Science.gov

Sample records for acromion marker cluster

  1. Evaluating the acromion marker cluster as a method for measuring scapular orientation in children with brachial plexus birth palsy.

    PubMed

    Nicholson, Kristen F; Russo, Stephanie A; Kozin, Scott H; Zlotolow, Dan A; Hulbert, Robert L; Rowley, K Michael; Richards, James G

    2014-02-01

    Several studies have described using an acromion marker cluster for measuring scapular orientation in healthy adults performing planar motions. It is unknown whether the acromion marker cluster method will provide the same level of accuracy in children with brachial plexus birth palsy. This study compared this method to palpation for calculating scapular orientation in children with brachial plexus birth palsy performing clinically relevant movements. Scapular orientation in ten patients was determined by palpation and an acromion marker cluster in neutral and six Modified Mallet positions. RMSEs and mean relative errors were calculated. Resultant RMSEs ranged from 5.2 degrees to 21.4 degrees. The averages of the mean relative errors across all positions for each axis were 177.4% for upward/downward rotation, 865.0% for internal/external rotation, and 166.2% for anterior/posterior tilt. The acromion marker cluster method did not accurately measure scapular rotation relative to the total movement on an individual or group basis in the population. With most relative errors over 100%, the acromion marker cluster method often produced errors larger than the actual measured motion. The accuracy of the acromion marker cluster method limits its use as a clinical tool for measuring scapular kinematics on children with brachial plexus birth palsy. PMID:24676519

  2. A comparison of acromion marker cluster calibration methods for estimating scapular kinematics during upper extremity ergometry.

    PubMed

    Richardson, R Tyler; Nicholson, Kristen F; Rapp, Elizabeth A; Johnston, Therese E; Richards, James G

    2016-05-01

    Accurate measurement of joint kinematics is required to understand the musculoskeletal effects of a therapeutic intervention such as upper extremity (UE) ergometry. Traditional surface-based motion capture is effective for quantifying humerothoracic motion, but scapular kinematics are challenging to obtain. Methods for estimating scapular kinematics include the widely-reported acromion marker cluster (AMC) which utilizes a static calibration between the scapula and the AMC to estimate the orientation of the scapula during motion. Previous literature demonstrates that including additional calibration positions throughout the motion improves AMC accuracy for single plane motions; however this approach has not been assessed for the non-planar shoulder complex motion occurring during UE ergometry. The purpose of this study was to evaluate the accuracy of single, dual, and multiple AMC calibration methods during UE ergometry. The orientations of the UE segments of 13 healthy subjects were recorded with motion capture. Scapular landmarks were palpated at eight evenly-spaced static positions around the 360° cycle. The single AMC method utilized one static calibration position to estimate scapular kinematics for the entire cycle, while the dual and multiple AMC methods used two and four static calibration positions, respectively. Scapulothoracic angles estimated by the three AMC methods were compared with scapulothoracic angles determined by palpation. The multiple AMC method produced the smallest RMS errors and was not significantly different from palpation about any axis. We recommend the multiple AMC method as a practical and accurate way to estimate scapular kinematics during UE ergometry. PMID:26976228

  3. Three-Dimensional Rotations of the Scapula During Arm Abduction: Evaluation of the Acromion Marker Cluster Method in Comparison With a Model-Based Approach Using Biplanar Radiograph Images.

    PubMed

    Duprey, Sonia; Billuart, Fabien; Sah, Sungjin; Ohl, Xavier; Robert, Thomas; Skalli, Wafa; Wang, Xuguang

    2015-10-01

    Noninvasive methods enabling measurement of shoulder bone positions are paramount in clinical and ergonomics applications. In this study, the acromion marker cluster (AMC) method is assessed in comparison with a model-based approach allowing scapula tracking from low-dose biplanar radiograph images. Six healthy male subjects participated in this study. Data acquisition was performed for 6 arm abduction positions (0°, 45°, 90°, 120°, 150°, 180°). Scapula rotations were calculated using the coordinate systems and angle sequence was defined by the ISB. The comparison analysis was based on root mean square error (RMSE) calculation and nonparametric statistical tests. RMSE remained under 8° for 0° to 90° arm abduction and under 13.5° for 0° to 180° abduction; no significant differences were found between the 2 methods. Compared with previous works, an improved accuracy of the AMC approach at high arm abduction positions was obtained. This could be explained by the different sources of data used as the "gold standard." PMID:26099159

  4. Acromion-fixation of glenoid components in total shoulder arthroplasty.

    PubMed

    Murphy, Linda A; Prendergast, Patrick J

    2005-08-01

    Successful design of components for total shoulder arthroplasty has proven to be challenging. This is because of the difficulties in maintaining fixation of the component that inserts into the scapula; i.e., the glenoid component. Glenoid components that are fixated to both the glenoid and acromion (a long process extending medially on the dorsal aspect of the scapula) have the possible advantage of greater stability over those that are fixated to the glenoid alone. In this study, a finite element analysis is used to investigate whether or not acromion fixation is advantageous for glenoid components. Full muscle loading and joint reaction forces are included in the finite element model. Reflective photoelasticity of five scapulae is used to obtain experimental data to compare with results from the finite element analysis, and it confirms the structural behaviour of the finite element model. When implanted with an acromion-fixated prosthesis, it is found that high unphysiological stresses occur in the scapula bone, and that stresses in the fixation are not reduced. Very high stresses are predicted in that part of the prosthesis which connects the acromion to the glenoid. It is found that the very high stresses are partly in response to the muscle and joint reaction forces acting at the acromion. It is concluded that, because of the relatively high forces acting at the acromion, fixation to it may not be the way forward in glenoid component design. PMID:15958228

  5. Stress injury of the acromion: case report and literature review.

    PubMed

    Taneja, Atul Kumar; Negromonte, Francisco Pires; Skaf, Abdalla

    2013-11-01

    We report a case of stress injury of the acromion related to golf practicing in a 40-year-old male. Fractures of the scapula are unusual, with stress injury of the acromion being even rarer. The probable mechanism would be a strong contraction of posterior fibers of the deltoid during golf swing. There are few published reports of similar injuries, and to our knowledge, this is the first to demonstrate its features by magnetic resonance imaging. A review of the literature is also presented. PMID:23412322

  6. Extra-articular Synovial Chondromatosis Eroding and Penetrating the Acromion

    PubMed Central

    El Rassi, George; Matta, Jihad; Hijjawi, Ayman; Khair, Ousama Abou; Fahs, Sara

    2015-01-01

    Synovial chondromatosis of the shoulder is an uncommon disorder. It usually affects the glenohumeral joint and is characterized by metaplasia of the synovium leading to the formation of osteochondral loose bodies. Few cases of extra-articular subacromial synovial chondromatosis involving the rotator cuff tendon have been reported in the literature. The treatment of previously reported cases consisted of open bursectomy and removal of loose bodies. We report a case of subacromial synovial chondromatosis without rotator cuff involvement but with severe erosion and fracture of the acromion. Treatment consisted of shoulder arthroscopy to remove all loose bodies, total bursectomy, and debridement of the acromion. Potential benefits of arthroscopy were also evaluated. PMID:26697302

  7. Extra-articular Synovial Chondromatosis Eroding and Penetrating the Acromion.

    PubMed

    El Rassi, George; Matta, Jihad; Hijjawi, Ayman; Khair, Ousama Abou; Fahs, Sara

    2015-10-01

    Synovial chondromatosis of the shoulder is an uncommon disorder. It usually affects the glenohumeral joint and is characterized by metaplasia of the synovium leading to the formation of osteochondral loose bodies. Few cases of extra-articular subacromial synovial chondromatosis involving the rotator cuff tendon have been reported in the literature. The treatment of previously reported cases consisted of open bursectomy and removal of loose bodies. We report a case of subacromial synovial chondromatosis without rotator cuff involvement but with severe erosion and fracture of the acromion. Treatment consisted of shoulder arthroscopy to remove all loose bodies, total bursectomy, and debridement of the acromion. Potential benefits of arthroscopy were also evaluated. PMID:26697302

  8. Osteoid osteoma of the acromion simulating acromioclavicular pain☆☆☆

    PubMed Central

    Miyazaki, Alberto Naoki; Fregoneze, Marcelo; Santos, Pedro Doneux; da Silva, Luciana Andrade; do Val Sella, Guilherme; Neto, Douglas Lobato Lopes; Muchiuti Junior, Melvis; Checchia, Sergio Luiz

    2014-01-01

    The osteoid osteoma is a benign bone tumour that usually presents with nocturnal pain in young adults, relieved by rest and anti‐inflammatories. It can affect any bone; however, their occurrence is rare in the acromion. The authors describe a case of osteoid osteoma located in the acromion, with symptoms that simulated acromion claviculararthrosis. The diagnosis was made by CT scan and treatment was excision of the nidus through arthroscopy. The diagnosis was confirmed by histopathology. In the outpatient segment, the patient remained asymptomatic, with complete recovery of function of the affected limb. PMID:26229778

  9. PERPENDICULAR DOUBLE-PLATE FIXATION WITH LOCKING SYSTEM FOR ACROMION PEDICLE FRACTURE

    PubMed Central

    Zhu, Junkun; Pan, Zhijun; Zheng, Rongzong; Lan, Shuhua

    2016-01-01

    Objective : To describe the surgical technique and preliminary clinical outcomes in a series of open reduction internal fixation of basal acromion process fractures applying a double-plating technique. Methods : Nine consecutive patients, mean age 33.4 years old (range, 23-61 years old) with unilateral acromion fracture (Type 3 AO/OTA) with more than 1cm displacement who underwent fixation utilizing a locked double-plating technique, were evaluated on average at 7.8 months (range, 3-15 months) for outcomes related to pain, shoulder function, and surgical complications. Results : Eight patients recovered with complete radiographic union and favorable shoulder function. One case failed to be fully evaluated for more than 3 months follow-up. The overall scores of Constant, Shoulder Pain and Disability Index (SPADI) and DASH for the eight patients reviewed were 91.9± 6.31, 3.11± 3.79 and 5.2± 6.35, respectively. No post-operative infection or surgical hardware irritation was identified at final follow-up of these eight patients. Conclusion : While more evidence is needed to justify its advantages over traditional implants, perpendicular double-plate with a locking system may be indicated for acromion pedicle fracture treatment, since it performed well for fracture healing and joint function rehabilitation. Level of Evidence IV, Therapeutic Study. PMID:26981047

  10. ANATOMICAL RELATIONSHIP OF THE SUPRASCAPULAR NERVE TO THE CORACOID PROCESS, ACROMIOCLAVICULAR JOINT AND ACROMION

    PubMed Central

    Terra, Bernardo Barcellos; Gaspar, Eric Figueiredo; Siqueira, Karina Levy; Filho, Nivaldo Souza Cardozo; Monteiro, Gustavo Cará; Andreoli, Carlos Vicente; Ejnisman, Benno

    2015-01-01

    Objective: To establish the anatomical relationship of the suprascapular nerve (SSN) located in the suprascapular notch, to the medial border of the base of the coracoid process, the acromial joint surface of the acromioclavicular joint and the anterolateral border of the acromion. Methods: We dissected 16 shoulders of 16 cadavers (9 males and 7 females). The distances from the suprascapular nerve (at its passage beneath the transverse ligament) to certain fixed points on the medial border of the base of the coracoid process, the acromial joint surface of the acromioclavicular joint, and the anterolateral border of the acromion were measured with the aid of calipers and correlated with age and sex. Cadavers with previous surgical interventions were excluded. Results: The mean measurements from the notch of the suprascapular nerve were: 3.9 cm to the medial border of the base of the coracoid process (ranging from 3.1 cm to 5.2 cm); 4.7 cm to the acromioclavicular joint (ranging from 3.9 cm to 5.2 cm); and 6.1 cm to the anterolateral border of the acromion (ranging from 5.7 cm to 6.8 cm). Conclusion: Accurate anatomical knowledge of the nerves of the anterior region of the shoulder is essential in order to avoid iatrogenic injuries and to achieve satisfactory results in surgical treatment for shoulder diseases, whether performed as open or arthroscopic procedures. PMID:27022551

  11. COMPARATIVE ANATOMICAL STUDY BETWEEN THE RIGHT AND LEFT SIDES OF THE AXILLARY NERVE IN RELATION TO DELTOPECTORAL APPROACH AND ACROMION

    PubMed Central

    Junior, Antonio Carlos Tenor; Ribeiro, Fabiano Rebouças; Filho, Rômulo Brasil; Filho, Cantídio Salvador Filardi; Lutfi, Hilton Vargas; Magri, Eduardo Angoti

    2015-01-01

    Objective: To establish anatomical parameters for the axillary nerve by measuring the distances to the acromion and the deltopectoral access, and to ascertain whether there are any differences in comparative measurements between the left and right sides. Method: An anatomical study on the path of the axillary nerve was conducted by dissecting 30 shoulders of 20 fresh adult cadavers. For comparative study, bilateral dissection was performed on 10 cadavers. Digital caliper gauges, accurate to the nearest 0.05 cm, were used to measure the distances between the lateral extremity of the acromion and the anterior and posterior branches of the axillary nerve, and between the deltopectoral space and the anterior branch of the axillary nerve. Results: The shortest distance between the acromion and the axillary nerve was 5.47 cm, and the greatest distance was 7.06 cm. The shortest distance between the deltopectoral groove and the axillary nerve was 3.94 cm. A statistically significant difference was found using Wilcoxon’s test in comparative measurements between the left and right sides for the distances between the posterior branch of the axillary nerve and the midpoint of the lateral border of the acromion (A-E), and between the anterior branch of the axillary nerve and the anterior extremity of the acromion (B-C), both of which were larger on the right side. Conclusions: The axillary nerve was situated between 5.47 and 7.06 cm distally to the acromion, and 3.94 cm laterally to the deltopectoral space. There was a statistically significant difference in the comparison between the left and right sides, and both measurements were larger on the right side. PMID:27047824

  12. Strain rates, stress markers and earthquake clustering (Invited)

    NASA Astrophysics Data System (ADS)

    Fry, B.; Gerstenberger, M.; Abercrombie, R. E.; Reyners, M.; Eberhart-Phillips, D. M.

    2013-12-01

    The 2010-present Canterbury earthquakes comprise a well-recorded sequence in a relatively low strain-rate shallow crustal region. We present new scientific results to test the hypothesis that: Earthquake sequences in low-strain rate areas experience high stress drop events, low-post seismic relaxation, and accentuated seismic clustering. This hypothesis is based on a physical description of the aftershock process in which the spatial distribution of stress accumulation and stress transfer are controlled by fault strength and orientation. Following large crustal earthquakes, time dependent forecasts are often developed by fitting parameters defined by Omori's aftershock decay law. In high-strain rate areas, simple forecast models utilizing a single p-value fit observed aftershock sequences well. In low-strain rate areas such as Canterbury, assumptions of simple Omori decay may not be sufficient to capture the clustering (sub-sequence) nature exhibited by the punctuated rise in activity following significant child events. In Canterbury, the moment release is more clustered than in more typical Omori sequences. The individual earthquakes in these clusters also exhibit somewhat higher stress drops than in the average crustal sequence in high-strain rate regions, suggesting the earthquakes occur on strong Andersonian-oriented faults, possibly juvenile or well-healed . We use the spectral ratio procedure outlined in (Viegas et al., 2010) to determine corner frequencies and Madariaga stress-drop values for over 800 events in the sequence. Furthermore, we will discuss the relevance of tomographic results of Reyners and Eberhart-Phillips (2013) documenting post-seismic stress-driven fluid processes following the three largest events in the sequence as well as anisotropic patterns in surface wave tomography (Fry et al., 2013). These tomographic studies are both compatible with the hypothesis, providing strong evidence for the presence of widespread and hydrated regional

  13. Hox gene clusters of early vertebrates: do they serve as reliable markers for genome evolution?

    PubMed

    Kuraku, Shigehiro

    2011-06-01

    Hox genes, responsible for regional specification along the anteroposterior axis in embryogenesis, are found as clusters in most eumetazoan genomes sequenced to date. Invertebrates possess a single Hox gene cluster with some exceptions of secondary cluster breakages, while osteichthyans (bony vertebrates) have multiple Hox clusters. In tetrapods, four Hox clusters, derived from the so-called two-round whole genome duplications (2R-WGDs), are observed. Overall, the number of Hox gene clusters has been regarded as a reliable marker of ploidy levels in animal genomes. In fact, this scheme also fits the situations in teleost fishes that experienced an additional WGD. In this review, I focus on cyclostomes and cartilaginous fishes as lineages that would fill the gap between invertebrates and osteichthyans. A recent study highlighted a possible loss of the HoxC cluster in the galeomorph shark lineage, while other aspects of cartilaginous fish Hox clusters usually mark their conserved nature. In contrast, existing resources suggest that the cyclostomes exhibit a different mode of Hox cluster organization. For this group of species, whose genomes could have differently responded to the 2R-WGDs from jawed vertebrates, therefore the number of Hox clusters may not serve as a good indicator of their ploidy level. PMID:21802046

  14. Markers

    ERIC Educational Resources Information Center

    Healthy Schools Network, Inc., 2011

    2011-01-01

    Dry erase whiteboards come with toxic dry erase markers and toxic cleaning products. Dry erase markers labeled "nontoxic" are not free of toxic chemicals and can cause health problems. Children are especially vulnerable to environmental health hazards; moreover, schools commonly have problems with indoor air pollution, as they are more densely…

  15. Rigid and non-rigid geometrical transformations of a marker-cluster and their impact on bone-pose estimation.

    PubMed

    Bonci, T; Camomilla, V; Dumas, R; Chèze, L; Cappozzo, A

    2015-11-26

    When stereophotogrammetry and skin-markers are used, bone-pose estimation is jeopardised by the soft tissue artefact (STA). At marker-cluster level, this can be represented using a modal series of rigid (RT; translation and rotation) and non-rigid (NRT; homothety and scaling) geometrical transformations. The NRT has been found to be smaller than the RT and claimed to have a limited impact on bone-pose estimation. This study aims to investigate this matter and comparatively assessing the propagation of both STA components to bone-pose estimate, using different numbers of markers. Twelve skin-markers distributed over the anterior aspect of a thigh were considered and STA time functions were generated for each of them, as plausibly occurs during walking, using an ad hoc model and represented through the geometrical transformations. Using marker-clusters made of four to 12 markers affected by these STAs, and a Procrustes superimposition approach, bone-pose and the relevant accuracy were estimated. This was done also for a selected four marker-cluster affected by STAs randomly simulated by modifying the original STA NRT component, so that its energy fell in the range 30-90% of total STA energy. The pose error, which slightly decreased while increasing the number of markers in the marker-cluster, was independent from the NRT amplitude, and was always null when the RT component was removed. It was thus demonstrated that only the RT component impacts pose estimation accuracy and should thus be accounted for when designing algorithms aimed at compensating for STA. PMID:26555716

  16. Bladder Carcinoma Data with Clinical Risk Factors and Molecular Markers: A Cluster Analysis

    PubMed Central

    Redondo-Gonzalez, Enrique; de Castro, Leandro Nunes; Moreno-Sierra, Jesús; Maestro de las Casas, María Luisa; Vera-Gonzalez, Vicente; Ferrari, Daniel Gomes; Corchado, Juan Manuel

    2015-01-01

    Bladder cancer occurs in the epithelial lining of the urinary bladder and is amongst the most common types of cancer in humans, killing thousands of people a year. This paper is based on the hypothesis that the use of clinical and histopathological data together with information about the concentration of various molecular markers in patients is useful for the prediction of outcomes and the design of treatments of nonmuscle invasive bladder carcinoma (NMIBC). A population of 45 patients with a new diagnosis of NMIBC was selected. Patients with benign prostatic hyperplasia (BPH), muscle invasive bladder carcinoma (MIBC), carcinoma in situ (CIS), and NMIBC recurrent tumors were not included due to their different clinical behavior. Clinical history was obtained by means of anamnesis and physical examination, and preoperative imaging and urine cytology were carried out for all patients. Then, patients underwent conventional transurethral resection (TURBT) and some proteomic analyses quantified the biomarkers (p53, neu, and EGFR). A postoperative follow-up was performed to detect relapse and progression. Clusterings were performed to find groups with clinical, molecular markers, histopathological prognostic factors, and statistics about recurrence, progression, and overall survival of patients with NMIBC. Four groups were found according to tumor sizes, risk of relapse or progression, and biological behavior. Outlier patients were also detected and categorized according to their clinical characters and biological behavior. PMID:25866762

  17. Heterozygosis deficit of polymorphic markers linked to the β-globin gene cluster region in the Iranian population

    PubMed Central

    Moradi, Tahereh; Vallian, Reihaneh; Fazeli, Zahra; Haghighatnia, Asieh; Vallian, Sadeq

    2015-01-01

    Objective(s): Iran is considered as one of the high-prevalence areas for β-thalassemia with a rate of about 10% carrier frequency. Molecular diagnosis of the disease is performed both by direct sequencing and indirectly by the use of polymorphic markers present in the beta globin gene cluster. However, to date there is no reliable information on the application of the markers in the Iranian population. Here we report the results of an extended molecular analysis of five RFLP markers, XmnI, HindIIIA, HindIIIG, RsaI and HinfI, located within the β-globin gene cluster region in four subpopulations of Iran. Materials and Methods: A total of 552 blood samples taken from the Iranian subpopulations including Isfahan, Chaharmahal-O-Bakhtiari, Khuzestan and Hormozgan were genotyped using PCR-RFLP and sequencing. The allele frequency, the expected and observed heterozygosity, and Shannon’s information index (I) of these markers were calculated. Results: Distribution of the allele frequencies for XmnI, HindIIIA, HindIIIG, RsaI and HinfI polymorphic markers did not differ significantly among the subpopulations examined. Overall observed heterozygosity ranged from 0.1706 for HindIIIA to 0.4484 for RsaI. The Shannon index was <1 for all the polymorphic markers in the populations studied. The data indicated that heterozygosity of these markers was low in the Iranian population. Conclusion: The results suggested that genotyping of these markers is not informative enough once used as single markers for prenatal diagnosis and carrier detection of β-thalassemia in the Iranian population. However, haplotyping of these markers may provide more useful data in linkage analysis and prenatal diagnosis as well as carrier detections for β-thalassemia in Iranians. PMID:26229579

  18. GENES FOR TUMOR MARKERS ARE CLUSTERED WITH CELLULAR PROTO-ONCOGENES ON HUMAN CHROMOSOMES

    EPA Science Inventory

    The relative mapping positions of genes for polypeptides expressed abnormally in tumors (tumor markers) and cellular proto-oncogenes were analyzed and a remarkable degree of co-mapping of tumor marker genes with oncogenes in the human karyotype were found. It is proposed that abe...

  19. Impaired Fasting Glucose in Nondiabetic Range: Is It a Marker of Cardiovascular Risk Factor Clustering?

    PubMed Central

    Valentino, Giovanna; Kramer, Verónica; Orellana, Lorena; Bustamante, María José; Casasbellas, Cinthia; Adasme, Marcela; Salazar, Alejandra; Navarrete, Carlos; Acevedo, Mónica

    2015-01-01

    Background. Impaired fasting glucose (IFG) through the nondiabetic range (100–125 mg/dL) is not considered in the cardiovascular (CV) risk profile. Aim. To compare the clustering of CV risk factors (RFs) in nondiabetic subjects with normal fasting glucose (NFG) and IFG. Material and Methods. Cross-sectional study in 3739 nondiabetic subjects. Demographics, medical history, and CV risk factors were collected and lipid profile, fasting glucose levels (FBG), C-reactive protein (hsCRP), blood pressure (BP), anthropometric measurements, and aerobic capacity were determined. Results. 559 (15%) subjects had IFG: they had a higher mean age, BMI, waist circumference, non-HDL cholesterol, BP, and hsCRP (p < 0.0001) and lower HDL (p < 0.001) and aerobic capacity (p < 0.001). They also had a higher prevalence of hypertension (34% versus 25%; p < 0.001), dyslipidemia (79% versus 74%; p < 0.001), and obesity (29% versus 16%; p < 0.001) and a higher Framingham risk score (8% versus 6%; p < 0.001). The probability of presenting 3 or more CV RFs adjusted by age and gender was significantly higher in the top quintile of fasting glucose (≥98 mg/dL; OR = 2.02; 1.62–2.51). Conclusions. IFG in the nondiabetic range is associated with increased cardiovascular RF clustering. PMID:26504260

  20. [Sequence of Escherichia coli O11 O-antigen gene cluster and identification of molecular markers specific to O11].

    PubMed

    Wang, Wei; Peng, Xia; Wang, Quan; Cheng, Jian-Song; Wang, Lei

    2006-06-01

    Escherichia coli O11 belongs to Shiga toxin-producing Escherichia coli (STEC), which can cause food-borne disease, hemorrhagic colitis, and hemolytic-uremic syndrome (HUS) in humans. Because of its character of specificity, the O-antigen gene cluster provides the best material for the selection of molecular markers which can be used for rapid genotyping of bacterial strain. In this study, the E.coli O11 O-antigen gene cluster was amplified by Long-range PCR and was sequenced using Shotgun-sequencing approach. Twelve open reading frames were assigned functions on the basis of homology in the E. coli O11 O-antigen gene cluster, including UDP-N-acetyl glucosamine-4-epimerase gene (gne), genes responsible for the biosynthesis of GDP-L-fucose (gmd, fcl, gmm, manC, manB), glycosyl transferase genes, O-unit flippase gene (wzx) and O-antigen polymerase gene (wzy). By polymerase chain reaction against representative stains for all the 166 E. coli and 43 Shigella O serotypes, two genes and four pairs of primers were identified to be specific to E. coli O11. Further PCR was done to detect E. coli O11 from the environmental specimens, and the sensitivities for detecting E.coli O11 from the pork and dejecta specimens were 0.25 cfu/g and 2.5 x 10(3) cfu/g, respectively. Moreover, eight probes were designed and proved to be unique to E. coli O11, which provides the basis for a sensitive test of the rapid detection of E. coli O11 by DNA microarray method. PMID:16933598

  1. First-principles calculation of the ultrafast spin manipulation of two-center metallic clusters with a CO molecule attached to one center as an infrared marker

    NASA Astrophysics Data System (ADS)

    Li, Chun; Hartenstein, Tobias; Lefkidis, Georgios; Hübner, Wolfgang

    2009-05-01

    We present a fully ab initio ultrafast spin manipulation calculation in two-magnetic-center clusters with CO attached to one of the magnetic centers. CO serves as an experimental marker for certain magnetic states between which spin flip and transfer can be achieved. The predicted spin-state-dependent CO vibrational frequencies indicate that spin manipulation can be readily monitored through the infrared spectrum. The feasibility is demonstrated by two charged clusters [CoMg2Ni-CO]+ and [NiCo-CO]+ . Spin transfer between magnetic centers is achieved with a fidelity of 99.8%.

  2. Inferring population structure and relationship using minimal independent evolutionary markers in Y-chromosome: a hybrid approach of recursive feature selection for hierarchical clustering

    PubMed Central

    Srivastava, Amit Kumar; Chopra, Rupali; Ali, Shafat; Aggarwal, Shweta; Vig, Lovekesh; Koul Bamezai, Rameshwar Nath

    2014-01-01

    Inundation of evolutionary markers expedited in Human Genome Project and 1000 Genome Consortium has necessitated pruning of redundant and dependent variables. Various computational tools based on machine-learning and data-mining methods like feature selection/extraction have been proposed to escape the curse of dimensionality in large datasets. Incidentally, evolutionary studies, primarily based on sequentially evolved variations have remained un-facilitated by such advances till date. Here, we present a novel approach of recursive feature selection for hierarchical clustering of Y-chromosomal SNPs/haplogroups to select a minimal set of independent markers, sufficient to infer population structure as precisely as deduced by a larger number of evolutionary markers. To validate the applicability of our approach, we optimally designed MALDI-TOF mass spectrometry-based multiplex to accommodate independent Y-chromosomal markers in a single multiplex and genotyped two geographically distinct Indian populations. An analysis of 105 world-wide populations reflected that 15 independent variations/markers were optimal in defining population structure parameters, such as FST, molecular variance and correlation-based relationship. A subsequent addition of randomly selected markers had a negligible effect (close to zero, i.e. 1 × 10−3) on these parameters. The study proves efficient in tracing complex population structures and deriving relationships among world-wide populations in a cost-effective and expedient manner. PMID:25030906

  3. Global methylation silencing of clustered proto-cadherin genes in cervical cancer: serving as diagnostic markers comparable to HPV

    PubMed Central

    Wang, Kai-Hung; Lin, Cuei-Jyuan; Liu, Chou-Jen; Liu, Dai-Wei; Huang, Rui-Lan; Ding, Dah-Ching; Weng, Ching-Feng; Chu, Tang-Yuan

    2015-01-01

    Epigenetic remodeling of cell adhesion genes is a common phenomenon in cancer invasion. This study aims to investigate global methylation of cell adhesion genes in cervical carcinogenesis and to apply them in early detection of cancer from cervical scraping. Genome-wide methylation array was performed on an investigation cohort, including 16 cervical intraepithelial neoplasia 3 (CIN3) and 20 cervical cancers (CA) versus 12 each of normal, inflammation and CIN1 as controls. Twelve members of clustered proto-cadherin (PCDH) genes were collectively methylated and silenced, which were validated in cancer cells of the cervix, endometrium, liver, head and neck, breast, and lung. In an independent cohort including 107 controls, 66 CIN1, 85 CIN2/3, and 38 CA, methylated PCDHA4 and PCDHA13 were detected in 2.8%, 24.2%, 52.9%, and 84.2% (P < 10−25), and 2.8%, 24.2%, 50.6%, and 94.7% (P < 10−29), respectively. In diagnosis of CIN2 or more severe lesion of the cervix, a combination test of methylated PCDHA4 or PCDHA13 from cervical scraping had a sensitivity, specificity, positive predictive value, and negative predictive value of 74.8%, 80.3%, 73%, and 81.8%, respectively. Testing of this combination from cervical scraping is equally sensitive but more specific than human papillomavirus (HPV) test in diagnosis of CIN2 or more severe lesions. The study disclosed a collective methylation of PCDH genes in cancer of cervix and other sites. At least two of them can be promising diagnostic markers for cervical cancer noninferior to HPV. PMID:25418975

  4. Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes

    PubMed Central

    Lin, Hsin-Hung; Liao, Yu-Chieh

    2016-01-01

    Metagenomics, the application of shotgun sequencing, facilitates the reconstruction of the genomes of individual species from natural environments. A major challenge in the genome recovery domain is to agglomerate or ‘bin’ sequences assembled from metagenomic reads into individual groups. Metagenomic binning without consideration of reference sequences enables the comprehensive discovery of new microbial organisms and aids in the microbial genome reconstruction process. Here we present MyCC, an automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the reconstructed genomic fragments. We demonstrate the superior performance of MyCC compared to other binning tools including CONCOCT, GroopM, MaxBin and MetaBAT on both synthetic and real human gut communities with a small sample size (one to 11 samples), as well as on a large metagenome dataset (over 250 samples). Moreover, we demonstrate the visualization of metagenomes in MyCC to aid in the reconstruction of genomes from distinct bins. MyCC is freely available at http://sourceforge.net/projects/sb2nhri/files/MyCC/. PMID:27067514

  5. Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes.

