing strata yielded 14C ages of late Pleistocene. These ages are comparable with previous radiocarbon dating results. Furthermore, the presence of the proboscidean footprints attributable to woolly mammoths in the footprint-bearing strata supports the radiocarbon dating results. Based on the new radiocarbon dates and the presence of the alleged mammoth footprints, the age of the hominid footprints found at Jeju Island is thought to be late Pleistocene (about 19,000–25,000 cal yr BP). Therefore, this is the second discovery of hominid footprints dated to the Pleistocene age in Asia, and the first to be discovered in Korea.

The FOXE1 locus is a major genetic determinant for radiation-related thyroid carcinoma in Chernobyl

Papillary thyroid cancer (PTC) among individuals exposed to radioactive iodine in their childhood or adolescence is a major internationally recognized health consequence of the Chernobyl accident. To identify genetic determinants affecting individual susceptibility to radiation-related PTC, we conducted a genome-wide association study employing Belarusian patients with PTC aged 0-18 years at the time of accident and age-matched Belarusian control subjects. Two series of genome scans were performed using independent sample sets, and association with radiation-related PTC was evaluated. Meta-analysis by the Mantel-Haenszel method combining the two studies identified four SNPs at chromosome 9q22.33 showing significant associations with the disease (Mantel-Haenszel P: mhp = 1.7 x 10(-9) to 4.9 x 10(-9)). The association was further reinforced by a validation analysis using one of these SNP markers, rs965513, with a new set of samples (overall mhp = 4.8 x 10(-12), OR = 1.65, 95% CI: 1.43-1.91). Rs965513 is located 57-kb upstream to FOXE1, a thyroid-specific transcription factor with pivotal roles in thyroid morphogenesis and was recently reported as the strongest genetic risk marker of sporadic PTC in European populations. Of interest, no association was obtained between radiation-related PTC and rs944289 (mhp = 0.17) at 14p13.3 which showed the second strongest association with sporadic PTC in Europeans. These results show that the complex pathway underlying the pathogenesis may be partly shared by the two etiological forms of PTC, but their genetic components do not completely overlap each other, suggesting the presence of other unknown etiology-specific genetic determinants in radiation-related PTC.

Last Interglacial Age for aeolian and marine deposits and the Nahoon fossil human footprints, Southeast Coast of South Africa

Three hominid footprints preserved as casts were found in 1964 in Pleistocene aeolianites of the Nahoon Formation near East London, South Africa. Dating of the footprint-bearing aeolianite proved a lengthy and problematic task. Previous age estimates included a radiocarbon age of 29,090 − 390 + 410 years BP [Deacon, H.J., 1966. The dating of the Nahoon footprints. South African Journal of Science 62, 111–113], an infrared stimulated luminescence (IRSL) age of 144 ± 4 ka, a thermoluminescence age of 236 ± 8 ka (TL) and a luminescence subtraction age based on the IRSL and TL estimates of 75 ± 9 ka [Vogel, J.C., Wintle, A.G., Woodborne, S.M., 1999. Luminescence dating of coastal sands: overcoming changes in environmental dose rate. Journal of Archaeological Science 26, 729–733]. Thus there was no consistency among the ages derived using different dating methods. Here we describe optically stimulated luminescence (OSL) dating of quartz grains from a new set of samples collected from the footprint-bearing aeolianite and from associated geological formations. We also re-assessed the dose rate parameters for the sample for which TL and IRSL ages were reported and analysed the OSL signal from this sample. The new OSL dating yielded a coherent series of ages consistent with the stratigraphy as well as global and local sea level history. The indicated footprint age of 124 ± 4 ka thus relates to an important period of modern human evolution.

Identification of Differentially Expressed Genes in Blood Cells of Narcolepsy Patients

A close association between the human leukocyte antigen (HLA)-DRB1*1501/DQB1*0602 and abnormalities in some inflammatory cytokines have been demonstrated in narcolepsy. Specific alterations in the immune system have been suggested to occur in this disorder. We attempted to identify alterations in gene expression underlying the abnormalities in the blood cells of narcoleptic patients. Total RNA from 12 narcolepsy-cataplexy patients and from 12 age- and sex-matched healthy controls were pooled. The pooled samples were initially screened for candidate genes for narcolepsy by differential display analysis using annealing control primers (ACP). The second screening of the samples was carried out by semiquantitative PCR using gene-specific primers. Finally, the expression levels of the candidate genes were further confirmed by quantitative real-time PCR using a new set of samples (20 narcolepsy-cataplexy patients and 20 healthy controls). The second screening revealed differential expression of 4 candidate genes. Among them, MX2 was confirmed as a significantly down-regulated gene in the white blood cells of narcoleptic patients by quantitative real-time PCR. We found the MX2 gene to be significantly less expressed in comparison with normal subjects in the white blood cells of narcoleptic patients. This gene is relevant to the immune system. Although differential display analysis using ACP technology has a limitation in that it does not help in determining the functional mechanism underlying sleep/wakefulness dysregulation, it is useful for identifying novel genetic factors related to narcolepsy, such as HLA molecules. Further studies are required to explore the functional relationship between the MX2 gene and narcolepsy pathophysiology.