    PubMed

    Lin, Hsin-Hung; Liao, Yu-Chieh

    2016-01-01

    Metagenomics, the application of shotgun sequencing, facilitates the reconstruction of the genomes of individual species from natural environments. A major challenge in the genome recovery domain is to agglomerate or 'bin' sequences assembled from metagenomic reads into individual groups. Metagenomic binning without consideration of reference sequences enables the comprehensive discovery of new microbial organisms and aids in the microbial genome reconstruction process. Here we present MyCC, an automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the reconstructed genomic fragments. We demonstrate the superior performance of MyCC compared to other binning tools including CONCOCT, GroopM, MaxBin and MetaBAT on both synthetic and real human gut communities with a small sample size (one to 11 samples), as well as on a large metagenome dataset (over 250 samples). Moreover, we demonstrate the visualization of metagenomes in MyCC to aid in the reconstruction of genomes from distinct bins. MyCC is freely available at http://sourceforge.net/projects/sb2nhri/files/MyCC/. PMID:27067514

  6. The APOA1/C3/A4/A5 cluster and markers of allostatic load in the Boston Puerto Rican Health Study

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The APOA1/C3/A4/A5 cluster encodes key regulators of plasma lipids. Interactions between dietary factors and single nucleotide polymorphisms (SNPs) in the cluster have been reported. Allostatic load, or physiological dysregulation in response to stress, has been implicated in shaping health disparit...

  7. Marker development

    SciTech Connect

    Adams, M.R.

    1987-05-01

    This report is to discuss the marker development for radioactive waste disposal sites. The markers must be designed to last 10,000 years, and place no undue burdens on the future generations. Barriers cannot be constructed that preclude human intrusion. Design specifications for surface markers will be discussed, also marker pictograms will also be covered.

  8. Bone Markers

    MedlinePlus

    ... Alkaline Phosphatase; Osteocalcin; P1NP; Procollagen Type 1 N-Terminal Propeptide Formal name: Biochemical Markers of Bone Remodeling ... tests for evaluating bone turnover: C-telopeptide (C-terminal telopeptide of type 1 collagen (CTx)) – a marker ...

  9. Long-term marker-free multiphoton imaging, targeted transfection, optical cleaning of stem cell clusters, and optical transport of microRNA with extreme ultrashort laser pulses

    NASA Astrophysics Data System (ADS)

    Uchugonova, Aisada; Földes-Papp, Zeno; Kostner, Gerhard M.; König, Karsten

    2010-02-01

    The novel utrashort femtosecond laser scanning microscope FemtOgene (JenLab GmbH, Germany) with 12 femtoseconds at the focal plane have been employed in marker-free imaging and optical manipulation of stem cells as well as for the non-contact introduction of microRNA in cancer cells. Human adult pancreatic stem cells, salivary gland stem cells, and human dental pulp stem cells have been investigated by femtosecond laser multiphoton microscopy. Autofluorescence based on NAD(P)H and flavoproteins and second harmonic generation due to collagen have been imaged with submicron spatial resolution, 270 ps temporal resolution, and 10 nm spectral resolution. Major emission peaks at 460 nm and 530 nm with typical mean fluorescence lifetimes of 1.8 ns and 2.0 ns, respectively, were measured in a variety of stem cells using spectral imaging and time-correlated single photon counting. During differentiation, the ratios of bound to free NAD(P)H and NAD(P)H/flavoproteins changed. In addition, the biosynthesis of lipids and collagen was detected over a long period of time of up to 5 weeks. Nanoprocessing was performed with 12 femtosecond laser pulses and low picojoule pulse energies to realize targeted transfection and optical cleaning of human adult stem cell populations. Multiphoton sub-20fs microscopes may become novel non-invasive tools for marker-free optical stem cell characterization, for on-line monitoring of differentiation within a three-dimensional microenvironment, and for optical manipulation.

  10. Disruption of a sugar transporter gene cluster in a hyperthermophilic archaeon using a host-marker system based on antibiotic resistance.

    PubMed

    Matsumi, Rie; Manabe, Kenji; Fukui, Toshiaki; Atomi, Haruyuki; Imanaka, Tadayuki

    2007-04-01

    We have developed a gene disruption system in the hyperthermophilic archaeon Thermococcus kodakaraensis using the antibiotic simvastatin and a fusion gene designed to overexpress the 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase gene (hmg(Tk)) with the glutamate dehydrogenase promoter. With this system, we disrupted the T. kodakaraensis amylopullulanase gene (apu(Tk)) or a gene cluster which includes apu(Tk) and genes encoding components of a putative sugar transporter. Disruption plasmids were introduced into wild-type T. kodakaraensis KOD1 cells, and transformants exhibiting resistance to 4 microM simvastatin were isolated. The transformants exhibited growth in the presence of 20 microM simvastatin, and we observed a 30-fold increase in intracellular HMG-CoA reductase activity. The expected gene disruption via double-crossover recombination occurred at the target locus, but we also observed recombination events at the hmg(Tk) locus when the endogenous hmg(Tk) gene was used. This could be avoided by using the corresponding gene from Pyrococcus furiosus (hmg(Pf)) or by linearizing the plasmid prior to transformation. While both gene disruption strains displayed normal growth on amino acids or pyruvate, cells without the sugar transporter genes could not grow on maltooligosaccharides or polysaccharides, indicating that the gene cluster encodes the only sugar transporter involved in the uptake of these compounds. The Deltaapu(Tk) strain could not grow on pullulan and displayed only low levels of growth on amylose, suggesting that Apu(Tk) is a major polysaccharide-degrading enzyme in T. kodakaraensis. PMID:17259314

  11. HOXD-AS1 is a novel lncRNA encoded in HOXD cluster and a marker of neuroblastoma progression revealed via integrative analysis of noncoding transcriptome

    PubMed Central

    2014-01-01

    Background Long noncoding RNAs (lncRNAs) constitute a major, but poorly characterized part of human transcriptome. Recent evidence indicates that many lncRNAs are involved in cancer and can be used as predictive and prognostic biomarkers. Significant fraction of lncRNAs is represented on widely used microarray platforms, however they have usually been ignored in cancer studies. Results We developed a computational pipeline to annotate lncRNAs on popular Affymetrix U133 microarrays, creating a resource allowing measurement of expression of 1581 lncRNAs. This resource can be utilized to interrogate existing microarray datasets for various lncRNA studies. We found that these lncRNAs fall into three distinct classes according to their statistical distribution by length. Remarkably, these three classes of lncRNAs were co-localized with protein coding genes exhibiting distinct gene ontology groups. This annotation was applied to microarray analysis which identified a 159 lncRNA signature that discriminates between localized and metastatic stages of neuroblastoma. Analysis of an independent patient cohort revealed that this signature differentiates also relapsing from non-relapsing primary tumors. This is the first example of the signature developed via the analysis of expression of lncRNAs solely. One of these lncRNAs, termed HOXD-AS1, is encoded in HOXD cluster. HOXD-AS1 is evolutionary conserved among hominids and has all bona fide features of a gene. Studying retinoid acid (RA) response of SH-SY5Y cell line, a model of human metastatic neuroblastoma, we found that HOXD-AS1 is a subject to morphogenic regulation, is activated by PI3K/Akt pathway and itself is involved in control of RA-induced cell differentiation. Knock-down experiments revealed that HOXD-AS1 controls expression levels of clinically significant protein-coding genes involved in angiogenesis and inflammation, the hallmarks of metastatic cancer. Conclusions Our findings greatly extend the number of

  12. CLUSTER CHEMISTRY

    SciTech Connect

    Muetterties, Earl L.

    1980-05-01

    Metal cluster chemistry is one of the most rapidly developing areas of inorganic and organometallic chemistry. Prior to 1960 only a few metal clusters were well characterized. However, shortly after the early development of boron cluster chemistry, the field of metal cluster chemistry began to grow at a very rapid rate and a structural and a qualitative theoretical understanding of clusters came quickly. Analyzed here is the chemistry and the general significance of clusters with particular emphasis on the cluster research within my group. The importance of coordinately unsaturated, very reactive metal clusters is the major subject of discussion.

  13. Discourse Markers across Language.

    ERIC Educational Resources Information Center

    Fraser, Bruce

    This paper discusses discourse markers (e.g., "and, so, anyway") and offers an overview of their characteristics and occurrence, using English for illustration. The role of discourse markers is to signal speaker comment on the current utterance. The discourse marker is not part of the sentence's propositional content. While absence of markers does…

  14. Glenohumeral joint kinematics measured by intracortical pins, reflective markers, and computed tomography: A novel technique to assess acromiohumeral distance.

    PubMed

    Dal Maso, Fabien; Blache, Yoann; Raison, Maxime; Lundberg, Arne; Begon, Mickaël

    2016-08-01

    Combination of biplane fluoroscopy and CT-scan provides accurate 3D measurement of the acromiohumeral distance (AHD) during dynamic tasks. However, participants performed only two and six trials in previous experiments to respect the recommended radiation exposure per year. Our objective was to propose a technique to assess the AHD in 3D during dynamic tasks without this limitation. The AHD was computed from glenohumeral kinematics obtained using markers fitted to pins drilled into the scapula and the humerus combined with 3D bone geometry obtained using CT-scan. Four participants performed range-of-motion, daily-living, and sports activities. Sixty-six out of 158trials performed by each participant were analyzed. Two participants were not considered due to experimental issues. AHD decreased with arm elevation. Overall, the smallest AHD occurred in abduction (1.1mm (P1) and 1.2mm (P2)). The smallest AHD were 2.4mm (P1) and 3.1mm (P2) during ADL. It was 2.8mm (P1) and 1.1mm (P2) during sports activities. The humeral head greater and lesser tuberosities came the nearest to the acromion. The proposed technique increases the number of trials acquired during one experiment compared to previous. The identification of movements maximizing AHD is possible, which may provide benefits for shoulder rehabilitation. PMID:26263837

  15. Ceramic subsurface marker prototypes

    SciTech Connect

    Lukens, C.E.

    1985-05-02

    The client submitted 5 sets of porcelain and stoneware subsurface (radioactive site) marker prototypes (31 markers each set). The following were determined: compressive strength, thermal shock resistance, thermal crazing resistance, alkali resistance, color retention, and chemical resistance.

  16. Meaningful Clusters

    SciTech Connect

    Sanfilippo, Antonio P.; Calapristi, Augustin J.; Crow, Vernon L.; Hetzler, Elizabeth G.; Turner, Alan E.

    2004-05-26

    We present an approach to the disambiguation of cluster labels that capitalizes on the notion of semantic similarity to assign WordNet senses to cluster labels. The approach provides interesting insights on how document clustering can provide the basis for developing a novel approach to word sense disambiguation.

  17. Identification and DUS Testing of Rice Varieties through Microsatellite Markers

    PubMed Central

    Pourabed, Ehsan; Jazayeri Noushabadi, Mohammad Reza; Jamali, Seyed Hossein; Moheb Alipour, Naser; Zareyan, Abbas; Sadeghi, Leila

    2015-01-01

    Identification and registration of new rice varieties are very important to be free from environmental effects and using molecular markers that are more reliable. The objectives of this study were, first, the identification and distinction of 40 rice varieties consisting of local varieties of Iran, improved varieties, and IRRI varieties using PIC, and discriminating power, second, cluster analysis based on Dice similarity coefficient and UPGMA algorithm, and, third, determining the ability of microsatellite markers to separate varieties utilizing the best combination of markers. For this research, 12 microsatellite markers were used. In total, 83 polymorphic alleles (6.91 alleles per locus) were found. In addition, the variation of PIC was calculated from 0.52 to 0.9. The results of cluster analysis showed the complete discrimination of varieties from each other except for IR58025A and IR58025B. Moreover, cluster analysis could detect the most of the improved varieties from local varieties. Based on the best combination of markers analysis, five pair primers together have shown the same results of all markers for detection among all varieties. Considering the results of this research, we can propose that microsatellite markers can be used as a complementary tool for morphological characteristics in DUS tests. PMID:25755666

  18. Quintuplet Cluster

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Penetrating 25,000 light-years of obscuring dust and myriad stars, NASA's Hubble Space Telescope has provided the clearest view yet of one of the largest young clusters of stars inside our Milky Way galaxy, located less than 100 light-years from the very center of the Galaxy. Having the equivalent mass greater than 10,000 stars like our sun, the monster cluster is ten times larger than typical young star clusters scattered throughout our Milky Way. It is destined to be ripped apart in just a few million years by gravitational tidal forces in the galaxy's core. But in its brief lifetime it shines more brightly than any other star cluster in the Galaxy. Quintuplet Cluster is 4 million years old. It has stars on the verge of blowing up as supernovae. It is the home of the brightest star seen in the galaxy, called the Pistol star. This image was taken in infrared light by Hubble's NICMOS camera in September 1997. The false colors correspond to infrared wavelengths. The galactic center stars are white, the red stars are enshrouded in dust or behind dust, and the blue stars are foreground stars between us and the Milky Way's center. The cluster is hidden from direct view behind black dust clouds in the constellation Sagittarius. If the cluster could be seen from earth it would appear to the naked eye as a 3rd magnitude star, 1/6th of a full moon's diameter apart.

  19. Identification of molecular markers associated with fruit traits in olive and assessment of olive core collection with AFLP markers and fruit traits.

    PubMed

    Ipek, M; Seker, M; Ipek, A; Gul, M K

    2015-01-01

    The purpose of this study was to characterize olive core collection with amplified fragment length polymorphism (AFLP) markers and fruit traits and to determine AFLP markers significantly associated with these fruit characters in olive. A total of 168 polymorphic AFLP markers generated by five primer combinations and nine fruit traits were used to characterize relationships between 18 olive cultivars. Although all olive cultivars were discriminated from each other by either AFLP markers (<0.75 similarity level) or fruit traits, clustering based on the AFLP markers and fruit traits was not significantly correlated (r = 0.13). Partial clustering of olive cultivars by AFLP markers according to their geographical origin was observed. Associations of AFLP markers with fruits were determined using a multiple-regression analysis with stepwise addition of AFLP markers. Significant associations between eight AFLP markers and fruit traits were identified. While five AFLP markers demonstrated significant negative correlation with fruit and stone weight, width and length and total polyphenols (P < 0.05), three AFLP markers displayed significant positive correlation with α-tocopherol and γ-tocopherol (P < 0.01). This is the first report on the association of molecular markers with fruit traits in olive. Molecular markers associated with morphological and agronomic traits could be utilized for the breeding of olive cultivars. However, the association power of these markers needs to be confirmed in larger populations, and highly correlated markers should then be converted to PCR-based DNA markers such as sequence-characterized amplified region markers for better utilization. PMID:25867425

  20. Galaxy Clusters

    NASA Astrophysics Data System (ADS)

    Miller, Christopher J. Miller

    2012-03-01

    There are many examples of clustering in astronomy. Stars in our own galaxy are often seen as being gravitationally bound into tight globular or open clusters. The Solar System's Trojan asteroids cluster at the gravitational Langrangian in front of Jupiter’s orbit. On the largest of scales, we find gravitationally bound clusters of galaxies, the Virgo cluster (in the constellation of Virgo at a distance of ˜50 million light years) being a prime nearby example. The Virgo cluster subtends an angle of nearly 8◦ on the sky and is known to contain over a thousand member galaxies. Galaxy clusters play an important role in our understanding of theUniverse. Clusters exist at peaks in the three-dimensional large-scale matter density field. Their sky (2D) locations are easy to detect in astronomical imaging data and their mean galaxy redshifts (redshift is related to the third spatial dimension: distance) are often better (spectroscopically) and cheaper (photometrically) when compared with the entire galaxy population in large sky surveys. Photometric redshift (z) [Photometric techniques use the broad band filter magnitudes of a galaxy to estimate the redshift. Spectroscopic techniques use the galaxy spectra and emission/absorption line features to measure the redshift] determinations of galaxies within clusters are accurate to better than delta_z = 0.05 [7] and when studied as a cluster population, the central galaxies form a line in color-magnitude space (called the the E/S0 ridgeline and visible in Figure 16.3) that contains galaxies with similar stellar populations [15]. The shape of this E/S0 ridgeline enables astronomers to measure the cluster redshift to within delta_z = 0.01 [23]. The most accurate cluster redshift determinations come from spectroscopy of the member galaxies, where only a fraction of the members need to be spectroscopically observed [25,42] to get an accurate redshift to the whole system. If light traces mass in the Universe, then the locations

  1. Occupational Clusters.

    ERIC Educational Resources Information Center

    Pottawattamie County School System, Council Bluffs, IA.

    The 15 occupational clusters (transportation, fine arts and humanities, communications and media, personal service occupations, construction, hospitality and recreation, health occupations, marine science occupations, consumer and homemaking-related occupations, agribusiness and natural resources, environment, public service, business and office…

  2. Data Clustering

    NASA Astrophysics Data System (ADS)

    Wagstaff, Kiri L.

    2012-03-01

    On obtaining a new data set, the researcher is immediately faced with the challenge of obtaining a high-level understanding from the observations. What does a typical item look like? What are the dominant trends? How many distinct groups are included in the data set, and how is each one characterized? Which observable values are common, and which rarely occur? Which items stand out as anomalies or outliers from the rest of the data? This challenge is exacerbated by the steady growth in data set size [11] as new instruments push into new frontiers of parameter space, via improvements in temporal, spatial, and spectral resolution, or by the desire to "fuse" observations from different modalities and instruments into a larger-picture understanding of the same underlying phenomenon. Data clustering algorithms provide a variety of solutions for this task. They can generate summaries, locate outliers, compress data, identify dense or sparse regions of feature space, and build data models. It is useful to note up front that "clusters" in this context refer to groups of items within some descriptive feature space, not (necessarily) to "galaxy clusters" which are dense regions in physical space. The goal of this chapter is to survey a variety of data clustering methods, with an eye toward their applicability to astronomical data analysis. In addition to improving the individual researcher’s understanding of a given data set, clustering has led directly to scientific advances, such as the discovery of new subclasses of stars [14] and gamma-ray bursts (GRBs) [38]. All clustering algorithms seek to identify groups within a data set that reflect some observed, quantifiable structure. Clustering is traditionally an unsupervised approach to data analysis, in the sense that it operates without any direct guidance about which items should be assigned to which clusters. There has been a recent trend in the clustering literature toward supporting semisupervised or constrained

  3. Cluster generator

    DOEpatents

    Donchev, Todor I.; Petrov, Ivan G.

    2011-05-31

    Described herein is an apparatus and a method for producing atom clusters based on a gas discharge within a hollow cathode. The hollow cathode includes one or more walls. The one or more walls define a sputtering chamber within the hollow cathode and include a material to be sputtered. A hollow anode is positioned at an end of the sputtering chamber, and atom clusters are formed when a gas discharge is generated between the hollow anode and the hollow cathode.

  4. [MUSCULOSKELETAL MARKERS, ARTHROPATY, TRAUMAS].

    PubMed

    Caldarini, Carla; Zavaroni, Federica; Benassi, Valentina

    2015-01-01

    The bone tissue remodeling due to strong physical/working activity is defined as ergonomic markers or MSM (Muscoloskeletal Stress Markers) (Capasso et al. 1999) and MOS (Markers of Occupational Stress). Among them we can find: enthesopaties, arthropaties, non metrical stress and traumas markers. In the present study, the analysis of these traits has been used to clarify habitual activity patterns of four imperial populations from Suburbium: Castel Malnome, Casal Bertone area Q, Via Padre Semeria e Quarto Cappello del Prete. The very high prevalence of activity-induced stress lesions occurred among the individuals of Castel Malnome and Casal Bertone area Q suggests that these groups were involved in strenuous occupations such as, respectively: the processing and storage of salt and the dyeing of textiles and hides discernible from the archaeological context. For the individuals of Via Padre Semeria and Quarto Cappello del Prete the alterations, instead, could be compatibles with agricultural work. PMID:27348990

  5. [Biological markers of alcoholism].

    PubMed

    Marcos Martín, M; Pastor Encinas, I; Laso Guzmán, F J

    2005-09-01

    Diagnosis of alcoholism is very important, given its high prevalence and possibility of influencing the disease course. For this reason, the so-called biological markers of alcoholism are useful. These are analytic parameters that alter in the presence of excessive alcohol consumption. The two most relevant markers are the gamma-glutamyltranspeptidase and carbohydrate deficient transferrin. With this clinical comment, we aim to contribute to the knowledge of these tests and promote its use in the clinical practice. PMID:16194480

  6. Analysis of the genetic diversity of super sweet corn inbred lines using SSR and SSAP markers.

    PubMed

    Ko, W R; Sa, K J; Roy, N S; Choi, H-J; Lee, J K

    2016-01-01

    In this study, we compared the efficiency of simple sequence repeat (SSR) and sequence specific amplified polymorphism (SSAP) markers for analyzing genetic diversity, genetic relationships, and population structure of 87 super sweet corn inbred lines from different origins. SSR markers showed higher average gene diversity and Shannon's information index than SSAP markers. To assess genetic relationships and characterize inbred lines using SSR and SSAP markers, genetic similarity (GS) matrices were constructed. The dendrogram using SSR marker data showed a complex pattern with nine clusters and a GS of 53.0%. For SSAP markers, three clusters were observed with a GS of 50.8%. Results of combined marker data showed six clusters with 53.5% GS. To analyze the genetic population structure of SSR and SSAP marker data, the 87 inbred lines were divided into groups I, II, and admixed based on the membership probability threshold of 0.8. Using combined marker data, the population structure was K = 3 and was divided into groups I, II, III, and admixed. This study represents a comparative analysis of SSR and SSAP marker data for the study of genetic diversity and genetic relationships in super sweet corn inbred lines. Our results would be useful for maize-breeding programs in Korea. PMID:26909914

  7. Informativeness of microsatellite markers.

    PubMed

    Reyes-Valdés, M Humberto

    2013-01-01

    Simple sequence repeats (SSR) are extensively used as genetic markers for studies of diversity, genetic mapping, and cultivar discrimination. The informativeness of a given SSR locus or a loci group depends on the number of alleles, their frequency distribution, as well as the kind of application. Here I describe several methods for calculating marker informativeness, all of them suitable for SSR polymorphisms, proposed by several authors and synthesized in an Information Theory framework. Additionally, free access software resources are described as well as their application through worked examples. PMID:23546797

  8. SVM clustering

    PubMed Central

    Winters-Hilt, Stephen; Merat, Sam

    2007-01-01

    Background Support Vector Machines (SVMs) provide a powerful method for classification (supervised learning). Use of SVMs for clustering (unsupervised learning) is now being considered in a number of different ways. Results An SVM-based clustering algorithm is introduced that clusters data with no a priori knowledge of input classes. The algorithm initializes by first running a binary SVM classifier against a data set with each vector in the set randomly labelled, this is repeated until an initial convergence occurs. Once this initialization step is complete, the SVM confidence parameters for classification on each of the training instances can be accessed. The lowest confidence data (e.g., the worst of the mislabelled data) then has its' labels switched to the other class label. The SVM is then re-run on the data set (with partly re-labelled data) and is guaranteed to converge in this situation since it converged previously, and now it has fewer data points to carry with mislabelling penalties. This approach appears to limit exposure to the local minima traps that can occur with other approaches. Thus, the algorithm then improves on its weakly convergent result by SVM re-training after each re-labeling on the worst of the misclassified vectors – i.e., those feature vectors with confidence factor values beyond some threshold. The repetition of the above process improves the accuracy, here a measure of separability, until there are no misclassifications. Variations on this type of clustering approach are shown. Conclusion Non-parametric SVM-based clustering methods may allow for much improved performance over parametric approaches, particularly if they can be designed to inherit the strengths of their supervised SVM counterparts. PMID:18047717

  9. GENETIC LINKAGE MAP FOR WATERMELON: SEGREGATION AND DISTRIBUTION OF DNA MARKERS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic linkage map is being constructed for watermelon based on a testcross population and an F2 population. About 51.0% and 31.8% of the markers in the testcross and F2 populations are skewed from the expected segregation ratios. AFLP markers appeared to be clustered on linkage regions, while IS...

  10. Analysis of genetic diversity in earthworms using DNA markers.

    PubMed

    Sharma, Anshul; Sonah, Humira; Deshmukh, Rupesh K; Gupta, Navneet K; Singh, Nagendra K; Sharma, Tilak R

    2011-01-01

    Earthworms are one of the most important and beneficial macrofauna, and are used extensively in organic farming. Earthworms mediate soil biological regulation systems, and produce biogenic structures. They help to maintain soil structure, water infiltration, and regulate the availability of nutrients assimilated by plants. The objectives of this study were to perform morphological and molecular characterizations of 24 earthworm individuals collected from geographically diverse locations to assess the level of genetic variation. For molecular analysis, the effectiveness of RAPD, ISSR, and Universal rice primers (URPs) markers was investigated to identify polymorphism among 24 isolates of earthworms. A total of 62 molecular markers were used for amplification of genomic DNA of earthworms. Of these, 10 RAPD, 10 ISSR, and 10 URPs markers were used for characterization, which showed 95.7%, 96.7% and 98.3% polymorphism, respectively. The dendrogram, generated from the DNA markers by the unweighted pair group method using arithmetic averages, grouped all the isolates into two main clusters. All Eisenia fetida isolates were clustered in group A, whereas group B included three isolates belonging to Eudrilus eugeniae. Molecular markers allowed a rapid assessment of genetic variation among these closely related isolates of earthworms. These results suggest that molecular markers are a good choice for diversity analysis of earthworm individuals. PMID:21186943

  11. Strategy Markers in Writing.

    ERIC Educational Resources Information Center

    Sindermann, Gerda; Horsella, Maria

    1989-01-01

    Part of a research project is presented that aims at identifying the difficulties tertiary level students encounter in reading scientific texts in a foreign language and the strategies they apply to overcome them. Strategy markers are identified and listed, and are then analyzed to interpret the linguistic difficulty and the strategy used.…

  12. The Swift Turbidity Marker

    ERIC Educational Resources Information Center

    Omar, Ahmad Fairuz; MatJafri, Mohd Zubir

    2011-01-01

    The Swift Turbidity Marker is an optical instrument developed to measure the level of water turbidity. The components and configuration selected for the system are based on common turbidity meter design concepts but use a simplified methodology to produce rapid turbidity measurements. This work is aimed at high school physics students and is the…

  13. Lipoprotein marker for hypertriglyceridemia

    DOEpatents

    Cubicciotti, Roger S.; Karu, Alexander E.; Krauss, Ronald M.

    1986-01-01

    Methods and compositions are provided for the detection of a particular low density lipoprotein which has been found to be a marker for patients suffering from type IV hypertriglyceridemia. A monoclonal antibody capable of specifically binding to a characteristic epitopic site on this LDL subspecies can be utilized in a wide variety of immunoassays. Hybridoma cell line SPL.IVA5A1 was deposited at the American Type Culture Collection on Mar. 29, 1984, and granted accession no. HB 8535.

  14. Identification of uterine leiomyoma-specific marker genes based on DNA methylation and their clinical application

    PubMed Central

    Sato, Shun; Maekawa, Ryo; Yamagata, Yoshiaki; Tamura, Isao; Lee, Lifa; Okada, Maki; Jozaki, Kosuke; Asada, Hiromi; Tamura, Hiroshi; Sugino, Norihiro

    2016-01-01

    Differential diagnosis of uterine leiomyomas and leiomyosarcomas is needed to determine whether the uterus can be retained. Therefore, biomarkers for uterine leiomyomas, and reliable and objective diagnostic methods have been desired besides the pathological diagnosis. In the present study, we identified 12 genes specific to uterine leiomyomas based on DNA methylation. Using these marker genes specific to uterine leiomyomas, we established a hierarchical clustering system based on the DNA methylation level of the marker genes, which could completely differentiate between uterine leiomyomas and normal myometrium. Furthermore, our hierarchical clustering system completely discriminated uterine cancers and differentiated between uterine leiomyosarcomas and leiomyomas with more than 70% accuracy. In conclusion, this study identified DNA methylation-based marker genes specific to uterine leiomyomas, and our hierarchical clustering system using these marker genes was useful for differential diagnosis of uterine leiomyomas and leiomyosarcomas. PMID:27498619

  15. Identification of uterine leiomyoma-specific marker genes based on DNA methylation and their clinical application.

    PubMed

    Sato, Shun; Maekawa, Ryo; Yamagata, Yoshiaki; Tamura, Isao; Lee, Lifa; Okada, Maki; Jozaki, Kosuke; Asada, Hiromi; Tamura, Hiroshi; Sugino, Norihiro

    2016-01-01

    Differential diagnosis of uterine leiomyomas and leiomyosarcomas is needed to determine whether the uterus can be retained. Therefore, biomarkers for uterine leiomyomas, and reliable and objective diagnostic methods have been desired besides the pathological diagnosis. In the present study, we identified 12 genes specific to uterine leiomyomas based on DNA methylation. Using these marker genes specific to uterine leiomyomas, we established a hierarchical clustering system based on the DNA methylation level of the marker genes, which could completely differentiate between uterine leiomyomas and normal myometrium. Furthermore, our hierarchical clustering system completely discriminated uterine cancers and differentiated between uterine leiomyosarcomas and leiomyomas with more than 70% accuracy. In conclusion, this study identified DNA methylation-based marker genes specific to uterine leiomyomas, and our hierarchical clustering system using these marker genes was useful for differential diagnosis of uterine leiomyomas and leiomyosarcomas. PMID:27498619

  16. CARTILAGE CELL CLUSTERS

    PubMed Central

    Lotz, Martin K.; Otsuki, Shuhei; Grogan, Shawn P.; Sah, Robert; Terkeltaub, Robert; D’Lima, Darryl

    2010-01-01

    The formation of new cell clusters is a histological hallmark of arthritic cartilage but the biology of clusters and their role in disease are poorly understood. This is the first comprehensive review of clinical and experimental conditions associated with cluster formation. Genes and proteins that are expressed in cluster cells, the cellular origin of the clusters, mechanisms that lead to cluster formation and the role of cluster cells in pathogenesis are discussed. PMID:20506158

  17. A microfluidic device for label-free, physical capture of circulating tumor cell clusters.

    PubMed

    Sarioglu, A Fatih; Aceto, Nicola; Kojic, Nikola; Donaldson, Maria C; Zeinali, Mahnaz; Hamza, Bashar; Engstrom, Amanda; Zhu, Huili; Sundaresan, Tilak K; Miyamoto, David T; Luo, Xi; Bardia, Aditya; Wittner, Ben S; Ramaswamy, Sridhar; Shioda, Toshi; Ting, David T; Stott, Shannon L; Kapur, Ravi; Maheswaran, Shyamala; Haber, Daniel A; Toner, Mehmet

    2015-07-01

    Cancer cells metastasize through the bloodstream either as single migratory circulating tumor cells (CTCs) or as multicellular groupings (CTC clusters). Existing technologies for CTC enrichment are designed to isolate single CTCs, and although CTC clusters are detectable in some cases, their true prevalence and significance remain to be determined. Here we developed a microchip technology (the Cluster-Chip) to capture CTC clusters independently of tumor-specific markers from unprocessed blood. CTC clusters are isolated through specialized bifurcating traps under low-shear stress conditions that preserve their integrity, and even two-cell clusters are captured efficiently. Using the Cluster-Chip, we identified CTC clusters in 30-40% of patients with metastatic breast or prostate cancer or with melanoma. RNA sequencing of CTC clusters confirmed their tumor origin and identified tissue-derived macrophages within the clusters. Efficient capture of CTC clusters will enable the detailed characterization of their biological properties and role in metastasis. PMID:25984697

  18. A remote camera operation system using a marker attached cap

    NASA Astrophysics Data System (ADS)

    Kawai, Hironori; Hama, Hiromitsu

    2005-12-01

    In this paper, we propose a convenient system to control a remote camera according to the eye-gazing direction of the operator, which is approximately obtained through calculating the face direction by means of image processing. The operator put a marker attached cap on his head, and the system takes an image of the operator from above with only one video camera. Three markers are set up on the cap, and 'three' is the minimum number to calculate the tilt angle of the head. The more markers are used, the robuster system may be made to occlusion, and the wider moving range of the head is tolerated. It is supposed that the markers must not exist on any three dimensional straight line. To compensate the marker's color change due to illumination conditions, the threshold for the marker extraction is adaptively decided using a k-means clustering method. The system was implemented with MATLAB on a personal computer, and the real-time operation was realized. Through the experimental results, robustness of the system was confirmed and tilt and pan angles of the head could be calculated with enough accuracy to use.

  19. Markers of vulnerability in schizophrenia

    PubMed Central

    Prelipceanu, D

    2009-01-01

    Vulnerability in schizophrenia is an integrative concept, which tries to explain the development of schizophrenia as an interaction between different individual susceptibility factors and environmental risk factors. Vulnerability markers used in genetic studies include biochemical indicators, neuroanatomical, neurophysiologic, and cognitive abnormalities. Among those, the most extensive studied markers were: evoked potentials, smooth pursuit eye movements, and attentional deficits. Some of the potential indicators presented in this paper satisfy most of the criteria necessary for a vulnerability marker, but none meets all of them. Nevertheless, they represent important markers of risk to schizophrenia. Key words: vulnerability, evoked potentials, eye movements, attentional deficits PMID:20108534

  20. Alterations in phenotypic biochemical markers in bladder epithelium during tumorigenesis.

    PubMed

    Rao, J Y; Hemstreet, G P; Hurst, R E; Bonner, R B; Jones, P L; Min, K W; Fradet, Y

    1993-09-01

    Phenotypic biochemical markers of oncogenesis and differentiation were mapped in bladder biopsies to investigate changes that occur in bladder tumorigenesis and to identify markers for increased bladder cancer risk. Touch preparations from biopsy specimens from 30 patients were obtained from tumors, the adjacent bladder epithelium, and random distant bladder epithelium. Markers, including DNA ploidy, epidermal growth factor receptor (EGFR), and oncoproteins, were quantified in individual cells by using quantitative fluorescence image analysis. Cluster analysis revealed the markers fell into three independent groups: (i) G-actin and EGFR; (ii) ploidy, cytology, and p185 (HER-2/neu oncoprotein) (ERBB2); and (iii) p300, a low-grade tumor antigen. Each marker displayed a gradient of abnormality from distant field to adjacent field to tumor. Different patterns for each marker suggested a developmental sequence of bladder cancer oncogenesis; G-actin was altered in 58% of distant biopsies (vs. 0/6 normals, P < 0.001), ploidy and cytology were altered in < 20% of distant fields and approximately 80% of tumors, and the other markers were intermediate. Patterns of EGFR and p185 suggest low-and high-grade tracks diverge early (P < 0.05 by Mann-Whitney U test for EGFR and ANOVA for p185). In conclusion, this study shows that a sequence of phenotypic changes accompanies development and progression of bladder cancers. Biochemical alterations in cells of the bladder field are often detectable before abnormal pathology, and markers previously thought to be limited to tumors were found in the field. The hierarchy of expression may be useful in identifying high-risk patients, assessing completeness of response to therapy, and monitoring and predicting recurrence. PMID:8367495

  1. Marker Assisted Selection in Legumes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Marker assisted selection (MAS) has begun to be implemented in some self-pollinating crops such as wheat. The promise of MAS has been on the breeding horizon for over two decades now. With the advent of the Medicago truncatula and Lotus japonicus genome sequences; numerous SSR mapped markers in M....

  2. Blueberry Microsatellite Markers Identify Cranberries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Forty-six blueberry simple sequence repeat (SSR) markers or microsatellites were tested for the ability to amplify a polymorphic marker in eight American cranberry accessions. Sixteen SSRs resulted in informative and polymorphic SSR primer pairs and were used to fingerprint 16 economically important...

  3. Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species.

    PubMed

    Buyyarapu, Ramesh; Kantety, Ramesh V; Yu, John Z; Saha, Sukumar; Sharma, Govind C

    2011-01-01

    New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum  EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps. PMID:22315588

  4. Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species

    PubMed Central

    Buyyarapu, Ramesh; Kantety, Ramesh V.; Yu, John Z.; Saha, Sukumar; Sharma, Govind C.

    2011-01-01

    New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum  EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps. PMID:22315588

  5. Foodservice Occupations Cluster Guide.

    ERIC Educational Resources Information Center

    Oregon State Dept. of Education, Salem.

    Intended to assist vocational teachers in developing and implementing a cluster program in food service occupations, this guide contains sections on cluster organization and implementation and instructional emphasis areas. The cluster organization and implementation section covers goal-based planning and includes a proposed cluster curriculum, a…

  6. Cluster-impact fusion

    SciTech Connect

    Echenique, P.M.; Manson, J.R.; Ritchie, R.H. )

    1990-03-19

    We present a model for the cluster-impact-fusion experiments of Buehler, Friedlander, and Friedman, Calculated fusion rates as a function of bombarding energy for constant cluster size agree well with experiment. The dependence of the fusion rate on cluster size at fixed bombarding energy is explained qualitatively. The role of correlated, coherent collisions in enhanced energy loss by clusters is emphasized.

  7. Chemotaxonomy of heterocystous cyanobacteria using FAME profiling as species markers.

    PubMed

    Shukla, Ekta; Singh, Satya Shila; Singh, Prashant; Mishra, Arun Kumar

    2012-07-01

    The fatty acid methyl ester (FAME) analysis of the 12 heterocystous cyanobacterial strains showed different fatty acid profiling based on the presence/absence and the percentage of 13 different types of fatty acids. The major fatty acids viz. palmitic acid (16:0), hexadecadienoic acid (16:2), stearic acid (18:0), oleic acid (18:1), linoleic (18:2), and linolenic acid (18:3) were present among all the strains except Cylindrospermum musicola where oleic acid (18:1) was absent. All the strains showed high levels of polyunsaturated fatty acid (PUFAs; 41-68.35%) followed by saturated fatty acid (SAFAs; 1.82-40.66%) and monounsaturated fatty acid (0.85-24.98%). Highest percentage of PUFAs and essential fatty acid (linolenic acid; 18:3) was reported in Scytonema bohnerii which can be used as fatty acid supplement in medical and biotechnological purpose. The cluster analysis based on FAME profiling suggests the presence of two distinct clusters with Euclidean distance ranging from 0 to 25. S. bohnerii of cluster I was distantly related to the other strains of cluster II. The genotypes of cluster II were further divided into two subclusters, i.e., IIa with C. musicola showing great divergence with the other genotypes of IIb which was further subdivided into two groups. Subsubcluster IIb(1) was represented by a genotype, Anabaena sp. whereas subsubcluster IIb(2) was distinguished by two groups, i.e., one group having significant similarity among their three genotypes showed distant relation with the other group having closely related six genotypes. To test the validity of the fatty acid profiles as a marker, cluster analysis has also been generated on the basis of morphological attributes. Our results suggest that FAME profiling might be used as species markers in the study of polyphasic approach based taxonomy and phylogenetic relationship. PMID:21761281

  8. Clustering of Expression Data in Chronic Lymphocytic Leukemia Reveals New Molecular Subdivisions

    PubMed Central

    Yepes, Sally; Torres, Maria Mercedes; Andrade, Rafael E.

    2015-01-01

    Although the identification of inherent structure in chronic lymphocytic leukemia (CLL) gene expression data using class discovery approaches has not been extensively explored, the natural clustering of patient samples can reveal molecular subdivisions that have biological and clinical implications. To explore this, we preprocessed raw gene expression data from two published studies, combined the data to increase the statistical power, and performed unsupervised clustering analysis. The clustering analysis was replicated in 4 independent cohorts. To assess the biological significance of the resultant clusters, we evaluated their prognostic value and identified cluster-specific markers. The clustering analysis revealed two robust and stable subgroups of CLL patients in the pooled dataset. The subgroups were confirmed by different methodological approaches (non-negative matrix factorization NMF clustering and hierarchical clustering) and validated in different cohorts. The subdivisions were related with differential clinical outcomes and markers associated with the microenvironment and the MAPK and BCR signaling pathways. It was also found that the cluster markers were independent of the immunoglobulin heavy chain variable (IGVH) genes mutational status. These findings suggest that the microenvironment can influence the clinical behavior of CLL, contributing to prognostic differences. The workflow followed here provides a new perspective on differences in prognosis and highlights new markers that should be explored in this context. PMID:26355846

  9. SSR markers: a tool for species identification in Psidium (Myrtaceae).

    PubMed

    Tuler, A C; Carrijo, T T; Nóia, L R; Ferreira, A; Peixoto, A L; da Silva Ferreira, M F

    2015-11-01

    Molecular DNA markers are used for detection of polymorphisms in individuals. As they are independent of developmental stage of the plant and environmental influences, they can be useful tools in taxonomy. The alleles of simple sequence repeat (SSR) markers (or microsatellites) are traditionally used to identify taxonomic units. This application demands the laborious and costly delimitation of exclusive alleles in order to avoid homoplasy. Here, we propose a method for identification of species based on the amplification profile of groups of SSR markers obtained by a transferability study. The approach considers that the SSR are conserved among related species. In this context, using Psidium as a model, 141 SSR markers developed for Psidium guajava were transferred to 13 indigenous species of Psidium from the Atlantic Rainforest. Transferability of the markers was high and 28 SSR were conserved in all species. Four SSR groups were defined and they can help in the identification of all 13 Psidium species studied. A group of 31 SSR was genotyped, with one to six alleles each. The H0 varied from 0.0 to 0.46, and PIC from 0.0 to 0.74. Cluster analysis revealed shared alleles among species. The high percentage of SSR transferability found in Psidium evidences the narrow phylogenetic relationship existing among these species since transferability occurs by the preservation of the microsatellites and anchoring regions. The proposed method was useful for distinguishing the species of Psidium, being useful in taxonomic studies. PMID:26476530

  10. Diagnostic marker signature for esophageal cancer from transcriptome analysis.

    PubMed

    Warnecke-Eberz, Ute; Metzger, Ralf; Hölscher, Arnulf H; Drebber, Uta; Bollschweiler, Elfriede

    2016-05-01

    Esophageal cancer is often diagnosed at an advanced stage. Diagnostic markers are needed for achieving a cure in esophageal cancer detecting and treating tumor cells earlier. In patients with locally advanced squamous cell carcinoma of the esophagus (ESCC), we profiled the gene expression of ESCC compared to corresponding normal biopsies for diagnostic markers by genome microarrays. Profiling of gene expression identified 4844 genes differentially expressed, 2122 upregulated and 2722 downregulated in ESCC. Twenty-three overexpressed candidates with best scores from significance analysis have been selected for further analysis by TaqMan low-density array-technique using a validation cohort of 40 patients. The verification rate was 100 % for ESCC. Twenty-two markers were additionally overexpressed in adenocarcinoma of the esophagus (EAC). The markers significantly overexpressed already in earlier tumor stages (pT1-2) of both histological subtypes (n = 19) have been clustered in a "diagnostic signature": PLA2G7, PRAME, MMP1, MMP3, MMP12, LIlRB2, TREM2, CHST2, IGFBP2, IGFBP7, KCNJ8, EMILIN2, CTHRC1, EMR2, WDR72, LPCAT1, COL4A2, CCL4, and SNX10. The marker signature will be translated to clinical practice to prove its diagnostic impact. This diagnostic signature may contribute to the earlier detection of tumor cells, with the aim to complement clinical techniques resulting in the development of better detection of concepts of esophageal cancer for earlier therapy and more favorite prognosis. PMID:26631031

  11. Screening and characterization of RAPD markers in viscerotropic Leishmania parasites.

    PubMed

    Mkada-Driss, Imen; Lahmadi, Ramzi; Chakroun, Ahmed S; Talbi, Chiraz; Guerbouj, Souheila; Driss, Mehdi; Elamine, Elwaleed M; Cupolillo, Elisa; Mukhtar, Moawia M; Guizani, Ikram

    2014-01-01

    Visceral leishmaniasis (VL) is mainly due to the Leishmania donovani complex. VL is endemic in many countries worldwide including East Africa and the Mediterranean region where the epidemiology is complex. Taxonomy of these pathogens is under controversy but there is a correlation between their genetic diversity and geographical origin. With steady increase in genome knowledge, RAPD is still a useful approach to identify and characterize novel DNA markers. Our aim was to identify and characterize polymorphic DNA markers in VL Leishmania parasites in diverse geographic regions using RAPD in order to constitute a pool of PCR targets having the potential to differentiate among the VL parasites. 100 different oligonucleotide decamers having arbitrary DNA sequences were screened for reproducible amplification and a selection of 28 was used to amplify DNA from 12 L. donovani, L. archibaldi and L. infantum strains having diverse origins. A total of 155 bands were amplified of which 60.65% appeared polymorphic. 7 out of 28 primers provided monomorphic patterns. Phenetic analysis allowed clustering the parasites according to their geographical origin. Differentially amplified bands were selected, among them 22 RAPD products were successfully cloned and sequenced. Bioinformatic analysis allowed mapping of the markers and sequences and priming sites analysis. This study was complemented with Southern-blot to confirm assignment of markers to the kDNA. The bioinformatic analysis identified 16 nuclear and 3 minicircle markers. Analysis of these markers highlighted polymorphisms at RAPD priming sites with mainly 5' end transversions, and presence of inter- and intra- taxonomic complex sequence and microsatellites variations; a bias in transitions over transversions and indels between the different sequences compared is observed, which is however less marked between L. infantum and L. donovani. The study delivers a pool of well-documented polymorphic DNA markers, to develop

  12. Survey on granularity clustering.

    PubMed

    Ding, Shifei; Du, Mingjing; Zhu, Hong

    2015-12-01

    With the rapid development of uncertain artificial intelligent and the arrival of big data era, conventional clustering analysis and granular computing fail to satisfy the requirements of intelligent information processing in this new case. There is the essential relationship between granular computing and clustering analysis, so some researchers try to combine granular computing with clustering analysis. In the idea of granularity, the researchers expand the researches in clustering analysis and look for the best clustering results with the help of the basic theories and methods of granular computing. Granularity clustering method which is proposed and studied has attracted more and more attention. This paper firstly summarizes the background of granularity clustering and the intrinsic connection between granular computing and clustering analysis, and then mainly reviews the research status and various methods of granularity clustering. Finally, we analyze existing problem and propose further research. PMID:26557926

  13. Beta-2 Microglobulin Tumor Marker

    MedlinePlus

    ... limited. Home Visit Global Sites Search Help? Beta-2 Microglobulin Tumor Marker Share this page: Was this page helpful? Also known as: B2M; B 2 M; β2-Microglobulin; Thymotaxin Formal name: Beta 2 ...

  14. Cancer markers: integratively annotated classification.

    PubMed

    Orsini, M; Travaglione, A; Capobianco, E

    2013-11-10

    Translational cancer genomics research aims to ensure that experimental knowledge is subject to computational analysis, and integrated with a variety of records from omics and clinical sources. The data retrieval from such sources is not trivial, due to their redundancy and heterogeneity, and the presence of false evidence. In silico marker identification, therefore, remains a complex task that is mainly motivated by the impact that target identification from the elucidation of gene co-expression dynamics and regulation mechanisms, combined with the discovery of genotype-phenotype associations, may have for clinical validation. Based on the reuse of publicly available gene expression data, our aim is to propose cancer marker classification by integrating the prediction power of multiple annotation sources. In particular, with reference to the functional annotation for colorectal markers, we indicate a classification of markers into diagnostic and prognostic classes combined with susceptibility and risk factors. PMID:23928109

  15. Cluster Morphology Analysis

    PubMed Central

    Jacquez, Geoffrey M.

    2009-01-01

    Most disease clustering methods assume specific shapes and do not evaluate statistical power using the applicable geography, at-risk population, and covariates. Cluster Morphology Analysis (CMA) conducts power analyses of alternative techniques assuming clusters of different relative risks and shapes. Results are ranked by statistical power and false positives, under the rationale that surveillance should (1) find true clusters while (2) avoiding false clusters. CMA then synthesizes results of the most powerful methods. CMA was evaluated in simulation studies and applied to pancreatic cancer mortality in Michigan, and finds clusters of flexible shape while routinely evaluating statistical power. PMID:20234799

  16. [Laboratory markers of melanoma progression].

    PubMed

    Bánfalvi, Teodóra; Edesné, Mariann B; Gergye, Mária; Udvarhelyi, Nóra; Orosz, Zsolt; Gilde, Katalin; Kremmer, Tibor; Ottó, Szabolcs; Tímár, József

    2003-01-01

    Extracellular tumour markers may have potential role in the follow-up of patients with malignant melanoma, in therapy monitoring and in prediction of prognosis. In our article circulating tumour markers in melanoma (melanoma inhibitory activity, lipid bound sialic acid, neuron specific enolase, TA90 immune complex, S-100B protein, 5-S-cysteinyldopa, tyrosinase, cytokines, metalloproteinases, LDH) were reviewed. Among laboratory melanoma markers the S-100B protein is the most investigated. S-100B protein has high specificity, appropriate sensitivity and proved to be significant prognostic factor independent from stages. High serum values are associated with shorter survival. However, before S-100B monitoring immunohistochemistry for the detection of S-100B is required. In the case of malignant melanomas with low expression serum S-100B monitoring may not be sensitive enough to follow disease progression. Although the serum concentration of 5-S-cysteinyldopa did not prove to be independent prognostic factor in our previous studies comprising the highest patient number in the literature, the marker was suggested for therapy monitoring. The survival analysis indicated that the elevated 5-S-cysteinyldopa level predicts shorter survival. In spite of the calculated low correlation between the two markers, parallel elevation of S-100B protein and 5-S-cysteinyldopa indicated shorter survival. On the basis of the literature LDH is the most appropriate tumour marker in stage IV to predict prognosis, but its sensitivity and specificity could not achieve that of S-100B protein. S-100B and LDH proved to be similarly reliable in respect to the clinical outcome. Determination of serum concentration of MIA and tyrosinase are also reliable markers in malignant melanoma. The other investigated markers are not well known yet or do not provide useful information to the clinicians. PMID:12704461

  17. Serum markers of intrahepatic cholangiocarcinoma.

    PubMed

    Malaguarnera, Giulia; Paladina, Isabella; Giordano, Maria; Malaguarnera, Michele; Bertino, Gaetano; Berretta, Massimiliano

    2013-01-01

    Cholangiocarcinoma (CCA) is a relatively rare type of primary liver cancer that originates in the bile duct epithelium. It is an aggressive malignancy typified by unresponsiveness to chemotherapy and radiotherapy. Despite advances in radiologic techniques and laboratory diagnostic test, the diagnosis of CCA remains highly challenging. Development in molecular techniques has led to go into the possible use of serum markers in diagnosing of cholangiocarcinoma. This review summarizes the principal characteristics of serum markers of cholangiocarcinoma. The tumour markers used frequently such as Carbohydrate antigen 19-9 (CA 19-9), Carcinogenic Embryonic antigen (CEA), and Cancer Antigen 125 have shown sufficient sensitivity and specificity to detect and monitor CCA. In particular, the combination of these tumour markers seems to increase their efficiency in diagnosing of cholangiocarcinoma. New markers such as Soluble fragment of cytokeratin 19 (CYFRA 21-1) Mucins, Tumour Markers_{2} pyruvate-Kinase (TuM_{2-} PK) and metalloproteinase-7 (MMP-7) have been recently shown to help in the diagnosis of CCA, with in some cases a prognostic value. PMID:23396291

  18. Space-Time Cluster Analysis of Invasive Meningococcal Disease

    PubMed Central

    de Melker, Hester; Spanjaard, Lodewijk; Dankert, Jacob; Nagelkerke, Nico

    2004-01-01

    Clusters are recognized when meningococcal cases of the same phenotypic strain (markers: serogroup, serotype, and subtype) occur in spatial and temporal proximity. The incidence of such clusters was compared to the incidence that would be expected by chance by using space-time nearest-neighbor analysis of 4,887 confirmed invasive meningococcal cases identified in the 9-year surveillance period 1993–2001 in the Netherlands. Clustering beyond chance only occurred among the closest neighboring cases (comparable to secondary cases) and was small (3.1%, 95% confidence interval 2.1%–4.1%). PMID:15498165

  19. Universal Cluster Deposition System

    NASA Astrophysics Data System (ADS)

    Qiang, You; Sun, Zhiguang; Sellmyer, David J.

    2001-03-01

    We have developed a universal cluster deposition system (UCDS), which combines a new kind of sputtering-gas-aggregation (SGA) cluster beam source with two atom beams from magnetron sputtering. A highly intense, very stable beam of nanoclusters (like Co, Fe, Ni, Si, CoSm or CoPt) are produced. A quadrupole and/or a new high transmission infinite range mass selector have been designed for the cluster beam. The size distribution (Δd/d) is between 0.05+/-0.10, measured in situ by TOF. A range of mean cluster size is 2 to 10 nm. Usually the deposition rate is about 5 deg/s. The cluster concentration in the film is adjusted through the ratio of cluster and atomic beam deposition rates, as measured in situ with a rotatable quartz microbalance. The UCDS can be used to prepare coated clusters. After exiting from the cluster source, the clusters can be coated first with an atomic or molecular species in an evaporation chamber, and deposited alone or co-deposited with another material. This system is used to deposit simultaneously or alternately mesoscopic thin films or multilayers, and offers the possibility to control independently the incident cluster size and concentration, and thereby the interaction between clusters and cluster-matrix material which is of interest for fundamental research and industry applications. Magnetic properties of Co cluster-assembled materials will be discussed. * Research supported by NSF, DARPA through ARO, and CMRA

  20. EINSTEIN Cluster Alignments Revisited

    NASA Astrophysics Data System (ADS)

    Chambers, S. W.; Melott, A. L.; Miller, C. J.

    2000-12-01

    We have examined whether the major axes of rich galaxy clusters tend to point (in projection) toward their nearest neighboring cluster. We used the data of Ulmer, McMillan and Kowalski, who used x-ray morphology to define position angles. Our cluster samples, with well measured redshifts and updated positions, were taken from the MX Northern Abell Cluster Survey. The usual Kolmogorov-Smirnov test shows no significant alignment signal for nonrandom angles for all separations less than 100 Mpc/h. Refining the null hypothesis, however, with the Wilcoxon rank-sum test, reveals a high confidence signal for alignment. This confidence is highest when we restrict our sample to small nearest neighbor separations. We conclude that we have identified a more powerful tool for testing cluster-cluster alignments. Moreover, there is a strong signal in the data for alignment, consistent with a picture of hierarchical cluster formation in which matter falls into clusters along large scale filamentary structures.

  1. Matlab Cluster Ensemble Toolbox

    SciTech Connect

    Sapio, Vincent De; Kegelmeyer, Philip

    2009-04-27

    This is a Matlab toolbox for investigating the application of cluster ensembles to data classification, with the objective of improving the accuracy and/or speed of clustering. The toolbox divides the cluster ensemble problem into four areas, providing functionality for each. These include, (1) synthetic data generation, (2) clustering to generate individual data partitions and similarity matrices, (3) consensus function generation and final clustering to generate ensemble data partitioning, and (4) implementation of accuracy metrics. With regard to data generation, Gaussian data of arbitrary dimension can be generated. The kcenters algorithm can then be used to generate individual data partitions by either, (a) subsampling the data and clustering each subsample, or by (b) randomly initializing the algorithm and generating a clustering for each initialization. In either case an overall similarity matrix can be computed using a consensus function operating on the individual similarity matrices. A final clustering can be performed and performance metrics are provided for evaluation purposes.

  2. Automated quantification of nuclear immunohistochemical markers with different complexity.

    PubMed

    López, Carlos; Lejeune, Marylène; Salvadó, María Teresa; Escrivà, Patricia; Bosch, Ramón; Pons, Lluis E; Alvaro, Tomás; Roig, Jordi; Cugat, Xavier; Baucells, Jordi; Jaén, Joaquín

    2008-03-01

    Manual quantification of immunohistochemically stained nuclear markers is still laborious and subjective and the use of computerized systems for digital image analysis have not yet resolved the problems of nuclear clustering. In this study, we designed a new automatic procedure for quantifying various immunohistochemical nuclear markers with variable clustering complexity. This procedure consisted of two combined macros. The first, developed with a commercial software, enabled the analysis of the digital images using color and morphological segmentation including a masking process. All information extracted with this first macro was automatically exported to an Excel datasheet, where a second macro composed of four different algorithms analyzed all the information and calculated the definitive number of positive nuclei for each image. One hundred and eighteen images with different levels of clustering complexity was analyzed and compared with the manual quantification obtained by a trained observer. Statistical analysis indicated a great reliability (intra-class correlation coefficient > 0.950) and no significant differences between the two methods. Bland-Altman plot and Kaplan-Meier curves indicated that the results of both methods were concordant around 90% of analyzed images. In conclusion, this new automated procedure is an objective, faster and reproducible method that has an excellent level of accuracy, even with digital images with a high complexity. PMID:18172664

  3. Assessment of genetic diversity in Brazilian barley using SSR markers

    PubMed Central

    Ferreira, Jéssica Rosset; Pereira, Jorge Fernando; Turchetto, Caroline; Minella, Euclydes; Consoli, Luciano; Delatorre, Carla Andréa

    2016-01-01

    Abstract Barley is a major cereal grown widely and used in several food products, beverage production and animal fodder. Genetic diversity is a key component in breeding programs. We have analyzed the genetic diversity of barley accessions using microsatellite markers. The accessions were composed of wild and domesticated barley representing genotypes from six countries and three breeding programs in Brazil. A total of 280 alleles were detected, 36 unique to Brazilian barley. The marker Bmag120 showed the greatest polymorphism information content (PIC), with the highest mean value found on chromosome three, and the lowest on chromosomes four and six. The wild accessions presented the highest diversity followed by the foreign genotypes. Genetic analysis was performed using Principal Coordinates Analysis, UPGMA clustering, and Bayesian clustering analysis implemented in Structure. All results obtained by the different methods were similar. Loss of genetic diversity has occurred in Brazilian genotypes. The number of alleles detected in genotypes released in 1980s was higher, whereas most of the cultivars released thereafter showed lower PIC and clustered in separate subgroups from the older cultivars. The use of a more diverse panel of genotypes should be considered in order to exploit novel alleles in Brazilian barley breeding programs. PMID:27007902

  4. [Pathophysiology of cluster headache].

    PubMed

    Donnet, Anne

    2015-11-01

    The aetiology of cluster headache is partially unknown. Three areas are involved in the pathogenesis of cluster headache: the trigeminal nociceptive pathways, the autonomic system and the hypothalamus. The cluster headache attack involves activation of the trigeminal autonomic reflex. A dysfunction located in posterior hypothalamic gray matter is probably pivotal in the process. There is a probable association between smoke exposure, a possible genetic predisposition and the development of cluster headache. PMID:26470883

  5. Imaging markers for Alzheimer disease

    PubMed Central

    Bocchetta, Martina; Chételat, Gael; Rabinovici, Gil D.; de Leon, Mony J.; Kaye, Jeffrey; Reiman, Eric M.; Scheltens, Philip; Barkhof, Frederik; Black, Sandra E.; Brooks, David J.; Carrillo, Maria C.; Fox, Nick C.; Herholz, Karl; Nordberg, Agneta; Jack, Clifford R.; Jagust, William J.; Johnson, Keith A.; Rowe, Christopher C.; Sperling, Reisa A.; Thies, William; Wahlund, Lars-Olof; Weiner, Michael W.; Pasqualetti, Patrizio; DeCarli, Charles

    2013-01-01

    Revised diagnostic criteria for Alzheimer disease (AD) acknowledge a key role of imaging biomarkers for early diagnosis. Diagnostic accuracy depends on which marker (i.e., amyloid imaging, 18F-fluorodeoxyglucose [FDG]-PET, SPECT, MRI) as well as how it is measured (“metric”: visual, manual, semiautomated, or automated segmentation/computation). We evaluated diagnostic accuracy of marker vs metric in separating AD from healthy and prognostic accuracy to predict progression in mild cognitive impairment. The outcome measure was positive (negative) likelihood ratio, LR+ (LR−), defined as the ratio between the probability of positive (negative) test outcome in patients and the probability of positive (negative) test outcome in healthy controls. Diagnostic LR+ of markers was between 4.4 and 9.4 and LR− between 0.25 and 0.08, whereas prognostic LR+ and LR− were between 1.7 and 7.5, and 0.50 and 0.11, respectively. Within metrics, LRs varied up to 100-fold: LR+ from approximately 1 to 100; LR− from approximately 1.00 to 0.01. Markers accounted for 11% and 18% of diagnostic and prognostic variance of LR+ and 16% and 24% of LR−. Across all markers, metrics accounted for an equal or larger amount of variance than markers: 13% and 62% of diagnostic and prognostic variance of LR+, and 29% and 18% of LR−. Within markers, the largest proportion of diagnostic LR+ and LR− variability was within 18F-FDG-PET and MRI metrics, respectively. Diagnostic and prognostic accuracy of imaging AD biomarkers is at least as dependent on how the biomarker is measured as on the biomarker itself. Standard operating procedures are key to biomarker use in the clinical routine and drug trials. PMID:23897875

  6. CLUSTERING OF RARE EVENTS

    EPA Science Inventory

    The clustering of cases of a rare disease is considered. The number of events observed for each unit is assumed to have a Poisson distribution, the mean of which depends upon the population size and the cluster membership of that unit. Here a cluster consists of those units that ...

  7. [Tumor markers for colorectal cancer].