Quantification of the intensity of virgin olive oil sensory attributes by direct coupling headspace-mass spectrometry and multivariate calibration techniques

The main sensory defects of virgin olive oils (rancid, vinegary, winey, muddy sediment, musty and vegetable water) and one positive attribute (fruity) characteristic of three monovarietal extra virgin olive oils (Arbequina, Picual and Frantoio) have been quantified using the direct coupling headspace-mass spectrometry. The results obtained were compared with those provided by the panel test for the same samples. Taking into account that no chromatographic separation exists, multivariate calibration techniques (partial least squares, PLS, and principal components regression, PCR) were used to create the appropriate models. The best results, in terms of standard error of prediction and prediction residual error sum of squares were obtained by PLS and therefore it was used for the prediction of a new set of samples with the above-mentioned positive and negative attributes at different concentration levels. The samples were also assessed by the panel test and good correlations were obtained in all cases. In order to extend the applicability of the model with the time, a multiplicative calibration transfer was used. The benefit of this approach was found to be more marked for the negative than the positive attributes.

The transcriptome of the uterine cervix before and after spontaneous term parturition

This study was designed to identify genes differentially expressed in the human uterine cervix after spontaneous term labor. The transcriptome of cervical tissue was characterized using Affymetrix HG-U133 plus 2 microarrays. Samples were collected from patients at term not in labor (n = 7) and after spontaneous labor (n = 9). Microarray statistical analysis included robust multiarray average, reduction of invariant probes, and permutation analysis for differential expression. Real-time quantitative reverse transcriptase-polymerase chain reaction assays of selected genes were performed on a new set of samples from term patients without labor (n = 10) and patients after spontaneous labor (n = 9). (1) The cervical transcriptome of term patients without labor was dramatically different from that of patients who underwent labor; (2) unique genes (n = 1192) were differentially expressed in the cervical tissue from patients after spontaneous labor, compared with that of the term patients without labor (false discovery rate less than 0.05, absolute fold change greater than 2); (3) Gene Ontology analysis indicated that multiple "Biological Process" categories were enriched, including "response to biotic stimulus," "apoptosis," "epidermis development," and "steroid metabolism"; (4) of major interest, genes involved in neutrophil chemotaxis were dramatically up-regulated in specimens from women after spontaneous labor; (5) real-time quantitative reverse transcriptase-polymerase chain reaction confirmed the increased expression of interleukin-8, interleukin-6, and vascular endothelial growth factor in patients after spontaneous labor; and (6) Toll-like receptor-3 and Toll-like receptor-5 showed decreased gene expression in patients after spontaneous labor. This was confirmed by real-time quantitative reverse transcriptase-polymerase chain reaction. (1) Cervical dilatation in term labor is associated with a stereotypic gene expression pattern determined by microarray, which is characterized by overexpression of genes involved in neutrophil chemotaxis, apoptosis, extracellular matrix regulation, and steroid metabolism; (2) Toll-like receptor-3 and Toll-like receptor-5 are differentially regulated during spontaneous parturition at term; and (3) this study provides an unbiased and comprehensive description of the changes in the cervical transcriptome before and after spontaneous term labor.

P2-202: URT: A new diagnostic approach for the early diagnosis of the Alzheimer’s disease

Today diagnosis of Alzheimer's disease (AD) is limited to the mental and cognitive examinations of patients and impedes preventive screening. Moreover, the diagnosis of patients is particularly difficult at the early stage of the disease when only minor cognitive impairment meets the criteria for being classified as dementia. These patients are generally considers to have mild cognitive impairment (MCI). The onset and/or progression of brain degeneration in MCI and AD have been linked to abnormal interactions between brain proteins resulting in the their aggregation. Unfortunately, the use of biomarkers to detect aggregated proteins has thus far not succeeded into early detection. As a consequence, new approaches are required to support existing clinical characterization. We recently investigated in two independent studies the potential of the Ultrasonic Resonator Technology (URT) for the diagnosis of AD. A clear differentiation of AD from healthy controls was obtained by comparison of the hydration profiles over increasing temperature. In the present study, we further evaluated the potential of URT in particular for the detection of very early AD stages. We therefore investigated a new set of samples from patients with MCI and age–matched and educational–matched healthy controls and characterized the disease specific hydration behaviour, during thermal destabilization. CSF samples classified according to Clinical Dementia Rating from volunteer subjects were obtained by lumbal puncture of healthy controls and individuals with MCI. All ultrasonic measurements were performed using the ResoScan® System. We could demonstrate the sensitivity of URT by detecting early stages of AD. The hydration behavior of the MCI group differed significantly from the control group. Quantification of the difference based on the selection of the hydration behavior at six defined temperatures allowed differentiation with more than 85% significance by simple cluster analysis. These results suggests that URT represents a new technical approach for the characterization of early stages of neurodegenerative disorders and may provide a new entry point for diagnostic strategies of misfolding disorders.