    PubMed

    Yamamoto, H; Miyake, Y; Noura, S; Ogawa, M; Yasui, M; Ikenaga, M; Sekimoto, M; Monden, M

    2001-09-01

    CEA and CA19-9 are the two most common tumor markers for colorectal cancer that are currently utilized clinically. The positive rate of CEA is 40-60% and that of CA19-9 is 30-50%. Simultaneous use of the two markers is useful in evaluating the therapeutic effect and monitoring the recurrence of advanced colorectal cancer. Surgical specimens may also provide useful information for the appropriate treatment of patients. Using surgically resected lymph nodes, we examined micrometastasis to assess the spread of the cancer cells and the malignant potential of colorectal cancer. Immunohistochemical analysis using anti-cytokeratin antibody revealed no significant impact of micrometastasis on patient prognosis, while RT-PCR assay using CEA as a genetic marker suggested a positive value in predicting a rapid recurrence. Among various molecular markers, we found that CDC25B phosphatase was a powerful prognostic factor for colorectal cancer. Diagnosis of the existence and malignant potential of cancer cells, together with serum tumor marker levels, may help to construct a more useful system for the better treatment of colorectal cancer. PMID:11579645

  8. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 1 2010-01-01 2010-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  9. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 1 2012-01-01 2012-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  10. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 1 2011-01-01 2011-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  11. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 1 2014-01-01 2014-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  12. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 1 2013-01-01 2013-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  13. Marker imputation in barley association studies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Association mapping requires higher marker density than linkage mapping, potentially leading to more missing marker data and to higher genotyping costs. In human genetics, methods exist to impute missing marker data and whole markers that were typed in a reference panel but not in the experimental d...

  14. Genetic diversity of Cosmos species revealed by RAPD and ISSR markers.

    PubMed

    Rodríguez-Bernal, A; Piña-Escutia, J L; Vázquez-García, L M; Arzate-Fernández, A M

    2013-01-01

    The genus Cosmos is native of America and is constituted by 34 species; 28 of them are endemic of Mexico. The cosmos are used as a nematicide, antimalarial, and antioxidative agent. The aim of this study was to estimate the genetic diversity among 7 cosmos species based on random amplified polymorphic DNA (RAPD) and inter-simple sequences repeats (ISSR) markers. With RAPD markers, the obtained polymorphism was 91.7 % and the genetic diversity was 0.33, whereas these values were 65.6%, and 0.22 from ISSR markers, respectively, indicating the presence of high genetic diversity among the Cosmos species that were analyzed. The unweighted pair group method with arithmetic mean dendrograms that were obtained with both markers were notably similar, revealing 2 clusters and indicating a clear genetic differentiation among the Cosmos species that were assessed. The first cluster comprised the species Cosmos sulphureus, Cosmos pacificus, and Cosmos diversifolius, while the second cluster included the species Cosmos purpureus, Cosmos crithmifolius, Cosmos bipinnatus, and Cosmos parviflorus. Besides this, the Cosmos species were clustered according to their collection sites. The Mantel test corroborates the correlation between the genetic distance and the geographic altitude of each Cosmos species. The results suggest that it is necessary to preserve the Cosmos species in their natural habitat in addition to the germoplasm collection for ex situ conservation. PMID:24338421

  15. A new clustering strategy

    NASA Astrophysics Data System (ADS)

    Feng, Jian-xin; Tang, Jia-fu; Wang, Guang-xing

    2007-04-01

    On the basis of the analysis of clustering algorithm that had been proposed for MANET, a novel clustering strategy was proposed in this paper. With the trust defined by statistical hypothesis in probability theory and the cluster head selected by node trust and node mobility, this strategy can realize the function of the malicious nodes detection which was neglected by other clustering algorithms and overcome the deficiency of being incapable of implementing the relative mobility metric of corresponding nodes in the MOBIC algorithm caused by the fact that the receiving power of two consecutive HELLO packet cannot be measured. It's an effective solution to cluster MANET securely.

  16. Tumor-derived circulating endothelial cell clusters in colorectal cancer.

    PubMed

    Cima, Igor; Kong, Say Li; Sengupta, Debarka; Tan, Iain B; Phyo, Wai Min; Lee, Daniel; Hu, Min; Iliescu, Ciprian; Alexander, Irina; Goh, Wei Lin; Rahmani, Mehran; Suhaimi, Nur-Afidah Mohamed; Vo, Jess H; Tai, Joyce A; Tan, Joanna H; Chua, Clarinda; Ten, Rachel; Lim, Wan Jun; Chew, Min Hoe; Hauser, Charlotte A E; van Dam, Rob M; Lim, Wei-Yen; Prabhakar, Shyam; Lim, Bing; Koh, Poh Koon; Robson, Paul; Ying, Jackie Y; Hillmer, Axel M; Tan, Min-Han

    2016-06-29

    Clusters of tumor cells are often observed in the blood of cancer patients. These structures have been described as malignant entities for more than 50 years, although their comprehensive characterization is lacking. Contrary to current consensus, we demonstrate that a discrete population of circulating cell clusters isolated from the blood of colorectal cancer patients are not cancerous but consist of tumor-derived endothelial cells. These clusters express both epithelial and mesenchymal markers, consistent with previous reports on circulating tumor cell (CTC) phenotyping. However, unlike CTCs, they do not mirror the genetic variations of matched tumors. Transcriptomic analysis of single clusters revealed that these structures exhibit an endothelial phenotype and can be traced back to the tumor endothelium. Further results show that tumor-derived endothelial clusters do not form by coagulation or by outgrowth of single circulating endothelial cells, supporting a direct release of clusters from the tumor vasculature. The isolation and enumeration of these benign clusters distinguished healthy volunteers from treatment-naïve as well as pathological early-stage (≤IIA) colorectal cancer patients with high accuracy, suggesting that tumor-derived circulating endothelial cell clusters could be used as a means of noninvasive screening for colorectal cancer. In contrast to CTCs, tumor-derived endothelial cell clusters may also provide important information about the underlying tumor vasculature at the time of diagnosis, during treatment, and throughout the course of the disease. PMID:27358499

  17. Markers of bile duct tumors

    PubMed Central

    Malaguarnera, Giulia; Giordano, Maria; Paladina, Isabella; Rando, Alessandra; Uccello, Mario; Basile, Francesco; Biondi, Antonio; Carnazzo, Santo; Alessandria, Innocenza; Mazzarino, Clorinda

    2011-01-01

    Biliary tract carcinomas are relatively rare, representing less than 1% of cancers. However, their incidence has increased in Japan and in industrialized countries like the USA. Biliary tract tumors have a poor prognosis and a high mortality rate because they are usually detected late in the course of the disease; therapeutic treatment options are often limited and of minimal utility. Recent studies have shown the importance of serum and molecular markers in the diagnosis and follow up of biliary tract tumors. This review aims to introduce the main features of the most important serum and molecular markers of biliary tree tumors. Some considerable tumor markers are cancer antigen 125, carbohydrate antigen 19-9, carcinoembryonic antigen, chromogranin A, mucin 1, mucin 5, alpha-fetoprotein, claudins and cytokeratins. PMID:21528090

  18. Unconventional methods for clustering

    NASA Astrophysics Data System (ADS)

    Kotyrba, Martin

    2016-06-01

    Cluster analysis or clustering is a task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more similar (in some sense or another) to each other than to those in other groups (clusters). It is the main task of exploratory data mining and a common technique for statistical data analysis used in many fields, including machine learning, pattern recognition, image analysis, information retrieval, and bioinformatics. The topic of this paper is one of the modern methods of clustering namely SOM (Self Organising Map). The paper describes the theory needed to understand the principle of clustering and descriptions of algorithm used with clustering in our experiments.

  19. Developing genome-wide microsatellite markers of bamboo and their applications on molecular marker assisted taxonomy for accessions in the genus Phyllostachys

    PubMed Central

    Zhao, Hansheng; Yang, Li; Peng, Zhenhua; Sun, Huayu; Yue, Xianghua; Lou, Yongfeng; Dong, Lili; Wang, Lili; Gao, Zhimin

    2015-01-01

    Morphology-based taxonomy via exiguously reproductive organ has severely limitation on bamboo taxonomy, mainly owing to infrequent and unpredictable flowering events of bamboo. Here, we present the first genome-wide analysis and application of microsatellites based on the genome of moso bamboo (Phyllostachys edulis) to assist bamboo taxonomy. Of identified 127,593 microsatellite repeat-motifs, the primers of 1,451 microsatellites were designed and 1,098 markers were physically mapped on the genome of moso bamboo. A total of 917 markers were successfully validated in 9 accessions with ~39.8% polymorphic potential. Retrieved from validated microsatellite markers, 23 markers were selected for polymorphic analysis among 78 accessions and 64 alleles were detected with an average of 2.78 alleles per primers. The cluster result indicated the majority of the accessions were consistent with their current taxonomic classification, confirming the suitability and effectiveness of the developed microsatellite markers. The variations of microsatellite marker in different species were confirmed by sequencing and in silico comparative genome mapping were investigated. Lastly, a bamboo microsatellites database (http://www.bamboogdb.org/ssr) was implemented to browse and search large information of bamboo microsatellites. Consequently, our results of microsatellite marker development are valuable for assisting bamboo taxonomy and investigating genomic studies in bamboo and related grass species. PMID:25620112

  20. Modeling Clustered Data with Very Few Clusters.

    PubMed

    McNeish, Daniel; Stapleton, Laura M

    2016-01-01

    Small-sample inference with clustered data has received increased attention recently in the methodological literature, with several simulation studies being presented on the small-sample behavior of many methods. However, nearly all previous studies focus on a single class of methods (e.g., only multilevel models, only corrections to sandwich estimators), and the differential performance of various methods that can be implemented to accommodate clustered data with very few clusters is largely unknown, potentially due to the rigid disciplinary preferences. Furthermore, a majority of these studies focus on scenarios with 15 or more clusters and feature unrealistically simple data-generation models with very few predictors. This article, motivated by an applied educational psychology cluster randomized trial, presents a simulation study that simultaneously addresses the extreme small sample and differential performance (estimation bias, Type I error rates, and relative power) of 12 methods to account for clustered data with a model that features a more realistic number of predictors. The motivating data are then modeled with each method, and results are compared. Results show that generalized estimating equations perform poorly; the choice of Bayesian prior distributions affects performance; and fixed effect models perform quite well. Limitations and implications for applications are also discussed. PMID:27269278

  1. Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers.

    PubMed

    Singh, Dharmendra; Singh, Chandan Kumar; Tomar, Ram Sewak Singh; Taunk, Jyoti; Singh, Ranjeet; Maurya, Sadhana; Chaturvedi, Ashish Kumar; Pal, Madan; Singh, Rajendra; Dubey, Sarawan Kumar

    2016-01-01

    The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8-27.6% and 9.5-23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2) and wild (ILWL-314 and ILWL-436) accessions showed 10.5-26.5% and 7.5%-15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48-49% and 30.5-45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321-0.854 and 0.299-0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05) different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil. PMID:26808306

  2. Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers

    PubMed Central

    Singh, Dharmendra; Singh, Chandan Kumar; Tomar, Ram Sewak Singh; Taunk, Jyoti; Singh, Ranjeet; Maurya, Sadhana; Chaturvedi, Ashish Kumar; Pal, Madan; Singh, Rajendra; Dubey, Sarawan Kumar

    2016-01-01

    The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8–27.6% and 9.5–23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2) and wild (ILWL-314 and ILWL-436) accessions showed 10.5–26.5% and 7.5%–15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48–49% and 30.5–45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321–0.854 and 0.299–0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05) different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil. PMID:26808306

  3. Association of Agronomic Traits with SNP Markers in Durum Wheat (Triticum turgidum L. durum (Desf.))

    PubMed Central

    Hu, Xin; Ren, Jing; Ren, Xifeng; Huang, Sisi; Sabiel, Salih A. I.; Luo, Mingcheng; Nevo, Eviatar; Fu, Chunjie; Peng, Junhua; Sun, Dongfa

    2015-01-01

    Association mapping is a powerful approach to detect associations between traits of interest and genetic markers based on linkage disequilibrium (LD) in molecular plant breeding. In this study, 150 accessions of worldwide originated durum wheat germplasm (Triticum turgidum spp. durum) were genotyped using 1,366 SNP markers. The extent of LD on each chromosome was evaluated. Association of single nucleotide polymorphisms (SNP) markers with ten agronomic traits measured in four consecutive years was analyzed under a mix linear model (MLM). Two hundred and one significant association pairs were detected in the four years. Several markers were associated with one trait, and also some markers were associated with multiple traits. Some of the associated markers were in agreement with previous quantitative trait loci (QTL) analyses. The function and homology analyses of the corresponding ESTs of some SNP markers could explain many of the associations for plant height, length of main spike, number of spikelets on main spike, grain number per plant, and 1000-grain weight, etc. The SNP associations for the observed traits are generally clustered in specific chromosome regions of the wheat genome, mainly in 2A, 5A, 6A, 7A, 1B, and 6B chromosomes. This study demonstrates that association mapping can complement and enhance previous QTL analyses and provide additional information for marker-assisted selection. PMID:26110423

  4. Toward a marker-dense meiotic map of the potato genome: lessons from linkage group I.

    PubMed Central

    Isidore, Edwige; van Os, Hans; Andrzejewski, Sandra; Bakker, Jaap; Barrena, Imanol; Bryan, Glenn J; Caromel, Bernard; van Eck, Herman; Ghareeb, Bilal; de Jong, Walter; van Koert, Paul; Lefebvre, Véronique; Milbourne, Dan; Ritter, Enrique; van der Voort, Jeroen Rouppe; Rousselle-Bourgeois, Françoise; van Vliet, Joke; Waugh, Robbie

    2003-01-01

    Segregation data were obtained for 1260 potato linkage group I-specific AFLP loci from a heterozygous diploid potato population. Analytical tools that identified potential typing errors and/or inconsistencies in the data and that assembled cosegregating markers into bins were applied. Bins contain multiple-marker data sets with an identical segregation pattern, which is defined as the bin signature. The bin signatures were used to construct a skeleton bin map that was based solely on observed recombination events. Markers that did not match any of the bin signatures exactly (and that were excluded from the calculation of the skeleton bin map) were placed on the map by maximum likelihood. The resulting maternal and paternal maps consisted of 95 and 101 bins, respectively. Markers derived from EcoRI/MseI, PstI/MseI, and SacI/MseI primer combinations showed different genetic distributions. Approximately three-fourths of the markers placed into a bin were considered to fit well on the basis of an estimated residual "error rate" of 0-3%. However, twice as many PstI-based markers fit badly, suggesting that parental PstI-site methylation patterns had changed in the population. Recombination frequencies were highly variable across the map. Inert, presumably centromeric, regions caused extensive marker clustering while recombination hotspots (or regions identical by descent) resulted in empty bins, despite the level of marker saturation. PMID:14704190

  5. Diversity Array Technology Markers: Genetic Diversity Analyses and Linkage Map Construction in Rapeseed (Brassica napus L.)

    PubMed Central

    Raman, Harsh; Raman, Rosy; Nelson, Matthew N.; Aslam, M.N.; Rajasekaran, Ravikesavan; Wratten, Neil; Cowling, Wallace A.; Kilian, A.; Sharpe, Andrew G.; Schondelmaier, Joerg

    2012-01-01

    We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified and used to assess molecular diversity among 89 accessions of B. napus, B. rapa, B. juncea, and B. carinata collected from different parts of the world. Hierarchical cluster and principal component analyses based on genetic distance matrices identified distinct populations clustering mainly according to their origin/pedigrees. DArT markers were also mapped in a new doubled haploid population comprising 131 lines from a cross between spring rapeseed lines ‘Lynx-037DH’ and ‘Monty-028DH’. Linkage groups were assigned on the basis of previously mapped simple sequence repeat (SSRs), intron polymorphism (IP), and gene-based markers. The map consisted of 437 DArT, 135 SSR, 6 IP, and 6 gene-based markers and spanned 2288 cM. Our results demonstrate that DArT markers are suitable for genetic diversity analysis and linkage map construction in rapeseed. PMID:22193366

  6. Diversity array technology markers: genetic diversity analyses and linkage map construction in rapeseed (Brassica napus L.).

    PubMed

    Raman, Harsh; Raman, Rosy; Nelson, Matthew N; Aslam, M N; Rajasekaran, Ravikesavan; Wratten, Neil; Cowling, Wallace A; Kilian, A; Sharpe, Andrew G; Schondelmaier, Joerg

    2012-01-01

    We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified and used to assess molecular diversity among 89 accessions of B. napus, B. rapa, B. juncea, and B. carinata collected from different parts of the world. Hierarchical cluster and principal component analyses based on genetic distance matrices identified distinct populations clustering mainly according to their origin/pedigrees. DArT markers were also mapped in a new doubled haploid population comprising 131 lines from a cross between spring rapeseed lines 'Lynx-037DH' and 'Monty-028DH'. Linkage groups were assigned on the basis of previously mapped simple sequence repeat (SSRs), intron polymorphism (IP), and gene-based markers. The map consisted of 437 DArT, 135 SSR, 6 IP, and 6 gene-based markers and spanned 2288 cM. Our results demonstrate that DArT markers are suitable for genetic diversity analysis and linkage map construction in rapeseed. PMID:22193366

  7. [Clustering of simple obesity].

    PubMed

    Yoshida, K; Matsuda, H; Kurita, M; Umetada, Y

    1988-05-01

    An attempt was made to classify persons with simple obesity from the viewpoint of health education. Subjects of the study were 1,278 male workers in a financing company who underwent health examination. At the time of health examinations, questionnaire survey concerning their life styles was carried out on all the subjects. The obese group consisted of 127 subjects whose obesity indices were over 15% and the control group consisted of 342 subjects whose obesity indices ranged from -5 to 5%. Subjects in the obese group were classified into four clusters based on cluster analysis using five life-style parameters; that is, frequency of taking breakfast, frequency of taking staple food, drinking habits, smoking habits, and frequency of exercise. The first cluster (N = 10) included inactive persons, the second cluster (N = 46) non smokers, the third cluster (N = 39) smokers and heavy drinkers, and the fourth cluster (N = 32) smokers and non-drinkers. Comparison of the four clusters of obese persons with the control group revealed the following findings: 1) All the four clusters had significantly high frequencies of abnormal values of triglyceride (TG) and fasting blood sugar (FBS). 2) The first cluster had significantly high frequencies of abnormal values of glutamic oxalacetic transaminase (GOT) and glutamic pyruvic transaminase (GPT). 3) The second cluster had significantly high frequencies of abnormal values of systolic and diastolic blood pressure, total cholesterol, TG, FBS, uric acid, GOT, GPT and gamma glutamyl transferase (GGT).(ABSTRACT TRUNCATED AT 250 WORDS) PMID:3172544

  8. Oxidative Stress Markers in Sputum

    PubMed Central

    Antus, Balazs

    2016-01-01

    Although oxidative stress is thought to play a pivotal role in the pathogenesis of inflammatory airway diseases, its assessment in clinical practice remains elusive. In recent years, it has been conceptualized that oxidative stress markers in sputum should be employed to monitor oxidative processes in patients with asthma, chronic obstructive pulmonary disease (COPD), or cystic fibrosis (CF). In this review, the use of sputum-based oxidative markers was explored and potential clinical applications were considered. Among lipid peroxidation-derived products, 8-isoprostane and malondialdehyde have been the most frequently investigated, while nitrosothiols and nitrotyrosine may serve as markers of nitrosative stress. Several studies have showed higher levels of these products in patients with asthma, COPD, or CF compared to healthy subjects. Marker concentrations could be further increased during exacerbations and decreased along with recovery of these diseases. Measurement of oxidized guanine species and antioxidant enzymes in the sputum could be other approaches for assessing oxidative stress in pulmonary patients. Collectively, even though there are promising findings in this field, further clinical studies using more established detection techniques are needed to clearly show the benefit of these measurements in the follow-up of patients with inflammatory airway diseases. PMID:26885248

  9. Electron: Cluster interactions

    SciTech Connect

    Scheidemann, A.A.; Kresin, V.V.; Knight, W.D.

    1994-02-01

    Beam depletion spectroscopy has been used to measure absolute total inelastic electron-sodium cluster collision cross sections in the energy range from E {approximately} 0.1 to E {approximately} 6 eV. The investigation focused on the closed shell clusters Na{sub 8}, Na{sub 20}, Na{sub 40}. The measured cross sections show an increase for the lowest collision energies where electron attachment is the primary scattering channel. The electron attachment cross section can be understood in terms of Langevin scattering, connecting this measurement with the polarizability of the cluster. For energies above the dissociation energy the measured electron-cluster cross section is energy independent, thus defining an electron-cluster interaction range. This interaction range increases with the cluster size.

  10. Information-based clustering

    PubMed Central

    Slonim, Noam; Atwal, Gurinder Singh; Tkačik, Gašper; Bialek, William

    2005-01-01

    In an age of increasingly large data sets, investigators in many different disciplines have turned to clustering as a tool for data analysis and exploration. Existing clustering methods, however, typically depend on several nontrivial assumptions about the structure of data. Here, we reformulate the clustering problem from an information theoretic perspective that avoids many of these assumptions. In particular, our formulation obviates the need for defining a cluster “prototype,” does not require an a priori similarity metric, is invariant to changes in the representation of the data, and naturally captures nonlinear relations. We apply this approach to different domains and find that it consistently produces clusters that are more coherent than those extracted by existing algorithms. Finally, our approach provides a way of clustering based on collective notions of similarity rather than the traditional pairwise measures. PMID:16352721

  11. An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

    PubMed Central

    2011-01-01

    Background Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety of sources and published cDNA markers into a composite P. taeda genetic map constructed from two reference mapping pedigrees. A dense genetic map that incorporates SSR loci will benefit complete pine genome sequencing, pine population genetics studies, and pine breeding programs. Careful marker annotation using a variety of references further enhances the utility of the integrated SSR map. Results The updated P. taeda genetic map, with an estimated genome coverage of 1,515 cM(Kosambi) across 12 linkage groups, incorporated 170 new SSR markers and 290 previously reported SSR, RFLP, and ESTP markers. The average marker interval was 3.1 cM. Of 233 mapped SSR loci, 84 were from cDNA-derived sequences (EST-SSRs) and 149 were from non-transcribed genomic sequences (genomic-SSRs). Of all 311 mapped cDNA-derived markers, 77% were associated with NCBI Pta UniGene clusters, 67% with RefSeq proteins, and 62% with functional Gene Ontology (GO) terms. Duplicate (i.e., redundant accessory) and paralogous markers were tentatively identified by evaluating marker sequences by their UniGene cluster IDs, clone IDs, and relative map positions. The average gene diversity, He, among polymorphic SSR loci, including those that were not mapped, was 0.43 for 94 EST-SSRs and 0.72 for 83 genomic-SSRs. The genetic map can be viewed and queried at http://www.conifergdb.org/pinemap. Conclusions Many polymorphic and genetically mapped SSR markers are now available for use in P. taeda population genetics, studies of adaptive traits, and various germplasm management applications. Annotating mapped genes with Uni

  12. Mini-clusters

    NASA Technical Reports Server (NTRS)

    Chinellato, J. A.; Dobrigkeit, C.; Bellandifilho, J.; Lattes, C. M. G.; Menon, M. J.; Navia, C. E.; Pamilaju, A.; Sawayanagi, K.; Shibuya, E. H.; Turtelli, A., Jr.

    1985-01-01

    Experimental results of mini-clusters observed in Chacaltaya emulsion chamber no.19 are summarized. The study was made on 54 single core shower upper and 91 shower clusters of E(gamma) 10 TeV from 30 families which are visible energy greater than 80 TeV and penetrate through both upper and lower detectors of the two-story chamber. The association of hadrons in mini-cluster is made clear from their penetrative nature and microscopic observation of shower continuation in lower chamber. Small P sub t (gamma) of hadrons in mini-clusters remained in puzzle.

  13. Management of cluster headache.

    PubMed

    Tfelt-Hansen, Peer C; Jensen, Rigmor H

    2012-07-01

    The prevalence of cluster headache is 0.1% and cluster headache is often not diagnosed or misdiagnosed as migraine or sinusitis. In cluster headache there is often a considerable diagnostic delay - an average of 7 years in a population-based survey. Cluster headache is characterized by very severe or severe orbital or periorbital pain with a duration of 15-180 minutes. The cluster headache attacks are accompanied by characteristic associated unilateral symptoms such as tearing, nasal congestion and/or rhinorrhoea, eyelid oedema, miosis and/or ptosis. In addition, there is a sense of restlessness and agitation. Patients may have up to eight attacks per day. Episodic cluster headache (ECH) occurs in clusters of weeks to months duration, whereas chronic cluster headache (CCH) attacks occur for more than 1 year without remissions. Management of cluster headache is divided into acute attack treatment and prophylactic treatment. In ECH and CCH the attacks can be treated with oxygen (12 L/min) or subcutaneous sumatriptan 6 mg. For both oxygen and sumatriptan there are two randomized, placebo-controlled trials demonstrating efficacy. In both ECH and CCH, verapamil is the prophylactic drug of choice. Verapamil 360 mg/day was found to be superior to placebo in one clinical trial. In clinical practice, daily doses of 480-720 mg are mostly used. Thus, the dose of verapamil used in cluster headache treatment may be double the dose used in cardiology, and with the higher doses the PR interval should be checked with an ECG. At the start of a cluster, transitional preventive treatment such as corticosteroids or greater occipital nerve blockade can be given. In CCH and in long-standing clusters of ECH, lithium, methysergide, topiramate, valproic acid and ergotamine tartrate can be used as add-on prophylactic treatment. In drug-resistant CCH, neuromodulation with either occipital nerve stimulation or deep brain stimulation of the hypothalamus is an alternative treatment strategy

  14. The youngest globular clusters

    NASA Astrophysics Data System (ADS)

    Beck, Sara

    2015-11-01

    It is likely that all stars are born in clusters, but most clusters are not bound and disperse. None of the many protoclusters in our Galaxy are likely to develop into long-lived bound clusters. The super star clusters (SSCs) seen in starburst galaxies are more massive and compact and have better chances of survival. The birth and early development of SSCs takes place deep in molecular clouds, and during this crucial stage the embedded clusters are invisible to optical or UV observations but are studied via the radio-infrared supernebulae (RISN) they excite. We review observations of embedded clusters and identify RISN within 10 Mpc whose exciting clusters have ≈ 106 M⊙ or more in volumes of a few pc3 and which are likely to not only survive as bound clusters, but to evolve into objects as massive and compact as Galactic globulars. These clusters are distinguished by very high star formation efficiency η, at least a factor of 10 higher than the few percent seen in the Galaxy, probably due to the violent disturbances their host galaxies have undergone. We review recent observations of the kinematics of the ionized gas in RISN showing outflows through low-density channels in the ambient molecular cloud; this may protect the cloud from feedback by the embedded H II region.

  15. Marker-Based Hierarchical Segmentation and Classification Approach for Hyperspectral Imagery

    NASA Technical Reports Server (NTRS)

    Tarabalka, Yuliya; Tilton, James C.; Benediktsson, Jon Atli; Chanussot, Jocelyn

    2011-01-01

    The Hierarchical SEGmentation (HSEG) algorithm, which is a combination of hierarchical step-wise optimization and spectral clustering, has given good performances for hyperspectral image analysis. This technique produces at its output a hierarchical set of image segmentations. The automated selection of a single segmentation level is often necessary. We propose and investigate the use of automatically selected markers for this purpose. In this paper, a novel Marker-based HSEG (M-HSEG) method for spectral-spatial classification of hyperspectral images is proposed. First, pixelwise classification is performed and the most reliably classified pixels are selected as markers, with the corresponding class labels. Then, a novel constrained marker-based HSEG algorithm is applied, resulting in a spectral-spatial classification map. The experimental results show that the proposed approach yields accurate segmentation and classification maps, and thus is attractive for hyperspectral image analysis.

  16. NETosis markers: Quest for specific, objective, and quantitative markers.

    PubMed

    Masuda, Sakiko; Nakazawa, Daigo; Shida, Haruki; Miyoshi, Arina; Kusunoki, Yoshihiro; Tomaru, Utano; Ishizu, Akihiro

    2016-08-01

    More than 10years have passed since the discovery of neutrophil extracellular traps (NETs) in 2004. NETs are extracellular web-like DNA decorated with antimicrobial proteins, which are released from activated neutrophils. The state of neutrophils with NET formation is called NETosis. It has been realized that NETosis includes suicidal NETosis and vital NETosis. The former state means cell death of neutrophils, whereas the latter state preserves living neutrophilic functions. Although both suicidal and vital NETosis play essential roles in elimination of microorganisms, excessive formation of NETs, especially the ones derived from suicidal NETosis, can harm the hosts. Therefore, the discovery of NETosis markers and development of evaluation methods are important. In this review, we compare the methods for evaluating NETosis, including immunocytological and immunohistological detection of co-localized neutrophil-derived proteins and extracellular DNA, and citrullinated histones, detection of NET remnants in fluid samples, and flow cytometric detection of cell-appendant NET components, with focus on the specificity, objectivity, and quantitativity. Since the gold standard marker of NETosis or method of NET detection has not been established yet, researchers should choose the most appropriate marker or method in each situation based on the knowledge of the respective virtues and faults. PMID:27259468

  17. Clustering versus non-clustering phase synchronizations.

    PubMed

    Liu, Shuai; Zhan, Meng

    2014-03-01

    Clustering phase synchronization (CPS) is a common scenario to the global phase synchronization of coupled dynamical systems. In this work, a novel scenario, the non-clustering phase synchronization (NPS), is reported. It is found that coupled systems do not transit to the global synchronization until a certain sufficiently large coupling is attained, and there is no clustering prior to the global synchronization. To reveal the relationship between CPS and NPS, we further analyze the noise effect on coupled phase oscillators and find that the coupled oscillator system can change from CPS to NPS with the increase of noise intensity or system disorder. These findings are expected to shed light on the mechanism of various intriguing self-organized behaviors in coupled systems. PMID:24697366

  18. Clustering versus non-clustering phase synchronizations

    SciTech Connect

    Liu, Shuai; Zhan, Meng

    2014-03-15

    Clustering phase synchronization (CPS) is a common scenario to the global phase synchronization of coupled dynamical systems. In this work, a novel scenario, the non-clustering phase synchronization (NPS), is reported. It is found that coupled systems do not transit to the global synchronization until a certain sufficiently large coupling is attained, and there is no clustering prior to the global synchronization. To reveal the relationship between CPS and NPS, we further analyze the noise effect on coupled phase oscillators and find that the coupled oscillator system can change from CPS to NPS with the increase of noise intensity or system disorder. These findings are expected to shed light on the mechanism of various intriguing self-organized behaviors in coupled systems.

  19. A nonparametric clustering technique which estimates the number of clusters

    NASA Technical Reports Server (NTRS)

    Ramey, D. B.

    1983-01-01

    In applications of cluster analysis, one usually needs to determine the number of clusters, K, and the assignment of observations to each cluster. A clustering technique based on recursive application of a multivariate test of bimodality which automatically estimates both K and the cluster assignments is presented.

  20. Reactive accelerated cluster erosion (RACE) by ionized cluster beams

    NASA Astrophysics Data System (ADS)

    Gspann, Jürgen

    1996-05-01

    Beams of ionized clusters accelerated up to about 120 keV kinetic energy per cluster are used for cluster impact lithography. Chemical reactions of clusters of CO 2, or of SF 6, respectively, are found to assist the physical erosion by hypervelocity cluster impacts in yielding volatile products. Natural diamond, silicon and Pyrex glass have been microstructured showing very smooth eroded surfaces.

  1. Performance of a lateral pelvic cluster technical system in evaluating running kinematics.

    PubMed

    Liew, Bernard X W; Morris, Susan; Robinson, Mark A; Netto, Kevin

    2016-06-14

    Valid measurement of pelvic and hip angles during posterior load carriage gait task requires placement of pelvic markers which will not be occluded or physically displaced by the load. One solution is the use of pure lateral pelvic clusters to track the pelvis segment. However, the validity of this method has not been compared against pelvic marker systems recommended by the International Society of Biomechanics (ISB) during high impact tasks, such as running. The purpose of this study was to validate the lateral tracking pelvic clusters against the ISB pelvis during running. Six participants performed overground running at a self-selected running speed with shoes. Three dimensional motion capture and synchronised in-ground force plates were used to determine lower limb joint angles and gait events respectively. Two biomechanical models were used to derive pelvic segment and hip joint angles. The ISB pelvis used the anterior and posterior iliac spines as anatomical and tracking markers, whilst the other model used lateral pelvic clusters as tracking markers. The between participant averaged coefficient of multiple correlation suggested good to excellent agreement between the angle waveforms generated from the two marker protocols. In addition, both marker protocols had similar sensitivity in detecting three dimensional pelvic and hip joint angles during the stance phase. This study suggests that in the event posterior load carriage is involved in running gait, pelvic and hip kinematics can be measured by the use of lateral pelvic clusters. PMID:27207384

  2. Root trait diversity, molecular marker diversity, and trait-marker associations in a core collection of Lupinus angustifolius.

    PubMed

    Chen, Yinglong; Shan, Fucheng; Nelson, Matthew N; Siddique, Kadambot Hm; Rengel, Zed

    2016-06-01

    Narrow-leafed lupin (Lupinus angustifolius L.) is the predominant grain legume crop in southern Australia, contributing half of the total grain legume production of Australia. Its yield in Australia is hampered by a range of subsoil constraints. The adaptation of lupin genotypes to subsoil constraints may be improved by selecting for optimal root traits from new and exotic germplasm sources. We assessed root trait diversity and genetic diversity of a core collection of narrow-leafed lupin (111 accessions) using 191 Diversity Arrays Technology (DArT) markers. The genetic relationship among accessions was determined using the admixture model in STRUCTURE. Thirty-eight root-associated traits were characterized, with 21 having coefficient of variation values >0.5. Principal coordinate analysis and cluster analysis of the DArT markers revealed broad diversity among the accessions. An ad hoc statistics calculation resulted in 10 distinct populations with significant differences among and within them (P < 0.001). The mixed linear model test in TASSEL showed a significant association between all root traits and some DArT markers, with the numbers of markers associated with an individual trait ranging from 2 to 13. The percentage of phenotypic variation explained by any one marker ranged from 6.4 to 21.8%, with 15 associations explaining >10% of phenotypic variation. The genetic variation values ranged from 0 to 7994, with 23 associations having values >240. Root traits such as deeper roots and lateral root proliferation at depth would be useful for this species for improved adaptation to drier soil conditions. This study offers opportunities for discovering useful root traits that can be used to increase the yield of Australian cultivars across variable environmental conditions. PMID:27049020

  3. Root trait diversity, molecular marker diversity, and trait-marker associations in a core collection of Lupinus angustifolius

    PubMed Central

    Chen, Yinglong; Shan, Fucheng; Nelson, Matthew N; Siddique, Kadambot HM; Rengel, Zed

    2016-01-01

    Narrow-leafed lupin (Lupinus angustifolius L.) is the predominant grain legume crop in southern Australia, contributing half of the total grain legume production of Australia. Its yield in Australia is hampered by a range of subsoil constraints. The adaptation of lupin genotypes to subsoil constraints may be improved by selecting for optimal root traits from new and exotic germplasm sources. We assessed root trait diversity and genetic diversity of a core collection of narrow-leafed lupin (111 accessions) using 191 Diversity Arrays Technology (DArT) markers. The genetic relationship among accessions was determined using the admixture model in STRUCTURE. Thirty-eight root-associated traits were characterized, with 21 having coefficient of variation values >0.5. Principal coordinate analysis and cluster analysis of the DArT markers revealed broad diversity among the accessions. An ad hoc statistics calculation resulted in 10 distinct populations with significant differences among and within them (P < 0.001). The mixed linear model test in TASSEL showed a significant association between all root traits and some DArT markers, with the numbers of markers associated with an individual trait ranging from 2 to 13. The percentage of phenotypic variation explained by any one marker ranged from 6.4 to 21.8%, with 15 associations explaining >10% of phenotypic variation. The genetic variation values ranged from 0 to 7994, with 23 associations having values >240. Root traits such as deeper roots and lateral root proliferation at depth would be useful for this species for improved adaptation to drier soil conditions. This study offers opportunities for discovering useful root traits that can be used to increase the yield of Australian cultivars across variable environmental conditions. PMID:27049020

  4. Susceptibility to Exercise-Induced Muscle Damage: a Cluster Analysis with a Large Sample.

    PubMed

    Damas, F; Nosaka, K; Libardi, C A; Chen, T C; Ugrinowitsch, C

    2016-07-01

    We investigated the responses of indirect markers of exercise-induced muscle damage (EIMD) among a large number of young men (N=286) stratified in clusters based on the largest decrease in maximal voluntary contraction torque (MVC) after an unaccustomed maximal eccentric exercise bout of the elbow flexors. Changes in MVC, muscle soreness (SOR), creatine kinase (CK) activity, range of motion (ROM) and upper-arm circumference (CIR) before and for several days after exercise were compared between 3 clusters established based on MVC decrease (low, moderate, and high responders; LR, MR and HR). Participants were allocated to LR (n=61), MR (n=152) and HR (n=73) clusters, which depicted significantly different cluster centers of 82%, 61% and 42% of baseline MVC, respectively. Once stratified by MVC decrease, all muscle damage markers were significantly different between clusters following the same pattern: small changes for LR, larger changes for MR, and the largest changes for HR. Stratification of individuals based on the magnitude of MVC decrease post-exercise greatly increases the precision in estimating changes in EIMD by proxy markers such as SOR, CK activity, ROM and CIR. This indicates that the most commonly used markers are valid and MVC orchestrates their responses, consolidating the role of MVC as the best EIMD indirect marker. PMID:27116346

  5. A and MdMYB1 allele-specific markers controlling apple (Malus x domestica Borkh.) skin color and suitability for marker-assisted selection.

    PubMed

    Zhang, X J; Wang, L X; Chen, X X; Liu, Y L; Meng, R; Wang, Y J; Zhao, Z Y

    2014-01-01

    Pre-selection for fruit skin color at the seedling stage would be highly advantageous, with marker-assisted selection offering a potential method for apple pre-selection. A and MdMYB1 alleles are allele-specific DNA markers that are potentially associated with apple skin color, and co-segregate with the Rf and Rni loci, respectively. Here, we assessed the potential application of these 2 alleles for marker-assisted breeding across 30 diverse cultivars and 2 apple seedling progenies. The red skin color phenotype was usually associated with the MdMYB1-1 allele and A(1) allele, respectively, while the 2 molecular markers provided approximately 91% predictability in the 'Fuji' x 'Cripps Pink' and 'Fuji' x 'Gala' progenies. The results obtained from the 30 cultivars and 2 progenies were consistent for the 2 molecular markers. Hence, the results supported that Rf and Rni could be located in a gene cluster, or even correspond to alleles of the same gene. Our results are consistent with the hypothesis that red/yellow dimorphism is controlled by a monogenic system, with the presence of the red anthocyanin pigmentation being dominant. In addition, our results supported that the practical utilization of the 2 function markers to efficiently and accurately select red-skinned apple cultivars in apple scion breeding programs. PMID:25366802

  6. Apoptotic markers in protozoan parasites

    PubMed Central

    2010-01-01

    The execution of the apoptotic death program in metazoans is characterized by a sequence of morphological and biochemical changes that include cell shrinkage, presentation of phosphatidylserine at the cell surface, mitochondrial alterations, chromatin condensation, nuclear fragmentation, membrane blebbing and the formation of apoptotic bodies. Methodologies for measuring apoptosis are based on these markers. Except for membrane blebbing and formation of apoptotic bodies, all other events have been observed in most protozoan parasites undergoing cell death. However, while techniques exist to detect these markers, they are often optimised for metazoan cells and therefore may not pick up subtle differences between the events occurring in unicellular organisms and multi-cellular organisms. In this review we discuss the markers most frequently used to analyze cell death in protozoan parasites, paying special attention to changes in cell morphology, mitochondrial activity, chromatin structure and plasma membrane structure/permeability. Regarding classical regulators/executors of apoptosis, we have reviewed the present knowledge of caspase-like and nuclease activities. PMID:21062457

  7. [Biology and markers of preeclampsia].

    PubMed

    Guibourdenche, Jean; Leguy, Marie-Clémence; Tsatsaris, Vassilis

    2013-11-01

    Preeclampsia is a syndrome specific of pregnancy and placenta diagnosed after 20 WG on the association of an hypertension and a proteinuria. It is responsible for significant maternal-fetal morbidity and mortality which justify the development of markers for screening, diagnosis and prognosis. These markers are actors or witnesses to the various stages and mechanisms of the disease : the initial defect of trophoblast invasion and remodeling of uterine arteries (proteases [PAPP-A, ADAM-12, uPA, MMPs], their inhibitors, and angiogenic factors [PlGF, sflt-1, s-eng]) which induces hydrostatic abnormalities (uterine doppler) and placental hypoperfusion with dysoxia (HIF-1α) and oxidative stress (free radicals, peroxynitrites, oxidized LDL). This results in impaired placental functions including endocrine and metabolic functions (hCG, leptin) with increase in placental apoptosis and necrosis with the release of exosomes and toxic placental fragments (STBM) and their content (RNA, DNA and proteins). This fragments amplify the gestational inflammation (IL6, TNFα ; activation of leukocytes and macrophages [elastase, neopterin] and complement) and lead to a deterioration of the maternal endothelium (vasoconstriction [ET2, TxA2]; platelet adhesion [sVCAM -1α), aggregation and activation; impaired vascular permeability) generating edema, hypertension, atherosclerosis and glomerular nephropathy (proteinuria, hyperuricemia). Other markers such as PP13 and PTX3 seem of interest even if their functions are poorly understood. Preeclampsia develops on a predisposed maternal environment (genetic, epigenetic infectious, and endocrine factors) characterized by a maternal inadequacy to pregnancy. PMID:24235331

  8. Serotonin, neural markers, and memory

    PubMed Central

    Meneses, Alfredo

    2015-01-01

    Diverse neuropsychiatric disorders present dysfunctional memory and no effective treatment exits for them; likely as result of the absence of neural markers associated to memory. Neurotransmitter systems and signaling pathways have been implicated in memory and dysfunctional memory; however, their role is poorly understood. Hence, neural markers and cerebral functions and dysfunctions are revised. To our knowledge no previous systematic works have been published addressing these issues. The interactions among behavioral tasks, control groups and molecular changes and/or pharmacological effects are mentioned. Neurotransmitter receptors and signaling pathways, during normal and abnormally functioning memory with an emphasis on the behavioral aspects of memory are revised. With focus on serotonin, since as it is a well characterized neurotransmitter, with multiple pharmacological tools, and well characterized downstream signaling in mammals' species. 5-HT1A, 5-HT4, 5-HT5, 5-HT6, and 5-HT7 receptors as well as SERT (serotonin transporter) seem to be useful neural markers and/or therapeutic targets. Certainly, if the mentioned evidence is replicated, then the translatability from preclinical and clinical studies to neural changes might be confirmed. Hypothesis and theories might provide appropriate limits and perspectives of evidence. PMID:26257650

  9. The LLNL Cluster Tool

    SciTech Connect

    Hunter, S L

    2007-03-27

    {lg_bullet} The Cluster Tool -is a set of linked vacuum chambers -can deposit multiple layers of metal and metal oxides {lg_bullet} Each layer can be deposited without breaking vacuum {lg_bullet} Shadow masks can give each layer a different pattern {lg_bullet} The Cluster Tool will be operational in April

  10. Cluster Interest Inventory.

    ERIC Educational Resources Information Center

    Herzog, Douglas

    The Cluster Interest Inventory is designed to familiarize students with representative occupations in 13 career clusters: (1) agribusiness and natural resources, (2) business marketing, and office occupations, (3) communications and media, (4) consumer and homemaker, (5) fine arts and humanities, (6) health, (7) manufacturing and processing, (8)…

  11. Coma cluster of galaxies

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Atlas Image mosaic, covering 34' x 34' on the sky, of the Coma cluster, aka Abell 1656. This is a particularly rich cluster of individual galaxies (over 1000 members), most prominently the two giant ellipticals, NGC 4874 (right) and NGC 4889 (left). The remaining members are mostly smaller ellipticals, but spiral galaxies are also evident in the 2MASS image. The cluster is seen toward the constellation Coma Berenices, but is actually at a distance of about 100 Mpc (330 million light years, or a redshift of 0.023) from us. At this distance, the cluster is in what is known as the 'Hubble flow,' or the overall expansion of the Universe. As such, astronomers can measure the Hubble Constant, or the universal expansion rate, based on the distance to this cluster. Large, rich clusters, such as Coma, allow astronomers to measure the 'missing mass,' i.e., the matter in the cluster that we cannot see, since it gravitationally influences the motions of the member galaxies within the cluster. The near-infrared maps the overall luminous mass content of the member galaxies, since the light at these wavelengths is dominated by the more numerous older stellar populations. Galaxies, as seen by 2MASS, look fairly smooth and homogeneous, as can be seen from the Hubble 'tuning fork' diagram of near-infrared galaxy morphology. Image mosaic by S. Van Dyk (IPAC).

  12. Probability and Cancer Clusters

    ERIC Educational Resources Information Center

    Hamilton-Keene, Rachael; Lenard, Christoper T.; Mills, Terry M.

    2009-01-01

    Recently there have been several news items about possible cancer clusters in the Australian media. The term "cancer cluster" is used when an unusually large number of people in one geographic area, often a workplace, are diagnosed with cancer in a short space of time. In this paper the authors explore this important health issue using probability…

  13. Illinois' Career Cluster Model

    ERIC Educational Resources Information Center

    Jankowski, Natasha A.; Kirby, Catherine L.; Bragg, Debra D.; Taylor, Jason L.; Oertle, Kathleen M.

    2009-01-01

    This booklet provides information to multiple stakeholders on the implementation of career clusters in Illinois. The booklet is an extension of the previous edition titled "An Introduction to Illinois CTE Programs of Study" (2008), and provides a resource for partners to understand Illinois' Career Cluster Model as its own adaptation of the…

  14. Matlab Cluster Ensemble Toolbox

    2009-04-27

    This is a Matlab toolbox for investigating the application of cluster ensembles to data classification, with the objective of improving the accuracy and/or speed of clustering. The toolbox divides the cluster ensemble problem into four areas, providing functionality for each. These include, (1) synthetic data generation, (2) clustering to generate individual data partitions and similarity matrices, (3) consensus function generation and final clustering to generate ensemble data partitioning, and (4) implementation of accuracy metrics. Withmore » regard to data generation, Gaussian data of arbitrary dimension can be generated. The kcenters algorithm can then be used to generate individual data partitions by either, (a) subsampling the data and clustering each subsample, or by (b) randomly initializing the algorithm and generating a clustering for each initialization. In either case an overall similarity matrix can be computed using a consensus function operating on the individual similarity matrices. A final clustering can be performed and performance metrics are provided for evaluation purposes.« less

  15. Mixed-Initiative Clustering

    ERIC Educational Resources Information Center

    Huang, Yifen

    2010-01-01

    Mixed-initiative clustering is a task where a user and a machine work collaboratively to analyze a large set of documents. We hypothesize that a user and a machine can both learn better clustering models through enriched communication and interactive learning from each other. The first contribution or this thesis is providing a framework of…

  16. Young Massive Star Clusters

    NASA Astrophysics Data System (ADS)

    Portegies Zwart, Simon F.; McMillan, Stephen L. W.; Gieles, Mark

    2010-09-01

    Young massive clusters (YMCs) are dense aggregates of young stars that form the fundamental building blocks of galaxies. Several examples exist in the Milky Way Galaxy and the Local Group, but they are particularly abundant in starburst and interacting galaxies. The few YMCs that are close enough to resolve are of prime interest for studying the stellar mass function and the ecological interplay between stellar evolution and stellar dynamics. The distant unresolved clusters may be effectively used to study the star-cluster mass function, and they provide excellent constraints on the formation mechanisms of young cluster populations. YMCs are expected to be the nurseries for many unusual objects, including a wide range of exotic stars and binaries. So far only a few such objects have been found in YMCs, although their older cousins, the globular clusters, are unusually rich in stellar exotica. In this review, we focus on star clusters younger than ˜100 Myr, more than a few current crossing times old, and more massive than ˜104M⊙; the size of the cluster and its environment are considered less relevant as distinguishing parameters. We describe the global properties of the currently known young massive star clusters in the Local Group and beyond, and discuss the state of the art in observations and dynamical modeling of these systems. In order to make this review readable by observers, theorists, and computational astrophysicists, we also review the cross-disciplinary terminology.

  17. Blue emitting undecaplatinum clusters

    NASA Astrophysics Data System (ADS)

    Chakraborty, Indranath; Bhuin, Radha Gobinda; Bhat, Shridevi; Pradeep, T.

    2014-07-01

    A blue luminescent 11-atom platinum cluster showing step-like optical features and the absence of plasmon absorption was synthesized. The cluster was purified using high performance liquid chromatography (HPLC). Electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI) mass spectrometry (MS) suggest a composition, Pt11(BBS)8, which was confirmed by a range of other experimental tools. The cluster is highly stable and compatible with many organic solvents.A blue luminescent 11-atom platinum cluster showing step-like optical features and the absence of plasmon absorption was synthesized. The cluster was purified using high performance liquid chromatography (HPLC). Electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI) mass spectrometry (MS) suggest a composition, Pt11(BBS)8, which was confirmed by a range of other experimental tools. The cluster is highly stable and compatible with many organic solvents. Electronic supplementary information (ESI) available: Details of experimental procedures, instrumentation, chromatogram of the crude cluster; SEM/EDAX, DLS, PXRD, TEM, FT-IR, and XPS of the isolated Pt11 cluster; UV/Vis, MALDI MS and SEM/EDAX of isolated 2 and 3; and 195Pt NMR of the K2PtCl6 standard. See DOI: 10.1039/c4nr02778g

  18. Brightest Cluster Galaxy Identification

    NASA Astrophysics Data System (ADS)

    Leisman, Luke; Haarsma, D. B.; Sebald, D. A.; ACCEPT Team

    2011-01-01

    Brightest cluster galaxies (BCGs) play an important role in several fields of astronomical research. The literature includes many different methods and criteria for identifying the BCG in the cluster, such as choosing the brightest galaxy, the galaxy nearest the X-ray peak, or the galaxy with the most extended profile. Here we examine a sample of 75 clusters from the Archive of Chandra Cluster Entropy Profile Tables (ACCEPT) and the Sloan Digital Sky Survey (SDSS), measuring masked magnitudes and profiles for BCG candidates in each cluster. We first identified galaxies by hand; in 15% of clusters at least one team member selected a different galaxy than the others.We also applied 6 other identification methods to the ACCEPT sample; in 30% of clusters at least one of these methods selected a different galaxy than the other methods. We then developed an algorithm that weighs brightness, profile, and proximity to the X-ray peak and centroid. This algorithm incorporates the advantages of by-hand identification (weighing multiple properties) and automated selection (repeatable and consistent). The BCG population chosen by the algorithm is more uniform in its properties than populations selected by other methods, particularly in the relation between absolute magnitude (a proxy for galaxy mass) and average gas temperature (a proxy for cluster mass). This work supported by a Barry M. Goldwater Scholarship and a Sid Jansma Summer Research Fellowship.

  19. Marketing Occupations. Cluster Guide.

    ERIC Educational Resources Information Center

    Oregon State Dept. of Education, Salem.

    This cluster guide, which is designed to show teachers what specific knowledge and skills qualify high school students for entry-level employment (or postsecondary training) in marketing occupations, is organized into three sections: (1) cluster organization and implementation, (2) instructional emphasis areas, and (3) assessment. The first…

  20. Muster: Massively Scalable Clustering

    2010-05-20

    Muster is a framework for scalable cluster analysis. It includes implementations of classic K-Medoids partitioning algorithms, as well as infrastructure for making these algorithms run scalably on very large systems. In particular, Muster contains algorithms such as CAPEK (described in reference 1) that are capable of clustering highly distributed data sets in-place on a hundred thousand or more processes.

  1. Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers.

    PubMed

    Rai, Ved Prakash; Kumar, Rajesh; Kumar, Sanjay; Rai, Ashutosh; Kumar, Sanjeet; Singh, Major; Singh, Sheo Pratap; Rai, Awadesh Bahadur; Paliwal, Rajneesh

    2013-10-01

    A sound knowledge of the genetic diversity among germplasm is vital for strategic germplasm collection, maintenance, conservation and utilisation. Genomic simple sequence repeats (SSRs) and random amplified microsatellite polymorphism (RAMPO) markers were used to analyse diversity and relationships among 48 pepper (Capsicum spp.) genotypes originating from nine countries. These genotypes covered 4 species including 13 germplasm accessions, 30 improved lines of 4 domesticated species and 5 landraces derived from natural interspecific crosses. Out of 106 SSR markers, 25 polymorphic SSR markers (24 %) detected a total of 76 alleles (average, 3.04; range, 2-5). The average polymorphic information content (PIC) was 0.69 (range, 0.29-0.92). Seventeen RAMPO markers produced 87 polymorphic fragments with average PIC of 0.63 (range, 0.44-0.81). Dendrograms based on SSRs and RAMPOs generated two clusters. All 38 Capsicum annuum genotypes and an interspecific landrace clustered together, whereas nine non-annuum (three Capsicum frutescens, one Capsicum chinense, one Capsicum baccatum and four interspecific landraces) genotypes clustered separately. Genetic variation within non-annuum genotypes was greater than the C. annuum genotypes. Distinctness of interspecific derivative landraces grown in northeast India was validated; natural crossing between sympatric Capsicum species has been proposed as the mechanism of their origin. PMID:24431527

  2. Cultivar identification and genetic relationship of pineapple (Ananas comosus) cultivars using SSR markers.

    PubMed

    Lin, Y S; Kuan, C S; Weng, I S; Tsai, C C

    2015-01-01

    The genetic relationships among 27 pineapple [Ananas comosus (L.) Merr.] cultivars and lines were examined using 16 simple sequence repeat (SSR) markers. The number of alleles per locus of the SSR markers ranged from 2 to 6 (average 3.19), for a total of 51 alleles. Similarity coefficients were calculated on the basis of 51 amplified bands. A dendrogram was created according to the 16 SSR markers by the unweighted pair-group method. The banding patterns obtained from the SSR primers allowed most of the cultivars and lines to be distinguished, with the exception of vegetative clones. According to the dendrogram, the 27 pineapple cultivars and lines were clustered into three main clusters and four individual clusters. As expected, the dendrogram showed that derived cultivars and lines are closely related to their parental cultivars; the genetic relationships between pineapple cultivars agree with the genealogy of their breeding history. In addition, the analysis showed that there is no obvious correlation between SSR markers and morphological characters. In conclusion, SSR analysis is an efficient method for pineapple cultivar identification and can offer valuable informative characters to identify pineapple cultivars in Taiwan. PMID:26634465

  3. Cosmology with galaxy clusters

    NASA Astrophysics Data System (ADS)

    Sartoris, Barbara

    2015-08-01

    Clusters of galaxies are powerful probes to constrain parameters that describe the cosmological models and to distinguish among different models. Since, the evolution of the cluster mass function and large-scale clustering contain the informations about the linear growth rate of perturbations and the expansion history of the Universe, clusters have played an important role in establishing the current cosmological paradigm. It is crucial to know how to determine the cluster mass from observational quantities when using clusters as cosmological tools. For this, numerical simulations are helpful to define and study robust cluster mass proxies that have minimal and well understood scatter across the mass and redshift ranges of interest. Additionally, the bias in cluster mass determination can be constrained via observations of the strong and weak lensing effect, X-ray emission, the Sunyaev- Zel’dovic effect, and the dynamics of galaxies.A major advantage of X-ray surveys is that the observable-mass relation is tight. Moreover, clusters can be easily identified in X-ray as continuous, extended sources. As of today, interesting cosmological constraints have been obtained from relatively small cluster samples (~102), X-ray selected by the ROSAT satellite over a wide redshift range (0clusters, the ROSAT All-Sky Survey.The next generation of X-ray telescopes will enhance the statistics of detected clusters and enlarge their redshift coverage. In particular, eROSITA will produce a catalog of >105 clusters with photometric redshifts from multi-band optical surveys (e.g. PanSTARRS, DES, and LSST). This will vastly improve upon current cosmological constraints, especially by the synergy with other cluster surveys that

  4. Cool Cluster Correctly Correlated

    SciTech Connect

    Sergey Aleksandrovich Varganov

    2005-12-17

    Atomic clusters are unique objects, which occupy an intermediate position between atoms and condensed matter systems. For a long time it was thought that physical and chemical properties of atomic dusters monotonically change with increasing size of the cluster from a single atom to a condensed matter system. However, recently it has become clear that many properties of atomic clusters can change drastically with the size of the clusters. Because physical and chemical properties of clusters can be adjusted simply by changing the cluster's size, different applications of atomic clusters were proposed. One example is the catalytic activity of clusters of specific sizes in different chemical reactions. Another example is a potential application of atomic clusters in microelectronics, where their band gaps can be adjusted by simply changing cluster sizes. In recent years significant advances in experimental techniques allow one to synthesize and study atomic clusters of specified sizes. However, the interpretation of the results is often difficult. The theoretical methods are frequently used to help in interpretation of complex experimental data. Most of the theoretical approaches have been based on empirical or semiempirical methods. These methods allow one to study large and small dusters using the same approximations. However, since empirical and semiempirical methods rely on simple models with many parameters, it is often difficult to estimate the quantitative and even qualitative accuracy of the results. On the other hand, because of significant advances in quantum chemical methods and computer capabilities, it is now possible to do high quality ab-initio calculations not only on systems of few atoms but on clusters of practical interest as well. In addition to accurate results for specific clusters, such methods can be used for benchmarking of different empirical and semiempirical approaches. The atomic clusters studied in this work contain from a few atoms to

  5. Hybridization schemes for clusters

    NASA Astrophysics Data System (ADS)

    Wales, David J.

    The concept of an optimum hybridization scheme for cluster compounds is developed with particular reference to electron counting. The prediction of electron counts for clusters and the interpretation of the bonding is shown to depend critically upon the presumed hybridization pattern of the cluster vertex atoms. This fact has not been properly appreciated in previous work, particularly in applications of Stone's tensor surface harmonic (TSH) theory, but is found to be a useful tool when dealt with directly. A quantitative definition is suggested for the optimum cluster hybridization pattern based directly upon the ease of interpretation of the molecular orbitals, and results are given for a range of species. The relationship of this scheme to the detailed cluster geometry is described using Löwdin's partitioned perturbation theory, and the success and range of application of TSH theory are discussed.

  6. Judging Quality through Substantive Conversations between Markers

    ERIC Educational Resources Information Center

    Grainger, Peter; Purnell, Ken; Zipf, Reyna

    2008-01-01

    Decisions by markers about quality in student work remain confusing to most students and markers. This may in part be due to the relatively subjective nature of what constitutes a quality response to an assessment task. This paper reports on an experiment that documented the process of decision-making by multiple markers at a university who…

  7. Mixtures with relatives and linked markers.

    PubMed

    Dørum, Guro; Kling, Daniel; Tillmar, Andreas; Vigeland, Magnus Dehli; Egeland, Thore

    2016-05-01

    Mixture DNA profiles commonly appear in forensic genetics, and a large number of statistical methods and software are available for such cases. However, most of the literature concerns mixtures where the contributors are assumed unrelated and the genetic markers are unlinked. In this paper, we consider mixtures of linked markers and related contributors. If no relationships are involved, linkage can be ignored. While unlinked markers can be treated independently, linkage introduces dependencies. The use of linked markers presents statistical and computational challenges, but may also lead to a considerable increase in power since the number of markers available is much larger if we do not require the markers to be unlinked. In addition, some cases that cannot be solved with an unlimited number of unlinked autosomal markers can be solved with linked markers. We focus on two special cases of linked markers: pairs of linked autosomal markers and X-chromosomal markers. A framework is presented for calculation of likelihood ratios for mixtures with general relationships and with linkage between any number of markers. Finally, we explore the effect of linkage disequilibrium, also called allelic association, on the likelihood ratio. PMID:26614310

  8. 49 CFR 195.410 - Line markers.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 3 2010-10-01 2010-10-01 false Line markers. 195.410 Section 195.410... PIPELINE Operation and Maintenance § 195.410 Line markers. (a) Except as provided in paragraph (b) of this section, each operator shall place and maintain line markers over each buried pipeline in accordance...

  9. Pseudoautosomal marker DXYS20 and manic depression

    SciTech Connect

    Noethen, M.M.; Cichon, S.; Erdmann, J.; Koerner, J.; Rietschel, M.; Propping, P. ); Rappold, G.A. ); Fritze, J. )

    1993-04-01

    Yoneda et al. (1992) observed a significant association between manic-depressive illness and a 13.5-kb band of the pseudoautosomal marker DXYS20 (probe 362A) in EcoRI digests of 49 Japanese patients compared with 119 controls. The 13.5-kb allele was designated [open quotes]A4 allele[close quotes] and was found on at least one chromosome in 46.9% of the patients, compared with 26.1% of the controls. The relative risk of the A4 allele for the disease was 2.51. The authors have genotyped the EcoRI RFLP in 73 patients (40 females and 33 males) who fulfill DSM-III-R criteria of manic-depressive illness (bipolar affective disorder) and in 79 controls (34 females and 45 males). All subjects included in the study were unrelated and were of German descent. They used the probe 3cos-PP, which, by sequence analysis, was shown to be directly homologous to the independently cloned probe 362A (Rappold et al. 1992). The pseudoautosomal locus DXYS20 represents a VNTR-like minisatellite, and many polymorphic bands are recognized by means of several restriction endonucleases (Page et al. 1987). In EcoRI digests, sizes of bands cluster, and the authors grouped their bands according to allele sizes used by Yoneda et al. In addition to the alleles reported by Yoneda et al., they observed a 10-kb band in five subjects. The results are shown in a table. The frequency of the A4 allele did not differ significantly between patients and controls. Thus, the data do not support a widespread or consistent association between DXYS20 and bipolar affective disorder. A large degree of ethnic variation is seen with DXYS20 (Rappold et al. 1992) and might explain the difference of allele frequencies in controls from Japan and Germany. Since VNTRs evolve rapidly, they may not always be the best markers to detect disease associations, where a positive effect requires linkage disequilibrium. In any case, it should be useful to study larger samples of Japanese patients and controls. 3 refs., 1 tab.