Current status of DIII-D real-time digital plasma control

This paper describes the current status of real-time digital plasma control for the DIII-D tokamak. The digital plasma control system (PCS) has been in place at DIII-D since the early 1990s and continues to expand and improve in it's capabilities to monitor and control plasma parameters for DIII-D fusion science experiments. The PCS monitors over 200 tokamak parameters from the DIII-D experiment using a real-time data acquisition system that acquires a new set of samples once every 60 /spl mu/s. This information is then used in a number of feedback control algorithms to compute and control a variety of parameters including those affecting plasma shape and position. A number of recent improvements to the control capabilities of the PCS along with general system enhancements have contributed to the advancement and understanding of fusion energy science at DIII-D. Among the more significant improvements to the PCS control capabilities has been the successful incorporation of advanced techniques for reconstruction of plasma equilibrium parameters in realtime. An isoflux control method using these improved plasma parameter calculations has greatly enhanced the ability of achieving desired shaped plasma on the DIII-D tokamak and even made it possible to achieve new and different ones. A number of system related improvements has improved the usability and flexibility of the DIII-D PCS. These include more graphical user interfaces to assist in entering and viewing the large and ever growing number of parameters controlled by the PCS, increased interaction and accessibility from other DIII-D applications, and upgrades to the computer hardware and vended software. Future plans for the system include possible upgrades of the real-time computers, further links to other DIII-D diagnostic measurements such as real-time Thomson scattering analysis, and joint collaborations with other tokamak experiments including the NSTX at Princeton.

Using an electronic nose for determining the spoilage of vacuum-packaged beef

The use of an electronic nose in the quantitative determination of the degree of spoilage of vacuum-packaged beef was evaluated. Beef from four different slaughterhouses was sliced, vacuum-packaged and stored at 4°C for 8 weeks. Samples were withdrawn for bacterial (aerobic bacteria, lactic acid bacteria, Brochothrix thermosphacta, Pseudomonas and Enterobacteriaceae) and sensorial analyses and analysis of the volatile compounds during the storage period. A trained panel was used for the sensorial evaluations. The volatile compounds were analysed using an electronic nose containing a sensory array composed of 10 metal oxide semiconductor field-effect transistors, four Tagushi type sensors and one CO 2-sensitive sensor. Four of the 15 sensors were excluded due to lack of response or overloading. Partial least-squares regression was used to define the mathematical relationships between the degree of spoilage of vacuum-packaged beef, as determined by the sensory panel, and the signal magnitudes of the sensors of the electronic nose. The mathematical models were validated after 6 months using a new set of samples. The stability of the sensors during this period was examined and it was shown that the sensitivity of five of the 11 sensors used had changed. Using the six remaining sensors, the signal patterns obtained from the meat from the different slaughterhouses did not change over a period of 6 months. It was shown that the degree of spoilage, as calculated using a model based on two Tagushi sensors, correlated well with the degree of spoilage determined by the sensory panel ( r 2=0.94).

Comparing two sets of community data: A method for testing reserve adequacy

Abstract Comparing a new set of samples to what may be considered a reference set is a common problem in ecology. The investigator may be interested in the degree of correspondence or any anomalies. For example, does a set of existing reserves adequately cover the range of communities sampled in a region? A technique for such comparisons is proposed. Being dependent solely on estimates of ecological resemblance, it is simple, efficient and robust. Significant difference is defined by means of a resemblance coefficient. A threshold value denoting significant difference can be defined either by species overlap or other attributes of the data. For presence/absence data the Czekanowski coefficient provides a suitable measure of ecological resemblance. Traditional discriminant analysis does not provide a viable alternative due to its limitations in accommodating ecological data.

Search for Pedogenic Phases During the Younger Pleistocene and Holocene (Soltanien and Rharbien) of Tunisia

Radiocarbon dates, obtained from paleosols, sediments, fossils, and groundwater samples of North Africa and especially, Tunisia, were investigated for information on phases of pedogenesis throughout the younger Pleistocene and Holocene in north and central Tunisia. This paper evaluates available data, while a larger set of new samples is under study, which, hopefully will exhaust the problem and will reveal whether extrapolations such as those made in this paper, eg, phases of pedogenesis from groundwater data, are correct.Frequency distribution of the dates from groundwaters taken by systematic sampling, as well as from random soil samples from open pits that yielded access to buried paleosols, indicate that organic matter was being produced for 7 or 8 periods. The evidence suggests major pedogenic activity at about 2000 BP, 4000 to 6000 BP, 8000 to 12,000 BP, and perhaps 21,000 to 25,000 BP.