  10. Merging and comparing three mitochondrial markers for phylogenetic studies of Eurasian reindeer (Rangifer tarandus).

    PubMed

    Kvie, Kjersti S; Heggenes, Jan; Røed, Knut H

    2016-07-01

    Phylogenetic analyses provide information that can be useful in the conservation of genetic variation by identifying intraspecific genetic structure. Reconstruction of phylogenetic relationships requires the use of markers with the appropriate amount of variation relative to the timeframe and purpose of the study. Here, genetic structure and clustering are inferred from comparative analyses of three widely used mitochondrial markers, the CR, cytb and the COI region, merged and separately, using Eurasian reindeer as a model. A Bayesian phylogeny and a MJ network, both based on the merged dataset, indicate several distinct maternal haplotype clusters within Eurasian reindeer. In addition to confirm previously described clusters, two new subclusters were found. When comparing the results from the merged dataset with the results from analyses of the three markers separately, similar clustering was found in the CR and COI phylogenies, whereas the cytb region showed poor resolution. Phylogenetic analyses of the merged dataset and the CR revealed congruent results, implying that single sequencing analysis of the CR is an applicable method for studying the haplotype structure in Eurasian reindeer. PMID:27386080

  11. Document clustering methods, document cluster label disambiguation methods, document clustering apparatuses, and articles of manufacture

    DOEpatents

    Sanfilippo, Antonio; Calapristi, Augustin J.; Crow, Vernon L.; Hetzler, Elizabeth G.; Turner, Alan E.

    2009-12-22

    Document clustering methods, document cluster label disambiguation methods, document clustering apparatuses, and articles of manufacture are described. In one aspect, a document clustering method includes providing a document set comprising a plurality of documents, providing a cluster comprising a subset of the documents of the document set, using a plurality of terms of the documents, providing a cluster label indicative of subject matter content of the documents of the cluster, wherein the cluster label comprises a plurality of word senses, and selecting one of the word senses of the cluster label.

  12. [Neuropathologic markers in degenerative dementias].

    PubMed

    Hauw, J J; Seilhean, D; Colle, M A; Hogenhuys, J; Duyckaerts, C

    1998-01-01

    The number of neuropathological markers used for the diagnosis of degenerative dementias is rapidly increasing, and this is somewhat confusing: some lesions described a long time ago, such as ballooned cells, proved to be less specific than they were supposed to be; this is also the case for Lewy bodies, that have been recognised in a larger spectrum of disorders than thought a few years ago. On the contrary, for an increasing number of neuropathologists, Pick bodies are now mandatory for the diagnosis of Pick disease, and this contrasts with the prevalent opinions of the late sixties or seventies. There are a number of reasons for the changing significance of neuropathological markers. Three of them can be easily identified: 1) the burst of immunohistochemistry into neuropathology allowed an easier recognition, a better delineation and new pathophysiological approaches to old lesions, and a dramatic increase in the description of new markers, especially in glial cells; 2) in some conditions characterized by the number and distribution of some lesions rather than by their mere presence, such as aging and Alzheimer disease, a better neuroanatomical point of view permitted new insights into the concept of disease versus age-related changes; 3) more accurate clinicopathologic correlations showed clearly the need of grouping or lumping together some entities: for example, obvious relationship aroused between progressive supranuclear palsy and corticobasal degeneration; in contrast, distinguishing different disorders in the frontal lobe dementias grouped together into "Pick disease" was felt necessary. This review summarizes the main criteria for identification, and the presumed meaning of the chief markers indicating the presence of abnormally phosphorylated tau proteins, A beta peptides, and PrP proteins. Abnormally phosphorylated tau proteins can be stored in the neurons, and participate in the constitution of many lesions (neurofibrillary tangles, neuropil threads

  13. Clinical tumour markers in ovarian cancer.

    PubMed

    Mazurek, A; Nikliński, J; Laudański, T; Pluygers, E

    1998-02-01

    Within past few years, the measurement of serological, histochemical and molecular genetic markers has had an increasing influence on clinical decisions about initial treatment and follow-up. This review presents data concerning the most studied and interesting markers in ovarian cancer. CA 125, CA 19.9, TATI, CASA, CEA, TPA, TPS and CYFRA21-1 are now the most widely used serological tumour markers for management of ovarian cancer patients. Ras oncogenes, C-erb2 proto-oncogene, p53 suppressor gene and Bcl-2 oncogene are examples of currently used molecular genetic markers. As histochemical markers-proliferation markers, flow cytometric analysis, thymidine labelling index, Ki-67 nuclear antigen or differentiation markers are nowadays the ones most often determined. Some of these markers might be useful adjuncts for monitoring response to therapy, including early detection of tumour reactivation to allow curative therapy and rapid detection of treatment failure. The study of these markers may also lead to a better understanding of the biological characteristics of ovarian cancer. Numerous tumour markers characterized in this paper have been recognized as promising prognostic factors. The information derived from studies of these markers also represents the most promising avenue towards new treatment strategies; nevertheless to validate these factors, prospective studies of a large patient population are needed. PMID:9511849

  14. Clines, Clusters, and the Effect of Study Design on the Inference of Human Population Structure

    PubMed Central

    2005-01-01

    Previously, we observed that without using prior information about individual sampling locations, a clustering algorithm applied to multilocus genotypes from worldwide human populations produced genetic clusters largely coincident with major geographic regions. It has been argued, however, that the degree of clustering is diminished by use of samples with greater uniformity in geographic distribution, and that the clusters we identified were a consequence of uneven sampling along genetic clines. Expanding our earlier dataset from 377 to 993 markers, we systematically examine the influence of several study design variables—sample size, number of loci, number of clusters, assumptions about correlations in allele frequencies across populations, and the geographic dispersion of the sample—on the “clusteredness” of individuals. With all other variables held constant, geographic dispersion is seen to have comparatively little effect on the degree of clustering. Examination of the relationship between genetic and geographic distance supports a view in which the clusters arise not as an artifact of the sampling scheme, but from small discontinuous jumps in genetic distance for most population pairs on opposite sides of geographic barriers, in comparison with genetic distance for pairs on the same side. Thus, analysis of the 993-locus dataset corroborates our earlier results: if enough markers are used with a sufficiently large worldwide sample, individuals can be partitioned into genetic clusters that match major geographic subdivisions of the globe, with some individuals from intermediate geographic locations having mixed membership in the clusters that correspond to neighboring regions. PMID:16355252

  15. Statistical properties of convex clustering

    PubMed Central

    Tan, Kean Ming; Witten, Daniela

    2016-01-01

    In this manuscript, we study the statistical properties of convex clustering. We establish that convex clustering is closely related to single linkage hierarchical clustering and k-means clustering. In addition, we derive the range of the tuning parameter for convex clustering that yields a non-trivial solution. We also provide an unbiased estimator of the degrees of freedom, and provide a finite sample bound for the prediction error for convex clustering. We compare convex clustering to some traditional clustering methods in simulation studies.

  16. Elucidating genetic diversity among sour orange rootstocks: a comparative study of the efficiency of RAPD and SSR markers.

    PubMed

    Lamine, Myriam; Mliki, Ahmed

    2015-03-01

    In order to compare the effectiveness of two molecular marker systems, a set of six RAPD and nine SSR markers were used to study the genetic diversity in a population of 46 sour orange accessions, a common rootstock used in almost all citrus orchards in Tunisia. Genetic diversity parameters [average and effective number of alleles, percentage of polymorphism, polymorphic information content (PIC), effective marker index (EMI), and marker index (MI) parameters] for RAPD, SSR, and RAPD + SSR were determined in order to assess the efficiency of the two marker systems. The results revealed that these parameters were significantly higher when using RAPD markers. Similarly, cluster analysis using the results of RAPD was practically the same as that obtained when combining data from the two marker systems (RAPD + SSR) demonstrating the efficiency of RAPD in discriminating between sour orange accessions. Therefore, the use of SSR markers, known to be more efficient and discriminatory, does not bring significant supplementary information in this work. Indeed, results would have been obtained using only the RAPD markers. Accordingly, this work highlights the efficiency and advantages of RAPD, as an easy and efficient technique, in studying citrus rootstock's genetic diversity, and establishing genetic relationships among citrus accessions. PMID:25586488

  17. Partially supervised speaker clustering.

    PubMed

    Tang, Hao; Chu, Stephen Mingyu; Hasegawa-Johnson, Mark; Huang, Thomas S

    2012-05-01

    Content-based multimedia indexing, retrieval, and processing as well as multimedia databases demand the structuring of the media content (image, audio, video, text, etc.), one significant goal being to associate the identity of the content to the individual segments of the signals. In this paper, we specifically address the problem of speaker clustering, the task of assigning every speech utterance in an audio stream to its speaker. We offer a complete treatment to the idea of partially supervised speaker clustering, which refers to the use of our prior knowledge of speakers in general to assist the unsupervised speaker clustering process. By means of an independent training data set, we encode the prior knowledge at the various stages of the speaker clustering pipeline via 1) learning a speaker-discriminative acoustic feature transformation, 2) learning a universal speaker prior model, and 3) learning a discriminative speaker subspace, or equivalently, a speaker-discriminative distance metric. We study the directional scattering property of the Gaussian mixture model (GMM) mean supervector representation of utterances in the high-dimensional space, and advocate exploiting this property by using the cosine distance metric instead of the euclidean distance metric for speaker clustering in the GMM mean supervector space. We propose to perform discriminant analysis based on the cosine distance metric, which leads to a novel distance metric learning algorithm—linear spherical discriminant analysis (LSDA). We show that the proposed LSDA formulation can be systematically solved within the elegant graph embedding general dimensionality reduction framework. Our speaker clustering experiments on the GALE database clearly indicate that 1) our speaker clustering methods based on the GMM mean supervector representation and vector-based distance metrics outperform traditional speaker clustering methods based on the “bag of acoustic features” representation and statistical

  18. Dwarfs in Coma Cluster

    NASA Technical Reports Server (NTRS)

    2007-01-01

    [figure removed for brevity, see original site] Click on image for larger poster version

    This false-color mosaic of the central region of the Coma cluster combines infrared and visible-light images to reveal thousands of faint objects (green). Follow-up observations showed that many of these objects, which appear here as faint green smudges, are dwarf galaxies belonging to the cluster. Two large elliptical galaxies, NGC 4889 and NGC 4874, dominate the cluster's center. The mosaic combines visible-light data from the Sloan Digital Sky Survey (color coded blue) with long- and short-wavelength infrared views (red and green, respectively) from NASA's Spitzer Space Telescope.

  19. H-cluster stars

    NASA Astrophysics Data System (ADS)

    Lai, X. Y.; Gao, C. Y.; Xu, R. X.

    2013-06-01

    The study of dense matter at ultrahigh density has a very long history, which is meaningful for us to understand not only cosmic events in extreme circumstances but also fundamental laws of physics. It is well known that the state of cold matter at supranuclear density depends on the non-perturbative nature of quantum chromodynamics (QCD) and is essential for modelling pulsars. A so-called H-cluster matter is proposed in this paper as the nature of dense matter in reality. In compact stars at only a few nuclear densities but low temperature, quarks could be interacting strongly with each other there. That might render quarks grouped in clusters, although the hypothetical quark clusters in cold dense matter have not been confirmed due to the lack of both theoretical and experimental evidence. Motivated by recent lattice QCD simulations of the H-dibaryons (with structure uuddss), we therefore consider here a possible kind of quark clusters, H-clusters, that could emerge inside compact stars during their initial cooling as the dominant components inside (the degree of freedom could then be H-clusters there). Taking into account the in-medium stiffening effect, we find that at baryon densities of compact stars H-cluster matter could be more stable than nuclear matter. We also find that for the H-cluster matter with lattice structure, the equation of state could be so stiff that it would seem to be `superluminal' in the most dense region. However, the real sound speed for H-cluster matter is in fact difficult to calculate, so at this stage we do not put constraints on our model from the usual requirement of causality. We study the stars composed of H-clusters, i.e. H-cluster stars, and derive the dependence of their maximum mass on the in-medium stiffening effect, showing that the maximum mass could be well above 2 M⊙ as observed and that the resultant mass-radius relation fits the measurement of the rapid burster under reasonable parameters. Besides a general

  20. Extending Beowulf Clusters

    USGS Publications Warehouse

    Steinwand, Daniel R.; Maddox, Brian; Beckmann, Tim; Hamer, George

    2003-01-01

    Beowulf clusters can provide a cost-effective way to compute numerical models and process large amounts of remote sensing image data. Usually a Beowulf cluster is designed to accomplish a specific set of processing goals, and processing is very efficient when the problem remains inside the constraints of the original design. There are cases, however, when one might wish to compute a problem that is beyond the capacity of the local Beowulf system. In these cases, spreading the problem to multiple clusters or to other machines on the network may provide a cost-effective solution.

  1. Smarter clustering methods for SNP genotype calling

    PubMed Central

    Lin, Yan; Tseng, George C.; Cheong, Soo Yeon; Bean, Lora J. H.; Sherman, Stephanie L.; Feingold, Eleanor

    2008-01-01

    Motivation: Most genotyping technologies for single nucleotide polymorphism (SNP) markers use standard clustering methods to ‘call’ the SNP genotypes. These methods are not always optimal in distinguishing the genotype clusters of a SNP because they do not take advantage of specific features of the genotype calling problem. In particular, when family data are available, pedigree information is ignored. Furthermore, prior information about the distribution of the measurements for each cluster can be used to choose an appropriate model-based clustering method and can significantly improve the genotype calls. One special genotyping problem that has never been discussed in the literature is that of genotyping of trisomic individuals, such as individuals with Down syndrome. Calling trisomic genotypes is a more complicated problem, and the addition of external information becomes very important. Results: In this article, we discuss the impact of incorporating external information into clustering algorithms to call the genotypes for both disomic and trisomic data. We also propose two new methods to call genotypes using family data. One is a modification of the K-means method and uses the pedigree information by updating all members of a family together. The other is a likelihood-based method that combines the Gaussian or beta-mixture model with pedigree information. We compare the performance of these two methods and some other existing methods using simulation studies. We also compare the performance of these methods on a real dataset generated by the Illumina platform (www.illumina.com). Availability: The R code for the family-based genotype calling methods (SNPCaller) is available to be downloaded from the following website: http://watson.hgen.pitt.edu/register. Contact: liny@upmc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:18826959

  2. Epididymal protein markers and fertility.

    PubMed

    Dacheux, Jean-Louis; Dacheux, Françoise; Druart, Xavier

    2016-06-01

    The last stages of male gamete differentiation occur outside the gonad in a specific environment controlled by the epididymal epithelium. All the fundamental characteristics of a fertile spermatozoon are acquired sequentially during transit through the epididymal tubule. Full understanding of the mechanisms involved in these gamete modifications is a key to understanding and controlling such important stages in male fertility. With the development of new large scale technologies, large amounts of information give hope of identifying the fundamental elements involved in such cellular events and of being able to obtain some markers predictive of male fertility that would be valuable both in human and/or animal reproduction. PMID:26963046

  3. Genetic markers as instrumental variables

    PubMed Central

    von Hinke, Stephanie; Davey Smith, George; Lawlor, Debbie A.; Propper, Carol; Windmeijer, Frank

    2016-01-01

    The use of genetic markers as instrumental variables (IV) is receiving increasing attention from economists, statisticians, epidemiologists and social scientists. Although IV is commonly used in economics, the appropriate conditions for the use of genetic variants as instruments have not been well defined. The increasing availability of biomedical data, however, makes understanding of these conditions crucial to the successful use of genotypes as instruments. We combine the econometric IV literature with that from genetic epidemiology, and discuss the biological conditions and IV assumptions within the statistical potential outcomes framework. We review this in the context of two illustrative applications. PMID:26614692

  4. Combining cluster number counts and galaxy clustering

    NASA Astrophysics Data System (ADS)

    Lacasa, Fabien; Rosenfeld, Rogerio

    2016-08-01

    The abundance of clusters and the clustering of galaxies are two of the important cosmological probes for current and future large scale surveys of galaxies, such as the Dark Energy Survey. In order to combine them one has to account for the fact that they are not independent quantities, since they probe the same density field. It is important to develop a good understanding of their correlation in order to extract parameter constraints. We present a detailed modelling of the joint covariance matrix between cluster number counts and the galaxy angular power spectrum. We employ the framework of the halo model complemented by a Halo Occupation Distribution model (HOD). We demonstrate the importance of accounting for non-Gaussianity to produce accurate covariance predictions. Indeed, we show that the non-Gaussian covariance becomes dominant at small scales, low redshifts or high cluster masses. We discuss in particular the case of the super-sample covariance (SSC), including the effects of galaxy shot-noise, halo second order bias and non-local bias. We demonstrate that the SSC obeys mathematical inequalities and positivity. Using the joint covariance matrix and a Fisher matrix methodology, we examine the prospects of combining these two probes to constrain cosmological and HOD parameters. We find that the combination indeed results in noticeably better constraints, with improvements of order 20% on cosmological parameters compared to the best single probe, and even greater improvement on HOD parameters, with reduction of error bars by a factor 1.4-4.8. This happens in particular because the cross-covariance introduces a synergy between the probes on small scales. We conclude that accounting for non-Gaussian effects is required for the joint analysis of these observables in galaxy surveys.

  5. On the influence of soft tissue coverage in the determination of bone kinematics using skin markers.

    PubMed

    Taylor, William R; Ehrig, Rainald M; Duda, Georg N; Schell, Hanna; Seebeck, Petra; Heller, Markus O

    2005-07-01

    Accurate measurement of underlying bone positions is important for the understanding of normal movement and function, as well as for addressing clinical musculoskeletal or post-injury problems. Non-invasive measurement techniques are limited by the analysis technique and movement of peripheral soft tissues that can introduce significant measurement errors in reproducing the kinematics of the underlying bones when using external skin markers. Reflective markers, skeletally mounted to the right hind limb of three Merino-mix sheep were measured simultaneously with markers attached to the skin of each segment, during repetitions of gait trials. The movement of the skin markers relative to the underlying bone positions was then assessed using the Point Cluster Technique (PCT), raw averaging and the Optimal Common Shape Technique (OCST), a new approach presented in this manuscript. Errors in the position of the proximal joint centre, predicted from the corresponding skin markers, were shown to be phasic and strongly associated with the amount soft tissue coverage, averaging 8.5 mm for the femur, 2.8 for the tibia and 2.0 for the metatarsus. Although the results show a better prediction of bone kinematics associated with the Optimal Common Shape Technique, these errors were large for all three assessment techniques and much greater than the differences between the various techniques. Whilst individual markers moved up to 4 mm from the optimal marker set configuration, average peak errors of up to 16, 5 and 3 mm (hip, knee and tibio-metatarsal joints respectively) were observed, suggesting that a large amount of kinematic noise is produced from the synchronous shifting of marker sets, potentially as a result of underlying muscle firing and the inertial effects of heel impact. Current techniques are therefore limited in their ability to determine the kinematics of underlying bones based on skin markers, particularly in segments with more pronounced soft tissue coverage

  6. Mantis BT Cluster Support

    2009-06-05

    The software is a modidication to the Mantis BT V1.5 open source application provided by the mantis BT group to support cluster web servers. It also provides various cosmetic modifications used a LLNL.

  7. Cyclostomes Lack Clustered Protocadherins.

    PubMed

    Ravi, Vydianathan; Yu, Wei-Ping; Pillai, Nisha E; Lian, Michelle M; Tay, Boon-Hui; Tohari, Sumanty; Brenner, Sydney; Venkatesh, Byrappa

    2016-02-01

    The brain, comprising billions of neurons and intricate neural networks, is arguably the most complex organ in vertebrates. The diversity of individual neurons is fundamental to the neuronal network complexity and the overall function of the vertebrate brain. In jawed vertebrates, clustered protocadherins provide the molecular basis for this neuronal diversity, through stochastic and combinatorial expression of their various isoforms in individual neurons. Based on analyses of transcriptomes from the Japanese lamprey brain and sea lamprey embryos, genome assemblies of the two lampreys, and brain expressed sequence tags of the inshore hagfish, we show that extant jawless vertebrates (cyclostomes) lack the clustered protocadherins. Our findings indicate that the clustered protocadherins originated from a nonclustered protocadherin in the jawed vertebrate ancestor, after the two rounds of whole-genome duplication. In the absence of clustered protocadherins, cyclostomes might have evolved novel molecules or mechanisms for generating neuronal diversity which remains to be discovered. PMID:26545918

  8. Dynamic Bayesian clustering.

    PubMed

    Fowler, Anna; Menon, Vilas; Heard, Nicholas A

    2013-10-01

    Clusters of time series data may change location and memberships over time; in gene expression data, this occurs as groups of genes or samples respond differently to stimuli or experimental conditions at different times. In order to uncover this underlying temporal structure, we consider dynamic clusters with time-dependent parameters which split and merge over time, enabling cluster memberships to change. These interesting time-dependent structures are useful in understanding the development of organisms or complex organs, and could not be identified using traditional clustering methods. In cell cycle data, these time-dependent structure may provide links between genes and stages of the cell cycle, whilst in developmental data sets they may highlight key developmental transitions. PMID:24131050

  9. [Cluster headache differential diagnosis].

    PubMed

    Guégan-Massardier, Evelyne; Laubier, Cécile

    2015-11-01

    Cluster headache is characterized by disabling stereotyped headache. Early diagnosis allows appropriate treatment, unfortunately diagnostic errors are frequent. The main differential diagnoses are other primary or essential headaches. Migraine, more frequent and whose diagnosis is carried by excess, trigeminal neuralgia or other trigemino-autonomic cephalgia. Vascular or tumoral underlying condition can mimic cluster headache, neck and brain imaging is recommended, ideally MRI. PMID:26549687

  10. Wild Duck Cluster

    NASA Technical Reports Server (NTRS)

    2005-01-01

    On April 7, 2005, the Deep Impact spacecraft's Impactor Target Sensor camera recorded this image of M11, the Wild Duck cluster, a galactic open cluster located 6 thousand light years away. The camera is located on the impactor spacecraft, which will image comet Tempel 1 beginning 22 hours before impact until about 2 seconds before impact. Impact with comet Tempel 1 is planned for July 4, 2005.

  11. Calpains: markers of tumor aggressiveness?

    PubMed

    Roumes, Hélène; Leloup, Ludovic; Dargelos, Elise; Brustis, Jean-Jacques; Daury, Laetitia; Cottin, Patrick

    2010-05-15

    Rhabdomyosarcoma (RMS) are soft-tissue sarcoma commonly encountered in childhood. RMS cells can acquire invasive behavior and form metastases. The metastatic dissemination implicates many proteases among which are mu-calpain and m-calpain. Study of calpain expression and activity underline the deregulation of calpain activity in RMS. Analysis of kinetic characteristics of RMS cells, compared to human myoblasts LHCN-M2 cells, shows an important migration velocity in RMS cells. One of the major results of this study is the positive linear correlation between calpain activity and migration velocity presenting calpains as a marker of tumor aggressiveness. The RMS cytoskeleton is disorganized. Specifying the role of mu- and m-calpain using antisense oligonucleotides led to show that both calpains up-regulate alpha- and beta-actin in ARMS cells. Moreover, the invasive behavior of these cells is higher than that of LHCN-M2 cells. However, it is similar to that of non-treated LHCN-M2 cells, when calpains are inhibited. In summary, calpains may be involved in the anarchic adhesion, migration and invasion of RMS. The direct relationship between calpain activity and migration velocities or invasive behavior indicates that calpains could be considered as markers of tumor aggressiveness and as potential targets for limiting development of RMS tumor as well as their metastatic behavior. PMID:20193680

  12. Cluster functional renormalization group

    NASA Astrophysics Data System (ADS)

    Reuther, Johannes; Thomale, Ronny

    2014-01-01

    Functional renormalization group (FRG) has become a diverse and powerful tool to derive effective low-energy scattering vertices of interacting many-body systems. Starting from a free expansion point of the action, the flow of the RG parameter Λ allows us to trace the evolution of the effective one- and two-particle vertices towards low energies by taking into account the vertex corrections between all parquet channels in an unbiased fashion. In this work, we generalize the expansion point at which the diagrammatic resummation procedure is initiated from a free UV limit to a cluster product state. We formulate a cluster FRG scheme where the noninteracting building blocks (i.e., decoupled spin clusters) are treated exactly, and the intercluster couplings are addressed via RG. As a benchmark study, we apply our cluster FRG scheme to the spin-1/2 bilayer Heisenberg model (BHM) on a square lattice where the neighboring sites in the two layers form the individual two-site clusters. Comparing with existing numerical evidence for the BHM, we obtain reasonable findings for the spin susceptibility, the spin-triplet excitation energy, and quasiparticle weight even in coupling regimes close to antiferromagnetic order. The concept of cluster FRG promises applications to a large class of interacting electron systems.

  13. Communication: The cluster vapor to cluster solid transition

    NASA Astrophysics Data System (ADS)

    Sweatman, Martin B.; Lue, Leo

    2016-05-01

    Until now, depletion induced transitions have been the hallmark of multicomponent systems only. Monte Carlo simulations reveal a depletion-induced phase transition from cluster vapor to cluster solid in a one-component fluid with competing short range and long range interactions. This confirms a prediction made by earlier theoretical work. Analysis of renormalized cluster-cluster and cluster-vapor interactions suggests that a cluster liquid is also expected within a very narrow range of model parameters. These insights could help identify the mechanisms of clustering in experiments and assist the design of colloidal structures through engineered self-assembly.

  14. The Clustering of Young Stellar Cluster Populations in Nearby Galaxies

    NASA Astrophysics Data System (ADS)

    Grasha, Kathryn; Calzetti, Daniela

    2016-01-01

    We present measurements of clustering among star clusters for several galaxies drawn from the Legacy ExtraGalactic UV Survey (LEGUS), in order to establish whether the clustering strength depends on properties of the cluster population. We use the two point autocorrelation function to study clustering as a function of spatial scale, age, concentration index (CI), and mass. We separate the clusters into different classes, defined by their (a)symmetry and number of peaks, comparing the trends of the autocorrelation functions between all the cluster classes. For one galaxy, NGC 628, we find that younger star clusters are more strongly clustered over small spatial scales and that the clustering disappears rapidly for ages as young as 40 Myr. We present here a similar analysis for the other galaxies. We also measure the power-law slope and amplitude of the autocorrelation functions and discuss the results.

  15. Relation chain based clustering analysis

    NASA Astrophysics Data System (ADS)

    Zhang, Cheng-ning; Zhao, Ming-yang; Luo, Hai-bo

    2011-08-01

    Clustering analysis is currently one of well-developed branches in data mining technology which is supposed to find the hidden structures in the multidimensional space called feature or pattern space. A datum in the space usually possesses a vector form and the elements in the vector represent several specifically selected features. These features are often of efficiency to the problem oriented. Generally, clustering analysis goes into two divisions: one is based on the agglomerative clustering method, and the other one is based on divisive clustering method. The former refers to a bottom-up process which regards each datum as a singleton cluster while the latter refers to a top-down process which regards entire data as a cluster. As the collected literatures, it is noted that the divisive clustering is currently overwhelming both in application and research. Although some famous divisive clustering methods are designed and well developed, clustering problems are still far from being solved. The k - means algorithm is the original divisive clustering method which initially assigns some important index values, such as the clustering number and the initial clustering prototype positions, and that could not be reasonable in some certain occasions. More than the initial problem, the k - means algorithm may also falls into local optimum, clusters in a rigid way and is not available for non-Gaussian distribution. One can see that seeking for a good or natural clustering result, in fact, originates from the one's understanding of the concept of clustering. Thus, the confusion or misunderstanding of the definition of clustering always derives some unsatisfied clustering results. One should consider the definition deeply and seriously. This paper demonstrates the nature of clustering, gives the way of understanding clustering, discusses the methodology of designing a clustering algorithm, and proposes a new clustering method based on relation chains among 2D patterns. In

  16. 75 FR 59620 - Natchez Fireworks Safety Zone; Lower Mississippi River, Mile Marker 365.5 to Mile Marker 363...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-28

    ..., Mile Marker 365.5 to Mile Marker 363, Natchez, MS AGENCY: Coast Guard, DHS. ACTION: Temporary final...; Lower Mississippi River, Mile Marker 365.5 to Mile Marker 363, Natchez, MS (a) Location. The...

  17. Phylogenetic relationships among Spanish Barbus species (Pisces, Cyprinidae) shown by RAPD markers.

    PubMed

    Callejas, C; Ochando, M D

    2002-07-01

    Random amplified polymorphic DNA (RAPD) markers were used to estimate the population structure and phylogenetic relationships among the eight species of the genus Barbus that inhabit the Iberian Peninsula. Ten random oligodecamers were used to amplify DNA from 232 fish sampled from 15 populations. A total of 270 markers were detected that revealed low levels of genetic variability. The conclusions of cluster analysis indicate two main branches and three well-differentiated groups: north-eastern, Mediterranean and Atlantic. This clustering mainly reflects the evolutionary history of the genus, which is closely related to the paleogeography of the Iberian Peninsula. The contribution and application of these results to the conservation of the species, to their taxonomic status and to the process of colonization of the Iberian Peninsula by the genus Barbus are discussed. PMID:12080368

  18. Evaluation of insertion-deletion markers suitable for genetic diversity studies and marker-trait correlation analyses in cultivated peanut (Arachis hypogaea L.).

    PubMed

    Meng, S; Yang, X L; Dang, P M; Cui, S L; Mu, G J; Chen, C Y; Liu, L F

    2016-01-01

    Peanut is one of the most important oil crops worldwide. We used insertion-deletion (InDel) markers to assess the genetic diversity and population structure in cultivated peanut. Fifty-four accessions from North China were genotyped using 48 InDel markers. The markers amplified 61 polymorphic loci with 1 to 8 alleles and an average of 2.6 alleles per marker. The polymorphism information content values ranged from 0.0364 to 0.9030, with an average of 0.5038. Population structure and neighbor-joining (NJ) tree analyses suggested that all accessions could be divided into four clusters (A1-A4), using the NJ method. Likewise, four subpopulations (G1-G4) were identified using STRUCTURE analysis. A principal component analysis was also used and results concordant with the other analysis methods were found. A multi-linear stepwise regression analysis revealed that 13 InDel markers correlated with five measured agronomical traits. Our results will provide important information for future peanut molecular breeding and genetic research. PMID:27525935

  19. Immunohistochemical Detection of Markers for Translational Studies of Lung Disease in Pigs and Humans.

    PubMed

    Meyerholz, David K; Lambertz, Allyn M; Reznikov, Leah R; Ofori-Amanfo, Georgina K; Karp, Phil H; McCray, Paul B; Welsh, Michael J; Stoltz, David A

    2016-04-01

    Genetically engineered pigs are increasingly recognized as valuable models for the study of human disease. Immunohistochemical study of cellular markers of disease is an important tool for the investigation of these novel models so as to evaluate genotype and treatment differences. Even so, there remains a lack of validated markers for pig tissues that can serve as a translational link to human disease in organs such as the lung. Herein, we evaluate markers of cellular inflammation (cluster of differentiation [CD]3, CD79a, B cell lymphoma [BCL] 6, ionized calcium-binding adapter molecule [IBA]1, and myeloperoxidase) and those that may be involved with tissue remodeling (alpha-smooth muscle actin, beta-tubulin-III, lactoferrin, mucin [MUC]5AC, MUC5B, and cystic fibrosis transmembrane conductance regulator [CFTR]) for study of lung tissues. We compare the utility of these markers between pig and human lungs to validate translational relevance of each marker. Our results suggest these markers can be a useful addition in the pathological evaluation of porcine models of human disease. PMID:26511846

  20. Metabolic markers in sports medicine.

    PubMed

    Banfi, Giuseppe; Colombini, Alessandra; Lombardi, Giovanni; Lubkowska, Anna

    2012-01-01

    Physical exercise induces adaptations in metabolism considered beneficial for health. Athletic performance is linked to adaptations, training, and correct nutrition in individuals with genetic traits that can facilitate such adaptations. Intense and continuous exercise, training, and competitions, however, can induce changes in the serum concentrations of numerous laboratory parameters. When these modifications, especially elevated laboratory levels, result outside the reference range, further examinations are ordered or participation in training and competition is discontinued or sports practice loses its appeal. In order to correctly interpret commonly used laboratory data, laboratory professionals and sport physicians need to know the behavior of laboratory parameters during and after practice and competition. We reviewed the literature on liver, kidney, muscle, heart, energy, and bone parameters in athletes with a view to increase the knowledge about clinical chemistry applied to sport and to stimulate studies in this field. In liver metabolism, the interpretation of serum aminotransferases concentration in athletes should consider the release of aspartate aminotransferase (AST) from muscle and of alanine aminotransferase (ALT) mainly from the liver, when bilirubin can be elevated because of continuous hemolysis, which is typical of exercise. Muscle metabolism parameters such as creatine kinase (CK) are typically increased after exercise. This parameter can be used to interpret the physiological release of CK from muscle, its altered release due to rhabdomyolysis, or incomplete recovery due to overreaching or trauma. Cardiac markers are released during exercise, and especially endurance training. Increases in these markers should not simply be interpreted as a signal of cardiac damage or wall stress but rather as a sign of regulation of myocardial adaptation. Renal function can be followed in athletes by measuring serum creatinine concentration, but it should

  1. Carotta: Revealing Hidden Confounder Markers in Metabolic Breath Profiles

    PubMed Central

    Hauschild, Anne-Christin; Frisch, Tobias; Baumbach, Jörg Ingo; Baumbach, Jan

    2015-01-01

    Computational breath analysis is a growing research area aiming at identifying volatile organic compounds (VOCs) in human breath to assist medical diagnostics of the next generation. While inexpensive and non-invasive bioanalytical technologies for metabolite detection in exhaled air and bacterial/fungal vapor exist and the first studies on the power of supervised machine learning methods for profiling of the resulting data were conducted, we lack methods to extract hidden data features emerging from confounding factors. Here, we present Carotta, a new cluster analysis framework dedicated to uncovering such hidden substructures by sophisticated unsupervised statistical learning methods. We study the power of transitivity clustering and hierarchical clustering to identify groups of VOCs with similar expression behavior over most patient breath samples and/or groups of patients with a similar VOC intensity pattern. This enables the discovery of dependencies between metabolites. On the one hand, this allows us to eliminate the effect of potential confounding factors hindering disease classification, such as smoking. On the other hand, we may also identify VOCs associated with disease subtypes or concomitant diseases. Carotta is an open source software with an intuitive graphical user interface promoting data handling, analysis and visualization. The back-end is designed to be modular, allowing for easy extensions with plugins in the future, such as new clustering methods and statistics. It does not require much prior knowledge or technical skills to operate. We demonstrate its power and applicability by means of one artificial dataset. We also apply Carotta exemplarily to a real-world example dataset on chronic obstructive pulmonary disease (COPD). While the artificial data are utilized as a proof of concept, we will demonstrate how Carotta finds candidate markers in our real dataset associated with confounders rather than the primary disease (COPD) and bronchial

  2. Carotta: Revealing Hidden Confounder Markers in Metabolic Breath Profiles.

    PubMed

    Hauschild, Anne-Christin; Frisch, Tobias; Baumbach, Jörg Ingo; Baumbach, Jan

    2015-01-01

    Computational breath analysis is a growing research area aiming at identifying volatile organic compounds (VOCs) in human breath to assist medical diagnostics of the next generation. While inexpensive and non-invasive bioanalytical technologies for metabolite detection in exhaled air and bacterial/fungal vapor exist and the first studies on the power of supervised machine learning methods for profiling of the resulting data were conducted, we lack methods to extract hidden data features emerging from confounding factors. Here, we present Carotta, a new cluster analysis framework dedicated to uncovering such hidden substructures by sophisticated unsupervised statistical learning methods. We study the power of transitivity clustering and hierarchical clustering to identify groups of VOCs with similar expression behavior over most patient breath samples and/or groups of patients with a similar VOC intensity pattern. This enables the discovery of dependencies between metabolites. On the one hand, this allows us to eliminate the effect of potential confounding factors hindering disease classification, such as smoking. On the other hand, we may also identify VOCs associated with disease subtypes or concomitant diseases. Carotta is an open source software with an intuitive graphical user interface promoting data handling, analysis and visualization. The back-end is designed to be modular, allowing for easy extensions with plugins in the future, such as new clustering methods and statistics. It does not require much prior knowledge or technical skills to operate. We demonstrate its power and applicability by means of one artificial dataset. We also apply Carotta exemplarily to a real-world example dataset on chronic obstructive pulmonary disease (COPD). While the artificial data are utilized as a proof of concept, we will demonstrate how Carotta finds candidate markers in our real dataset associated with confounders rather than the primary disease (COPD) and bronchial

  3. A microfluidic device for label-free, physical capture of circulating tumor cell-clusters

    PubMed Central

    Sarioglu, A. Fatih; Aceto, Nicola; Kojic, Nikola; Donaldson, Maria C.; Zeinali, Mahnaz; Hamza, Bashar; Engstrom, Amanda; Zhu, Huili; Sundaresan, Tilak K.; Miyamoto, David T.; Luo, Xi; Bardia, Aditya; Wittner, Ben S.; Ramaswamy, Sridhar; Shioda, Toshi; Ting, David T.; Stott, Shannon L.; Kapur, Ravi; Maheswaran, Shyamala; Haber, Daniel A.; Toner, Mehmet

    2015-01-01

    Cancer cells metastasize through the bloodstream either as single migratory circulating tumor cells (CTCs) or as multicellular groupings (CTC-clusters). Existing technologies for CTC enrichment are designed primarily to isolate single CTCs, and while CTC-clusters are detectable in some cases, their true prevalence and significance remain to be determined. Here, we developed a microchip technology (Cluster-Chip) specifically designed to capture CTC-clusters independent of tumor-specific markers from unprocessed blood. CTC-clusters are isolated through specialized bifurcating traps under low shear-stress conditions that preserve their integrity and even two-cell clusters are captured efficiently. Using the Cluster-Chip, we identify CTC-clusters in 30–40% of patients with metastatic cancers of the breast, prostate and melanoma. RNA sequencing of CTC-clusters confirms their tumor origin and identifies leukocytes within the clusters as tissue-derived macrophages. Together, the development of a device for efficient capture of CTC-clusters will enable detailed characterization of their biological properties and role in cancer metastasis. PMID:25984697

  4. Newer markers for hepatocellular carcinoma.

    PubMed

    Marrero, Jorge A; Lok, Anna S F

    2004-11-01

    The incidence of hepatocellular carcinoma (HCC) is increasing worldwide; the overall survival of patients with HCC is grim because most patients are diagnosed late, when curative treatment is not possible. Cirrhosis is the strongest risk factor for the development of HCC. HCC surveillance with alpha-fetoprotein (AFP) and ultrasonography has been recommended for persons with cirrhosis. However, AFP level is insensitive for the early detection of HCC, and ultrasonography is expensive and operator dependent. Clearly, there is a need for novel strategies for the early detection of HCC. The ideal biomarker assay for HCC would be sensitive, specific, noninvasive, reproducible, inexpensive, and acceptable to patients. The Early Detection Research Network of the National Cancer Institute has proposed 5 phases for biomarker validation: preclinical exploratory studies, clinical assay development for disease, retrospective longitudinal study to detect preclinical disease, prospective screening study, and cancer control studies. Several biomarkers, such as des-gamma carboxyprothrombin, lens culinaris agglutinin-reactive AFP, human hepatocyte growth factor, and insulin-like growth factor-1, are promising, but none of these markers has been validated for clinical use. Limitations of the current literature include inadequate sample size, heterogeneity in biomarker assay methods and result reporting, limited analysis of demographics and cause of liver disease as covariates in the expression of these markers, and a scarcity of longitudinal studies evaluating the ability of biomarkers to detect preclinical disease. There is an urgent need for novel biomarkers for the detection of early HCC; the National Cancer Institute proposal provides a framework for future validation studies. PMID:15508074

  5. Markers of exposure to carcinogens.

    PubMed Central

    Wogan, G N

    1989-01-01

    Methods have been developed for the detection of exposure to carcinogens and other DNA damaging agents in experimental animals and man through the detection of carcinogens or their metabolic derivatives in body fluids, or through adducts bound covalently to DNA or hemoglobin. The successful use of urinary markers of genotoxic exposures has been reported with respect to nitrosoproline as an indicator of exposure to N-nitroso compounds. The same approach has been used to detect AFB1 and AFB1-N7-Gua as markers of exposure to aflatoxin B1; of 3-methyladenine produced as a result of exposure to methylating agents; and thymine glycol as an indicator of exposure to agents causing oxidative damage to DNA. Detection of adducts formed between genotoxic agents and hemoglobin has been reported in studies of populations occupationally exposed to ethylene oxide, in which 3-hydroxyhistidine and 3-hydroxyvaline have been measured, and in smokers, whose hemoglobin has been found to contain levels of 4-aminobiphenyl and 3-hydroxyvaline that were correlated with the frequency of cigarette smoking. Detection of DNA adducts of genotoxic agents in the cells and tissues of exposed individuals has also been accomplished through the use of several types of analytical methods. Immunoassays and physicochemical methods have been applied to detect adducts formed through the major intermediate in the activation of benzo(a)pyrene, the 7,8-diol-9,10-epoxide (BPDE). This adduct has been found in the DNA of peripheral leukocytes of workers in foundries, aluminum manufacturing plants, roofers, and coke oven plants, and also in cigarette smokers.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2667991

  6. Clustering of complex shaped data sets via Kohonen maps and mathematical morphology

    NASA Astrophysics Data System (ADS)

    Ferreira Costa, Jose A.; de Andrade Netto, Marcio L.

    2001-03-01

    Clustering is the process of discovering groups within the data, based on similarities, with a minimal, if any, knowledge of their structure. The self-organizing (or Kohonen) map (SOM) is one of the best known neural network algorithms. It has been widely studied as a software tool for visualization of high-dimensional data. Important features include information compression while preserving topological and metric relationship of the primary data items. Although Kohonen maps had been applied for clustering data, usually the researcher sets the number of neurons equal to the expected number of clusters, or manually segments a two-dimensional map using some a-priori knowledge of the data. This paper proposes techniques for automatic partitioning and labeling SOM networks in clusters of neurons that may be used to represent the data clusters. Mathematical morphology operations, such as watershed, are performed on the U-matrix, which is a neuron-distance image. The direct application of watershed leads to an oversegmented image. It is used markers to identify significant clusters and homotopy modification to suppress the others. Markers are automatically found by performing a multilevel scan of connected regions of the U-matrix. Each cluster of neurons is a sub-graph that defines, in the input space, complex and non-parametric geometries which approximately describes the shape of the clusters. The process of map partitioning is extended recursively. Each cluster of neurons gives rise to a new map, which are trained with the subset of data that were classified to it. The algorithm produces dynamically a hierarchical tree of maps, which explains the cluster's structure in levels of granularity. The distributed and multiple prototypes cluster representation enables the discoveries of clusters even in the case when we have two or more non-separable pattern classes.

  7. Clustering in bubbly liquids

    NASA Astrophysics Data System (ADS)

    Figueroa, Bernardo; Zenit, Roberto

    2004-11-01

    We are conducting experiments to determine the amount of clustering that occurs when small gas bubbles ascend in clean water. In particular, we are interested in flows for which the liquid motion around the bubbles can be described, with a certain degree of accuracy, using potential flow theory. This model is applicable for the case of bubbly liquids in which the Reynolds number is large and the Weber number is small. To clearly observe the formation of bubble clusters we propose the use of a Hele-Shaw-type channel. In this thin channel the bubbles cannot overlap in the depth direction, therefore the identification of bubble clusters cannot be misinterpreted. Direct video image analysis is performed to calculate the velocity and size of the bubbles, as well as the formation of clusters. Although the walls do affect the motion of the bubbles, the clustering phenomena does occur and has the same qualitative behavior as in fully three-dimensional flows. A series of preliminary measurements are presented. A brief discussion of our plans to perform PIV measurements to obtain the liquid velocity fields is also presented.

  8. HST Cluster Supernova Survey

    NASA Astrophysics Data System (ADS)

    Suzuki, Nao; Aldering, G.; Amanullah, R.; Barbary, K.; Barrientos, L.; Brodwin, M.; Connolly, N.; Dawson, K.; de Jong, R.; Dey, A.; Doi, M.; Donahue, M.; Eisenhardt, P.; Ellingson, E.; Faccioli, L.; Fadeyev, V.; Fakhouri, H.; Fruchter, A.; Gilbank, D.; Gladders, M.; Goldhaber, G.; Gonzalez, A.; Goobar, A.; Gude, A.; Hennawi, J.; Hoekstra, H.; Hsiao, E.; Huang, X.; Ihara, Y.; Jannuzi, B.; Jee, M. J.; Koester, B.; Kowalski, M.; Lidman, C.; Linder, E.; Lubin, L.; Morokuma, T.; Perlmutter, S.; Postman, M.; Rhodes, J.; Rosati, P.; Ripoche, P.; Rubin, D.; Schlegel, D.; Spadafora, A.; Stanford, A.; Stern, D.; Yasuda, N.; Yee, H.; Cosmology Project, Supernova

    2010-01-01

    We report results from the Hubble Space Telescope (HST) Cluster Supernova Survey with the Advanced Camera for Surveys (ACS) (PI: Perlmutter; see Dawson et al. AJ, 2009). We have introduced a novel approach to discover and follow Type Ia supernovae (SNeIa). With HST, we monitored 25 massive clusters (0.9 < z < 1.4) found by the RCS, XMM, IRAC, and RDCS surveys and conducted spectroscopic observations with the Keck, Subaru, and VLT telescopes. Sixteen SNe were discovered at 0.95 < z < 1.41, nine of which were in galaxy clusters (for a discussion of the rates, see K. Barbary, oral presentation at this meeting). The SNe in galaxy clusters are found primarily in early type galaxies in the cluster red-sequence that have been shown to be nearly dust-free and uniform populations (see poster presentation by Meyers et al.). The reduction and control of systematic error is an urgent task for the study of dark energy today (see Rubin et al. poster presentation), and we discuss how this unique SNe Ia data set reduces both statistical and more importantly systematic uncertainty at the highest redshifts. This work has been supported by the Office of Science, U.S. Department of Energy, through contract DE-AC02-05CH11231 and in part by NASA through grants associated with HST-GO-10496.

  9. ROTATING GLOBULAR CLUSTERS

    SciTech Connect

    Bianchini, P.; Varri, A. L.; Bertin, G.; Zocchi, A.

    2013-07-20

    Internal rotation is thought to play a major role in the dynamics of some globular clusters. However, in only a few cases has internal rotation been studied by the quantitative application of realistic and physically justified global models. Here, we present a dynamical analysis of the photometry and three-dimensional kinematics of {omega} Cen, 47 Tuc, and M15, by means of a recently introduced family of self-consistent axisymmetric rotating models. The three clusters, characterized by different relaxation conditions, show evidence of differential rotation and deviations from sphericity. The combination of line-of-sight velocities and proper motions allows us to determine their internal dynamics, predict their morphology, and estimate their dynamical distance. The well-relaxed cluster 47 Tuc is interpreted very well by our model; internal rotation is found to explain the observed morphology. For M15, we provide a global model in good agreement with the data, including the central behavior of the rotation profile and the shape of the ellipticity profile. For the partially relaxed cluster {omega} Cen, the selected model reproduces the complex three-dimensional kinematics; in particular, the observed anisotropy profile, characterized by a transition from isotropy to weakly radial anisotropy and then to tangential anisotropy in the outer parts. The discrepancy found for the steep central gradient in the observed line-of-sight velocity dispersion profile and for the ellipticity profile is ascribed to the condition of only partial relaxation of this cluster and the interplay between rotation and radial anisotropy.

  10. Identification of Turkish and standard apple rootstocks by morphological and molecular markers.

    PubMed

    Koc, A; Akbulut, M; Orhan, E; Celik, Z; Bilgener, S; Ercisli, S

    2009-01-01

    Two local (Vezir-1 and Vezir-2) and two standard (M9 and MM106) clonal apple rootstocks were compared using both morphological and molecular markers. International Union for the Protection of New Varieties of Plants criteria were used for morphological evaluation, which did not clearly separate these rootstocks. We tested 47 random decamer primers for random amplified polymorphic DNA analysis; 15 of them gave reproducible polymorphic patterns, yielding 109 bands, which showed 78% polymorphism. Based on a dendrogram obtained by unweighted pair group method using arithmetic average analysis, three clusters were obtained. The highest genetic similarities were found between M9 and Vezir-2 (0.670). The random amplified polymorphic DNA markers proved to be more efficient than the standard morphological markers for the identification of rootstocks. PMID:19551628

  11. Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas

    PubMed Central

    Porter, Teresita M.; Shokralla, Shadi; Baird, Donald; Golding, G. Brian; Hajibabaei, Mehrdad

    2016-01-01

    Though the use of metagenomic methods to sample below-ground fungal communities is common, the use of similar methods to sample plants from their underground structures is not. In this study we use high throughput sequencing of the ribulose-bisphosphate carboxylase large subunit (rbcL) plastid marker to study the plant community as well as the internal transcribed spacer and large subunit ribosomal DNA (rDNA) markers to investigate the fungal community from two wetland sites. Observed community richness and composition varied by marker. The two rDNA markers detected complementary sets of fungal taxa and total fungal composition clustered according to primer rather than by site. The composition of the most abundant plants, however, clustered according to sites as expected. We suggest that future studies consider using multiple genetic markers, ideally generated from different primer sets, to detect a more taxonomically diverse suite of taxa compared with what can be detected by any single marker alone. Conclusions drawn from the presence of even the most frequently observed taxa should be made with caution without corroborating lines of evidence. PMID:26731732

  12. Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas.

    PubMed

    Porter, Teresita M; Shokralla, Shadi; Baird, Donald; Golding, G Brian; Hajibabaei, Mehrdad

    2016-01-01

    Though the use of metagenomic methods to sample below-ground fungal communities is common, the use of similar methods to sample plants from their underground structures is not. In this study we use high throughput sequencing of the ribulose-bisphosphate carboxylase large subunit (rbcL) plastid marker to study the plant community as well as the internal transcribed spacer and large subunit ribosomal DNA (rDNA) markers to investigate the fungal community from two wetland sites. Observed community richness and composition varied by marker. The two rDNA markers detected complementary sets of fungal taxa and total fungal composition clustered according to primer rather than by site. The composition of the most abundant plants, however, clustered according to sites as expected. We suggest that future studies consider using multiple genetic markers, ideally generated from different primer sets, to detect a more taxonomically diverse suite of taxa compared with what can be detected by any single marker alone. Conclusions drawn from the presence of even the most frequently observed taxa should be made with caution without corroborating lines of evidence. PMID:26731732

  13. DNA polymorphisms in chickpea accessions as revealed by PCR-based markers.

    PubMed

    Yadav, P; Koul, K K; Shrivastava, N; Mendaki, M J; Bhagyawant, S S

    2015-01-01

    Chickpea is a food legume which is alleged to be a preferred source of protein next only to milk. Germplasm of cultivated chickpea available is deficient in desired genetic variation. Genetic manipulations therefore, necessitate the genetic exploitation of its related annual and wild species. 42 RAPD and 41 ISSR markers were employed to ascertain polymorphism across 20 genotypes which were collected from 10 different geographical areas of the world. RAPD marker detected 51% genetic polymorphisms while ISSR marker detected 54 %. With an average of 6.5 each RAPD primer amplified 5—8 bands. Similarly with an average of 7.9 each ISSR primer amplified 4—12 bands. The cluster dendrogram demonstrated a similarity coefficient range from 0.80 to 0.92 due to RAPD markers, whereas with ISSR primers the cluster dendrogram showed similarity coefficient of 0.60 to 1.00. Accessions from same geographical area seem to be genetically similar than those from geographically distant and isolated ones. When however compared, interestingly the ISSR dendrogram showed more correlation with pedigree data than the RAPD dendrogram. The variability index worked out in the present study ranges from 0.79 to 0.96. Since the ultimate reason for such studies is selection of diverse genetic accessions for their recommendation to breeding programmers, the accessions like ICC6263, ICC6306 and ICC17160 can be recommended as parents. Further breeding programmes can therefore be planned to procure additional variation complexes in chickpea genetic stocks. PMID:26516116

  14. Micro- and minisatellite-expressed sequence tag (EST) markers discriminate between populations of Rhipicephalus appendiculatus.

    PubMed

    Kanduma, Esther G; Mwacharo, Joram M; Sunter, Jack D; Nzuki, Inosters; Mwaura, Stephen; Kinyanjui, Peter W; Kibe, Michael; Heyne, Heloise; Hanotte, Olivier; Skilton, Robert A; Bishop, Richard P

    2012-06-01

    Biological differences, including vector competence for the protozoan parasite Theileria parva have been reported among populations of Rhipicephalus appendiculatus (Acari: Ixodidae) from different geographic regions. However, the genetic diversity and population structure of this important tick vector remain unknown due to the absence of appropriate genetic markers. Here, we describe the development and evaluation of a panel of EST micro- and minisatellite markers to characterize the genetic diversity within and between populations of R. appendiculatus and other rhipicephaline species. Sixty-six micro- and minisatellite markers were identified through analysis of the R. appendiculatus Gene Index (RaGI) EST database and selected bacterial artificial chromosome (BAC) sequences. These were used to genotype 979 individual ticks from 10 field populations, 10 laboratory-bred stocks, and 5 additional Rhipicephalus species. Twenty-nine markers were polymorphic and therefore informative for genetic studies while 6 were monomorphic. Primers designed from the remaining 31 loci did not reliably generate amplicons. The 29 polymorphic markers discriminated populations of R. appendiculatus and also 4 other Rhipicephalus species, but not R. zambeziensis. The percentage Principal Component Analysis (PCA) implemented using Multiple Co-inertia Analysis (MCoA) clustered populations of R. appendiculatus into 2 groups. Individual markers however differed in their ability to generate the reference typology using the MCoA approach. This indicates that different panels of markers may be required for different applications. The 29 informative polymorphic micro- and minisatellite markers are the first available tools for the analysis of the phylogeography and population genetics of R. appendiculatus. PMID:22789728

  15. Genetic variability of oil palm parental genotypes and performance of its' progenies as revealed by molecular markers and quantitative traits.

    PubMed

    Abdullah, Norziha; Rafii Yusop, Mohd; Ithnin, Maizura; Saleh, Ghizan; Latif, M A

    2011-04-01

    Studies were conducted to assess the genetic relationships between the parental palms (dura and pisifera) and performance of their progenies based on nine microsatellite markers and 29 quantitative traits. Correlation analyses between genetic distances and hybrids performance were estimated. The coefficients of correlation values of genetic distances with hybrid performance were non-significant, except for mean nut weight and leaf number. However, the correlation coefficient of genetic distances with these characters was low to be used as predicted value. These results indicated that genetic distances based on the microsatellite markers may not be useful for predicting hybrid performance. The genetic distance analysis using UPGMA clustering system generated 5 genetic clusters with coefficient of 1.26 based on quantitative traits of progenies. The genotypes, DP16, DP14, DP4, DP13, DP12, DP15, DP8, DP1 and DP2 belonging to distant clusters and greater genetic distances could be selected for further breeding programs. PMID:21513898

  16. GENETIC VARIATION AND IDENTIFICATION OF PROMISING SOUR CHERRIES INFERRED FROM MICROSATELLITE MARKERS.

    PubMed

    Najafzadeh, R; Arzani, K; Bouzari, N; Saei, A

    2016-01-01

    The aim of this study was to identify the group of highly polymorphic microsatellite markers for identification of promising sour cherries. From among 30 tested microsatellite (SSR) markers, 19 were selected to profile genetic variation in sour cherries due to high polymorphisms. Results indicated a high level of polymorphism of the accessions based on these markers. Totally 148 alleles were generated at 19 SSR loci which 122 alleles were polymorphic. The number of total alleles per locus ranged from 2 to 15 with an average of 7.78 and polymorphism percentage varied from 50 to 100% with an average of 78.76%. Also, PIC varied from 0.47 to 0.89 with an average of 0.79 and heterozygosity ranged from 0.35 to 0.55 with a mean of 0.45. According to these results, these markers specially PMS3, PS12A02, PceGA34, BPPCT021, EMPA004, EMPA018, and Pchgms3 produced good and various levels of amplifications and showed high heterozygosity levels. By the way, the genetic similarity showed a high diversity among the sour cherries. Cluster analysis separated improved cultivars from promising sour cherries, and the PCoA supported the cluster analysis results. Since the studied sour cherries were superior to the improved cultivars and were separated from them in most groups, these sour cherries can be considered as distinct genotypes for further evaluations in the framework of breeding programs and new cultivar identification in cherries. Results also confirmed that the set of microsatellite markers employed in this study demonstrated usefulness of microsatellite markers for the identification of sour cherry genotypes. PMID:27183795

  17. Genetic variability and structure of Quercus brantii assessed by ISSR, IRAP and SCoT markers.

    PubMed

    Alikhani, Leila; Rahmani, Mohammad-Shafie; Shabanian, Naghi; Badakhshan, Hedieh; Khadivi-Khub, Abdollah

    2014-11-15

    Persian oak (Quercus brantii Lindl.) is one of the most important woody species of the Zagros forests in Iran. Three molecular marker techniques: start codon targeted (SCoT), inter-simple sequence repeat (ISSR) and inter-retrotransposon amplified polymorphism (IRAP) markers were compared for fingerprinting of 125 individuals of this species collected from different geographical locations of north-west of Iran. A total of 233 bands were amplified by 18 ISSR primers, of which 224 (96.10%) were polymorphic, and 126 polymorphic bands (97.65%) were observed in 129 bands amplified by 10 IRAP primers. Besides, 118 bands were observed for all 10 SCoT primers, of which 113 were polymorphic (95.71%). Average polymorphism information content (PIC) for ISSR, IRAP and SCoT markers was 0.30, 0.32 and 0.38, respectively, and this revealed that SCoT markers were more informative than IRAP and ISSR for the assessment of diversity among individuals. Based on the three different molecular types, cluster analysis revealed that 125 individuals taken for the analysis can be divided into three distinct clusters. The Jaccard's genetic similarity based on the combined data ranged from 0.23 to 0.76. These results suggest that efficiency of SCoT, IRAP and ISSR markers was relatively the same in fingerprinting of individuals. All molecular marker types revealed a low genetic differentiation among populations, indicating the possibility of gene flow between the studied populations. These results have an important implication for Persian oak (Q. brantii) germplasm characterization, improvement, and conservation. PMID:25241382

  18. [Measurement of Liver Fibrosis Marker Targeting Sugar Chain Marker].

    PubMed

    Shibata, Hiroshi; Kakuda, Hirokazu; Morikawa, Takashi; Funakoshi, Kunihiro

    2015-01-01

    The degree of liver fibrosis progression is an important factor in hepatocarcinogenesis, and monitoring liver fibrosis is important for predicting and preventing hepatocellular carcinoma. It is proportional to the appearance of a new hepatitis C therapy, or the expectation of liver fibrosis therapy, and liver fibrosis research is attracting attention. Although the Gold Standard for the diagnosis of liver fibrosis is liver biopsy, various problems, such as in the difficulty of invasive and frequent measurement, exist. The present non-invasive examination methods for the assessment of liver fibrosis also have a problem in the fields of organ specificity and diagnostic performance. Using a fully automated immunoassay system "HISCL", an assay system based on the lectin bound sugar reaction which is not an antigen-bound antibody reaction was developed. Measurements using the fully automated immunoassay system "HISCL" series and HISCL M2BPGi assay kit facilitated rapid assay (17 minutes) with a small sample volume (10 μL). Serum M2BPGi values can be used in various ways, such as for assessment of the risk and treatment associated with hepatocellular carcinoma, reflecting the liver fibrosis stage. Furthermore, many studies are currently in progress. The development of a new assay system for the detection of a cancer production sugar chain marker is expected in the future owing to the advent of a lectin-bound sugar chain reaction system. PMID:26524881

  19. Vanadogermanate cluster anions.

    PubMed

    Whitfield, T; Wang, X; Jacobson, A J

    2003-06-16

    Three novel vanadogermanate cluster anions have been synthesized by hydrothermal reactions. The cluster anions are derived from the (V(18)O(42)) Keggin cluster shell by substitution of V=O(2+) "caps" by Ge(2)O(OH)(2)(4+) species. In Cs(8)[Ge(4)V(16)O(42)(OH)(4)].4.7H(2)O, 1, (monoclinic, space group C2/c (No. 15), Z = 8, a = 44.513(2) A, b = 12.7632(7) A, c = 22.923(1) A, beta = 101.376(1) degrees ) and (pipH(2))(4)(pipH)(4)[Ge(8)V(14)O(50).(H(2)O)] (pip = C(4)N(2)H(10)), 2 (tetragonal, space group P4(2)/nnm (No. 134), Z = 2, a = 14.9950(7) A, c = 18.408(1) A), two and four VO(2+) caps are replaced, respectively, and each cluster anion encapsulates a water molecule. In K(5)H(8)Ge(8)V(12)SO(52).10H(2)O, 3, (tetragonal, space group I4/m (No. 87), Z = 2, a = 15.573(1) A, c = 10.963(1) A), four VO(2+) caps are replaced by Ge(2)O(OH)(2)(4+) species, and an additional two are omitted. The cluster ion in 3 contains a sulfate anion disordered over two positions. The cluster anions are analogous to the vanadoarsenate anions [V(18)(-)(n)()As(2)(n)()O(42)(X)](m)(-) (X = SO(3), SO(4), Cl; n = 3, 4) previously reported. PMID:12793808

  20. Clusters in storage rings

    SciTech Connect

    Hvelplund, P.; Andersen, J. U.; Hansen, K.

    1999-01-15

    Anions of fullerenes and small metal clusters have been stored in the storage rings ASTRID and ELISA. Decays on a millisecond time scale are due to electron emission from metastable excited states. For the fullerenes the decay curves have been interpreted in terms of thermionic emission quenched by radiative cooling. The stored clusters were heated by a Nd:YAG laser resulting in increased emission rates. With an OPO laser this effect was used to study the wavelength dependence of the absorption of light in hot C{sub 60}{sup -} ion molecules.

  1. Clustering of Resting State Networks

    PubMed Central

    Lee, Megan H.; Hacker, Carl D.; Snyder, Abraham Z.; Corbetta, Maurizio; Zhang, Dongyang; Leuthardt, Eric C.; Shimony, Joshua S.

    2012-01-01

    Background The goal of the study was to demonstrate a hierarchical structure of resting state activity in the healthy brain using a data-driven clustering algorithm. Methodology/Principal Findings The fuzzy-c-means clustering algorithm was applied to resting state fMRI data in cortical and subcortical gray matter from two groups acquired separately, one of 17 healthy individuals and the second of 21 healthy individuals. Different numbers of clusters and different starting conditions were used. A cluster dispersion measure determined the optimal numbers of clusters. An inner product metric provided a measure of similarity between different clusters. The two cluster result found the task-negative and task-positive systems. The cluster dispersion measure was minimized with seven and eleven clusters. Each of the clusters in the seven and eleven cluster result was associated with either the task-negative or task-positive system. Applying the algorithm to find seven clusters recovered previously described resting state networks, including the default mode network, frontoparietal control network, ventral and dorsal attention networks, somatomotor, visual, and language networks. The language and ventral attention networks had significant subcortical involvement. This parcellation was consistently found in a large majority of algorithm runs under different conditions and was robust to different methods of initialization. Conclusions/Significance The clustering of resting state activity using different optimal numbers of clusters identified resting state networks comparable to previously obtained results. This work reinforces the observation that resting state networks are hierarchically organized. PMID:22792291

  2. Precision Photometric Redshifts Of Clusters

    NASA Astrophysics Data System (ADS)

    Holden, L.; Annis, J.

    2006-06-01

    Clusters of galaxies provide a means to achieve more precise photometric redshifts than achievable using individual galaxies simply because of the numbers of galaxies available in clusters. Here we examine the expectation that one can achieve root-N improvement using the N galaxies in a cluster. We extracted from a maxBCG SDSS cluster catalog 28,000 clusters and used SDSS DR4 spectra to find spectroscopic redshifts for the cluster. We examined both using the brightest cluster galaxy redshift as the proxy for the cluster and using the mean of a collection of galaxies within a given angular diameter and redshift (about the cluster photo-z) range. We find that the BCG provides a better estimate of the cluster redshift, to be understood in the context of a handful of spectra in the neighborhood of the cluster. We find that the cluster photo-z has an approximate root-N scaling behavior with the normalization for maxBCG techniques being 0.07. We predict what ``afterburner photo-z'' techniques, which use individual galaxy photo-z's good to 0.03-0.05, can achieve for cluster catalogs and for cluster cosmology.

  3. Inflammatory markers in primary aldosteronism.

    PubMed

    Šomlóová, Z; Petrák, O; Rosa, J; Štrauch, B; Indra, T; Zelinka, T; Haluzík, M; Zikán, V; Holaj, R; Widimský, J

    2016-06-20

    Primary aldosteronism (PA) is the most common cause of endocrine hypertension with a high frequency of cardiovascular complications. The unfavorable cardiometabolic profile may be due to aldosterone-mediated activation of inflammatory cells, circulatory cytokines and activation of collagen synthesis in the vessel wall. Aim of our study was to evaluate differences in the levels of hsCRP, IL-6, TNF-alpha and N-terminal propeptide of collagen I (PINP) in patients with PA and essential hypertension (EH) as a control group, and between the subtypes of PA (aldosterone producing adenoma - APA, idiopathic hyperaldosteronism - IHA). We studied 28 patients with PA (IHA - 10 patients, APA - 12 patients, 6 unclassified) and 28 matched patients with EH. There were no differences in the levels of inflammatory markers between the followed groups [EH vs. PA: TNF-alpha (5.09 [3.68-6.32] vs. 4.84 [3.62-6.50] pg/ml), IL-6 (0.94 [0.70-1.13] vs. 0.97 [0.71-1.28] pg/ml), hsCRP (0.53 [0.25-1.54] vs. 0.37 [0.31-0.61] mg/l), leukocytes (6.35+/-1.42 vs. 5.97+/-1.29 10(9) l); APA vs. IHA: TNF-alpha (4.54 [3.62-7.03] vs. 5.19 [4.23-5.27] pg/ml), IL-6 (0.96 [0.63-1.21] vs. 0.90 [0.65-1.06] pg/ml), hsCRP (0.34 [0.29-0.47] vs. 0.75 [0.36-1.11] mg/l), leukocytes (6.37+/-1.41 vs. 5.71+/-1.21 10(9) l)]. Significant differences in the levels of PINP between PA and EH group were observed (35.18 [28.46-41.16] vs. 45.21 [36.95-62.81] microg/l, pmarkers were observed between the followed groups, we confirmed higher levels of PINP in patients with PA. PMID:26447510

  4. Characterizing Safflower Germplasm with AFLP Molecular Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Safflower (Carthamus tinctorius L.) accessions from the U.S. germplasm collection were characterized using AFLP (Amplified Length Polymorphisms) markers. Separation and scoring of 392 markers was completed using the Beckman CEQ8000 capillary electrophoresis system. Twelve plants from each of eight...

  5. MICROSATELLITE MARKERS FOR VERIFYING PARENTAGE OF PECANS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite or Simple Sequence Repeat (SSR) markers are being developed in ongoing research in the USDA ARS Pecan Breeding Program. These co-dominant markers provide a powerful tool for the verification of parentage. To confirm their utility, SSR profiles were used to confirm the parentage of 1...

  6. Update on genetic markers for pork quality

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To determine the robustness of reported marker associations with pork quality traits, assay systems were developed for as many polymorphisms from the literature as possible. These assays were genotyped across pigs (n = 1,291) with pork quality data available from four populations. Genetic marker-phe...

  7. 21 CFR 878.4660 - Skin marker.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Skin marker. 878.4660 Section 878.4660 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES GENERAL AND PLASTIC SURGERY DEVICES Surgical Devices § 878.4660 Skin marker. (a) Identification. A...

  8. 21 CFR 878.4660 - Skin marker.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Skin marker. 878.4660 Section 878.4660 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES GENERAL AND PLASTIC SURGERY DEVICES Surgical Devices § 878.4660 Skin marker. (a) Identification. A...

  9. 21 CFR 878.4660 - Skin marker.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Skin marker. 878.4660 Section 878.4660 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES GENERAL AND PLASTIC SURGERY DEVICES Surgical Devices § 878.4660 Skin marker. (a) Identification. A...

  10. 21 CFR 878.4660 - Skin marker.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Skin marker. 878.4660 Section 878.4660 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES GENERAL AND PLASTIC SURGERY DEVICES Surgical Devices § 878.4660 Skin marker. (a) Identification. A...

  11. 21 CFR 878.4660 - Skin marker.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Skin marker. 878.4660 Section 878.4660 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES GENERAL AND PLASTIC SURGERY DEVICES Surgical Devices § 878.4660 Skin marker. (a) Identification. A...

  12. 43 CFR 15.6 - Markers.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Markers. 15.6 Section 15.6 Public Lands: Interior Office of the Secretary of the Interior KEY LARGO CORAL REEF PRESERVE § 15.6 Markers. No person shall willfully mark, deface or injure in any way, or displace, remove or tamper with any Preserve...

  13. 43 CFR 15.6 - Markers.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 43 Public Lands: Interior 1 2013-10-01 2013-10-01 false Markers. 15.6 Section 15.6 Public Lands: Interior Office of the Secretary of the Interior KEY LARGO CORAL REEF PRESERVE § 15.6 Markers. No person shall willfully mark, deface or injure in any way, or displace, remove or tamper with any Preserve...

  14. 43 CFR 15.6 - Markers.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 43 Public Lands: Interior 1 2014-10-01 2014-10-01 false Markers. 15.6 Section 15.6 Public Lands: Interior Office of the Secretary of the Interior KEY LARGO CORAL REEF PRESERVE § 15.6 Markers. No person shall willfully mark, deface or injure in any way, or displace, remove or tamper with any Preserve...

  15. 43 CFR 15.6 - Markers.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 1 2011-10-01 2011-10-01 false Markers. 15.6 Section 15.6 Public Lands: Interior Office of the Secretary of the Interior KEY LARGO CORAL REEF PRESERVE § 15.6 Markers. No person shall willfully mark, deface or injure in any way, or displace, remove or tamper with any Preserve...

  16. 43 CFR 15.6 - Markers.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 43 Public Lands: Interior 1 2012-10-01 2011-10-01 true Markers. 15.6 Section 15.6 Public Lands: Interior Office of the Secretary of the Interior KEY LARGO CORAL REEF PRESERVE § 15.6 Markers. No person shall willfully mark, deface or injure in any way, or displace, remove or tamper with any Preserve...

  17. Smart magnetic markers use in hydraulic fracturing.

    PubMed

    Zawadzki, Jarosław; Bogacki, Jan

    2016-11-01

    One of the main challenges and unknowns during shale gas exploration is to assess the range and efficiency of hydraulic fracturing. It is also essential to assess the distribution of proppant, which keeps the fracture pathways open. Solving these problems may considerably increase the efficiency of the shale gas extraction. Because of that, the idea of smart magnetic marker, which can be detected when added to fracturing fluid, has been considered for a long time. This study provides overview of the possibilities of magnetic marker application for shale gas extraction. The imaging methods using electromagnetic markers, are considered or developed in two directions. The first possibility is the markers' electromagnetic activity throughout the whole volume of the fracturing fluid. Thus, it can be assumed that the whole fracturing fluid is the marker. Among these type of hydraulic fracturing solutions, ferrofluid could be considered. The second possibility is marker, which is just one of many components of the fracturing fluid. In this case feedstock magnetic materials, ferrites and nanomaterials could be considered. Magnetic properties of magnetite could be too low and ferrofluids' or nanomaterials' price is unacceptably high. Because of that, ferrites, especially ZnMn ferrites seems to be the best material for magnetic marker. Because of the numerous applications in electronics, it is cheap and easily available, although the price is higher, then that of magnetite. The disadvantage of using ferrite, could be too small mechanical strength. It creates an essential need for combining magnetic marker with proppant into magnetic-ceramic composite. PMID:27475294

  18. Bilingual Discourse Markers in Indigenous Languages

    ERIC Educational Resources Information Center

    Torres, Lourdes

    2006-01-01

    This review of research considers the occurrence and function of Spanish discourse markers and other particles in indigenous speech. I discuss important research that has examined these phenomena and refer to studies of bilingual discourse markers in other non-indigenous language contact situations to address unresolved issues concerning the form…

  19. Development of microsatellite markers in Parthenium ssp.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular markers provide the most efficient means to study genetic diversity within and among species of a particular genus. In addition, molecular markers can facilitate breeding efforts by providing tools necessary to reduce the time required to obtain recombinant genotypes with improved agricu...

  20. A molecular marker of artemisinin-resistant Plasmodium falciparum malaria

    NASA Astrophysics Data System (ADS)

    Ariey, Frédéric; Witkowski, Benoit; Amaratunga, Chanaki; Beghain, Johann; Langlois, Anne-Claire; Khim, Nimol; Kim, Saorin; Duru, Valentine; Bouchier, Christiane; Ma, Laurence; Lim, Pharath; Leang, Rithea; Duong, Socheat; Sreng, Sokunthea; Suon, Seila; Chuor, Char Meng; Bout, Denis Mey; Ménard, Sandie; Rogers, William O.; Genton, Blaise; Fandeur, Thierry; Miotto, Olivo; Ringwald, Pascal; Le Bras, Jacques; Berry, Antoine; Barale, Jean-Christophe; Fairhurst, Rick M.; Benoit-Vical, Françoise; Mercereau-Puijalon, Odile; Ménard, Didier

    2014-01-01

    Plasmodium falciparum resistance to artemisinin derivatives in southeast Asia threatens malaria control and elimination activities worldwide. To monitor the spread of artemisinin resistance, a molecular marker is urgently needed. Here, using whole-genome sequencing of an artemisinin-resistant parasite line from Africa and clinical parasite isolates from Cambodia, we associate mutations in the PF3D7_1343700 kelch propeller domain (`K13-propeller') with artemisinin resistance in vitro and in vivo. Mutant K13-propeller alleles cluster in Cambodian provinces where resistance is prevalent, and the increasing frequency of a dominant mutant K13-propeller allele correlates with the recent spread of resistance in western Cambodia. Strong correlations between the presence of a mutant allele, in vitro parasite survival rates and in vivo parasite clearance rates indicate that K13-propeller mutations are important determinants of artemisinin resistance. K13-propeller polymorphism constitutes a useful molecular marker for large-scale surveillance efforts to contain artemisinin resistance in the Greater Mekong Subregion and prevent its global spread.

  1. Genetic relationships among Heliconia (Heliconiaceae) species based on RAPD markers.

    PubMed

    Marouelli, L P; Inglis, P W; Ferreira, M A; Buso, G S C

    2010-01-01

    The family Heliconiaceae contains a single genus, Heliconia, with approximately 180 species of Neotropical origin. This genus was formerly allocated to the family Musaceae, but today forms its own family, in the order Zingiberales. The combination of inverted flowers, a single staminode and drupe fruits is an exclusive characteristic of Heliconia. Heliconias are cultivated as ornamental garden plants, and are of increasing importance as cut flowers. However, there are taxonomic confusions and uncertainties about the number of species and the relationships among them. Molecular studies are therefore necessary for better understanding of the species boundaries of these plants. We examined the genetic variability and the phylogenetic relationships of 124 accessions of the genus Heliconia based on RAPD markers. Phenetic and cladistic analyses, using 231 polymorphic RAPD markers, demonstrated that the genus Heliconia is monophyletic. Groupings corresponding to currently recognized species and some subgenera were found, and cultivars and hybrids were found to cluster with their parents. RAPD analysis generally agreed with morphological species classification, except for the position of the subgenus Stenochlamys, which was found to be polyphyletic. PMID:20645261

  2. A molecular marker of artemisinin-resistant Plasmodium falciparum malaria

    PubMed Central

    Ariey, Frédéric; Witkowski, Benoit; Amaratunga, Chanaki; Beghain, Johann; Langlois, Anne-Claire; Khim, Nimol; Kim, Saorin; Duru, Valentine; Bouchier, Christiane; Ma, Laurence; Lim, Pharath; Leang, Rithea; Duong, Socheat; Sreng, Sokunthea; Suon, Seila; Chuor, Char Meng; Bout, Denis Mey; Ménard, Sandie; Rogers, William O.; Genton, Blaise; Fandeur, Thierry; Miotto, Olivo; Ringwald, Pascal; Le Bras, Jacques; Berry, Antoine; Barale, Jean-Christophe; Fairhurst, Rick M.; Benoit-Vical, Françoise; Mercereau-Puijalon, Odile; Ménard, Didier

    2016-01-01

    Plasmodium falciparum resistance to artemisinin derivatives in southeast Asia threatens malaria control and elimination activities worldwide. To monitor the spread of artemisinin resistance, a molecular marker is urgently needed. Here, using whole-genome sequencing of an artemisinin-resistant parasite line from Africa and clinical parasite isolates from Cambodia, we associate mutations in the PF3D7_1343700 kelch propeller domain (‘K13-propeller’) with artemisinin resistance in vitro and in vivo. Mutant K13-propeller alleles cluster in Cambodian provinces where resistance is prevalent, and the increasing frequency of a dominant mutant K13-propeller allele correlates with the recent spread of resistance in western Cambodia. Strong correlations between the presence of a mutant allele, in vitro parasite survival rates and in vivo parasite clearance rates indicate that K13-propeller mutations are important determinants of artemisinin resistance. K13-propeller polymorphism constitutes a useful molecular marker for large-scale surveillance efforts to contain artemisinin resistance in the Greater Mekong Subregion and prevent its global spread. PMID:24352242

  3. Molecular Diversity Assessment Using Sequence Related Amplified Polymorphism (SRAP) Markers in Vicia faba L.

    PubMed Central

    Alghamdi, Salem S.; Al-Faifi, Sulieman A.; Migdadi, Hussein M.; Khan, Muhammad Altaf; El-Harty, Ehab H.; Ammar, Megahed H.

    2012-01-01

    Sequence-related amplified polymorphism (SRAP) markers were used to assess the genetic diversity and relationship among 58 faba bean (Vicia faba L.) genotypes. Fourteen SRAP primer combinations amplified a total of 1036 differently sized well-resolved peaks (fragments), of which all were polymorphic with a 0.96 PIC value and discriminated all of the 58 faba bean genotypes. An average pairwise similarity of 21% was revealed among the genotypes ranging from 2% to 65%. At a similarity of 28%, UPGMA clustered the genotypes into three main groups comprising 78% of the genotypes. The local landraces and most of the Egyptian genotypes in addition to the Sudan genotypes were grouped in the first main cluster. The advanced breeding lines were scattered in the second and third main clusters with breeding lines from the ICARDA and genotypes introduced from Egypt. At a similarity of 47%, all the genotypes formed separated clusters with the exceptions of Hassawi 1 and Hassawi 2. Group analysis of the genotypes according to their geographic origin and type showed that the landraces were grouped according to their origin, while others were grouped according to their seed type. To our knowledge, this is the first application of SRAP markers for the assessment of genetic diversity in faba bean. Such information will be useful to determine optimal breeding strategies to allow continued progress in faba bean breeding. PMID:23211669

  4. Genetic diversity analysis of Capparis spinosa L. populations by using ISSR markers.

    PubMed

    Liu, C; Xue, G P; Cheng, B; Wang, X; He, J; Liu, G H; Yang, W J

    2015-01-01

    Capparis spinosa L. is an important medicinal species in the Xinjiang Province of China. Ten natural populations of C. spinosa from 3 locations in North, Central, and South Xinjiang were studied using morphological trait inter simple sequence repeat (ISSR) molecular markers to assess the genetic diversity and population structure. In this study, the 10 ISSR primers produced 313 amplified DNA fragments, with 52% of fragments being polymorphic. Unweighted pair-group method with arithmetic average (UPGMA) cluster analysis indicated that 10 C. spinosa populations were clustered into 3 geographically distinct groups. The Nei gene of C. spinosa populations in different regions had Diversity and Shannon's information index ranges of 0.1312-0.2001 and 0.1004-0.1875, respectively. The 362 markers were used to construct the dendrogram based on the UPGMA cluster analysis. The dendrogram indicated that 10 populations of C. spinosa were clustered into 3 geographically distinct groups. The results showed these genotypes have high genetic diversity, and can be used for an alternative breeding program. PMID:26662446

  5. Genetic traceability of black pig meats using microsatellite markers.

    PubMed

    Oh, Jae-Don; Song, Ki-Duk; Seo, Joo-Hee; Kim, Duk-Kyung; Kim, Sung-Hoon; Seo, Kang-Seok; Lim, Hyun-Tae; Lee, Jae-Bong; Park, Hwa-Chun; Ryu, Youn-Chul; Kang, Min-Soo; Cho, Seoae; Kim, Eui-Soo; Choe, Ho-Sung; Kong, Hong-Sik; Lee, Hak-Kyo

    2014-07-01

    Pork from Jeju black pig (population J) and Berkshire (population B) has a unique market share in Korea because of their high meat quality. Due to the high demand of this pork, traceability of the pork to its origin is becoming an important part of the consumer demand. To examine the feasibility of such a system, we aim to provide basic genetic information of the two black pig populations and assess the possibility of genetically distinguishing between the two breeds. Muscle samples were collected from slaughter houses in Jeju Island and Namwon, Chonbuk province, Korea, for populations J and B, respectively. In total 800 Jeju black pigs and 351 Berkshires were genotyped at thirteen microsatellite (MS) markers. Analyses on the genetic diversity of the two populations were carried out in the programs MS toolkit and FSTAT. The population structure of the two breeds was determined by a Bayesian clustering method implemented in structure and by a phylogenetic analysis in Phylip. Population J exhibited higher mean number of alleles, expected heterozygosity and observed heterozygosity value, and polymorphism information content, compared to population B. The FIS values of population J and population B were 0.03 and -0.005, respectively, indicating that little or no inbreeding has occurred. In addition, genetic structure analysis revealed the possibility of gene flow from population B to population J. The expected probability of identify value of the 13 MS markers was 9.87×10(-14) in population J, 3.17×10(-9) in population B, and 1.03×10(-12) in the two populations. The results of this study are useful in distinguishing between the two black pig breeds and can be used as a foundation for further development of DNA markers. PMID:25050032

  6. Colorimetric Immunoassay for Detection of Tumor Markers

    PubMed Central

    Yin, Yongmei; Cao, Ya; Xu, Yuanyuan; Li, Genxi

    2010-01-01

    Tumor markers are substances, usually proteins, produced by the body in response to cancer growth, or by the cancer tissue itself. They can be detected in blood, urine, or tissue samples, and the discovery and detection of tumor markers may provide earlier diagnosis of cancer and improved therapeutic intervention. Colorimetric immunoassays for tumor marker detection have attracted considerable attention, due to their simplicity and high efficiency. The traditionally used colorimetric immunoassays for the detection of tumor markers are based on enzyme-linked immunosorbent assays, and the great achievement of nanotechnology has further opened opportunities for the development of such kind of immunoassays. This paper will summarize recent advances in the field of colorimetric immunoassays for detecting tumor markers, which is aimed to provide an overview in this field, as well as experimental guidance for the learner. PMID:21614193

  7. Nanometer scale marker for fluorescent microscopy

    SciTech Connect

    Hiraga, Takashi; Iketaki, Yoshinori; Watanabe, Takeshi; Ohyi, Hideyuki; Kobayashi, Kazumasa; Yamamoto, Noritaka; Mizokuro, Toshiko; Fujii, Masaaki

    2005-07-15

    To establish a calibration method of optical performance in fluorescence microscopy, we fabricated a fluorescent nanometer-scale marker by combining a dry dye method for polymer film and fine lithography. The marker has a 50 nm line-and-space fluorescent pattern, finer than the optical diffraction limit. A spin-coated poly(methyl methacrylate) thin film on a silicon wafer was densely doped with Rhodamine 6G using a simple vacuum process, named the vapor-transportation method, and then the pattern was formed on the film using electron-beam lithography. The figure accuracy of the fabricated marker was calibrated by electron microscopes. Using this marker, one can quantitatively evaluate the optical properties; i.e., the contrast-transfer function, the point-spread function, magnification, and so on. To show practical use of the marker, we demonstrated the evaluation of a fluorescent microscope system.

  8. Tumor markers in prostate cancer I: blood-based markers

    PubMed Central

    Shariat, Shahrokh F.; Semjonow, Axel; Lilja, Hans; Savage, Caroline; Vickers, Andrew J.; Bjartell, Anders

    2013-01-01

    INTRODUCTION The introduction of total prostate specific antigen (total PSA) testing in blood has revolutionized the detection and management of men with prostate cancer (PCa). The objective of this review was to discuss the challenges of PCa biomarker research, definition of the type of PCa biomarkers, the statistical considerations for biomarker discovery and validation, and to review the literature regarding total PSA velocity and novel blood-based biomarkers. METHODS An English-language literature review of the Medline database (1990 to August 2010) of published data on blood-based biomarkers and PCa was undertaken. RESULTS The inherent biological variability of total PSA levels affects the interpretation of any single result. Men who will eventually develop PCa have increased total PSA levels years or decades before the cancer is diagnosed. Total PSA velocity improves predictiveness of total PSA only marginally, limiting its value for PCa screening and prognostication. The combination of PSA molecular forms and other biomarkers improve PCa detection substantially. Several novel blood-based biomarkers such as human glandular kallikrein 2 (hK2), urokinase plasminogen activator (uPA) and its receptor (uPAR), transforming growth factor-beta 1 (TGF-β1); interleukin-6 (IL-6) and its receptor (IL-6R) may help PCa diagnosis, staging, prognostication, and monitoring. Panels of biomarkers that capture the biologic potential of PCa are in the process of being validated for PCa prognostication. CONCLUSIONS PSA is a strong prognostic marker for long-term risk of clinically relevant cancer. However, there is a need for novel biomarkers that aid clinical decision making about biopsy and initial treatment. There is no doubt that progress will continue based on the integrated collaboration of researchers, clinicians and biomedical firms. PMID:21604943

  9. Fiducial marker for correlating images

    DOEpatents

    Miller, Lisa Marie; Smith, Randy J.; Warren, John B.; Elliott, Donald

    2011-06-21

    The invention relates to a fiducial marker having a marking grid that is used to correlate and view images produced by different imaging modalities or different imaging and viewing modalities. More specifically, the invention relates to the fiducial marking grid that has a grid pattern for producing either a viewing image and/or a first analytical image that can be overlaid with at least one other second analytical image in order to view a light path or to image different imaging modalities. Depending on the analysis, the grid pattern has a single layer of a certain thickness or at least two layers of certain thicknesses. In either case, the grid pattern is imageable by each imaging or viewing modality used in the analysis. Further, when viewing a light path, the light path of the analytical modality cannot be visualized by viewing modality (e.g., a light microscope objective). By correlating these images, the ability to analyze a thin sample that is, for example, biological in nature but yet contains trace metal ions is enhanced. Specifically, it is desired to analyze both the organic matter of the biological sample and the trace metal ions contained within the biological sample without adding or using extrinsic labels or stains.

  10. Serotonergic Markers in Atopic Dermatitis.

    PubMed

    Rasul, Aram; El-Nour, Husameldin; Lonne-Rahm, Sol-Britt; Fransson, Oscar; Johansson, Charlotta; Johansson, Björn; Zubeidi, Marwe; Seeberg, Emma; Djurfeldt, Diana Radu; Azmitia, Efrain C; Nordlind, Klas

    2016-08-23

    Stress and anxiety may worsen atopic dermatitis (AD) through the serotonin system. Serotonergic expression was measured in 28 patients with AD in relation to extent of the disease (SCORing of Atopic Dermatitis; SCORAD), pruritus intensity (visual analogue scale; VAS), anxiety traits (Swedish Universities Scales of Personality; SSP) and depression (Montgomery-Åsberg Depression Rating Scale-Self assessment; MADRS-S). Biopsies were taken from lesional and non-lesional AD skin, and investigated for expression of serotonin, its receptors 5-HT1A and 5-HT2, and serotonin transporter protein (SERT), using immunohistochemistry. 5-HT1AR-immunoreactivity (ir) was higher in lesional skin in apical epidermis and in mast cell-like cells in dermis, and 5-HT2AR-ir in apical epidermis and on blood vessels. In contrast, a basement membrane 5-HT2AR-ir signal was higher in non-lesional skin. The distribution of SERT-ir in the basal epidermal layer was higher in lesional skin. Positive and negative correlations were found between serotonergic markers and SCORAD, inflammation, pruritus intensity, anxiety traits, and depression score, indicating that serotonergic mechanisms are involved in AD. PMID:26831833

  11. Construction Cluster Skills Standards.

    ERIC Educational Resources Information Center

    DePaul Univ., Chicago, IL. Built Environment Partnership.

    Twelve construction cluster skill standards and associated benchmarks were developed as part of a federally funded school-to-work initiative that included the following parties: the Chicago Public Schools; City Colleges of Chicago; and business, labor, and community organizations. The standards, which include core academic, generic workplace…

  12. Clustered for Success

    ERIC Educational Resources Information Center

    Brulles, Dina; Winebrenner, Susan

    2012-01-01

    Schools need to address the needs of their students with high ability. Not only does this raise achievement levels schoolwide, it also attracts students from surrounding districts and recaptures advanced learners who left the school because their needs weren't being met. One practical intervention--cluster grouping--provides an inclusive…

  13. Nuclear Cluster Physics

    SciTech Connect

    Kamimura, Masayasu

    2011-05-06

    Predictive power of theory needs good models and accurate calculation methods to solve the Schroedinger equations of the systems concerned. We present some examples of successful predictions based on the nuclear cluster models of light nuclei and hypernuclei and on the calculation methods that have been developed by Kyushu group.

  14. Detecting alternative graph clusterings.

    PubMed

    Mandala, Supreet; Kumara, Soundar; Yao, Tao

    2012-07-01

    The problem of graph clustering or community detection has enjoyed a lot of attention in complex networks literature. A quality function, modularity, quantifies the strength of clustering and on maximization yields sensible partitions. However, in most real world networks, there are an exponentially large number of near-optimal partitions with some being very different from each other. Therefore, picking an optimal clustering among the alternatives does not provide complete information about network topology. To tackle this problem, we propose a graph perturbation scheme which can be used to identify an ensemble of near-optimal and diverse clusterings. We establish analytical properties of modularity function under the perturbation which ensures diversity. Our approach is algorithm independent and therefore can leverage any of the existing modularity maximizing algorithms. We numerically show that our methodology can systematically identify very different partitions on several existing data sets. The knowledge of diverse partitions sheds more light into the topological organization and helps gain a more complete understanding of the underlying complex network. PMID:23005495

  15. Detecting alternative graph clusterings

    NASA Astrophysics Data System (ADS)

    Mandala, Supreet; Kumara, Soundar; Yao, Tao

    2012-07-01

    The problem of graph clustering or community detection has enjoyed a lot of attention in complex networks literature. A quality function, modularity, quantifies the strength of clustering and on maximization yields sensible partitions. However, in most real world networks, there are an exponentially large number of near-optimal partitions with some being very different from each other. Therefore, picking an optimal clustering among the alternatives does not provide complete information about network topology. To tackle this problem, we propose a graph perturbation scheme which can be used to identify an ensemble of near-optimal and diverse clusterings. We establish analytical properties of modularity function under the perturbation which ensures diversity. Our approach is algorithm independent and therefore can leverage any of the existing modularity maximizing algorithms. We numerically show that our methodology can systematically identify very different partitions on several existing data sets. The knowledge of diverse partitions sheds more light into the topological organization and helps gain a more complete understanding of the underlying complex network.

  16. The Cluster Active Archive

    NASA Astrophysics Data System (ADS)

    Laakso, H.; Perry, C. H.; Escoubet, C. P.; McCaffrey, S.; Herment, D.; Esson, S.; Bowen, H.; Buggy, O.; Taylor, M. G.

    2008-05-01

    The four-satellite Cluster mission investigates small-scale structures (in three dimensions) of the Earth's plasma environment, such as those involved in the interaction between the solar wind and the magnetospheric plasma, in global magnetotail dynamics, in cross-tail currents, and in the formation and dynamics of the neutral line and of plasmoids. The Cluster Active Archive CAA (http://caa.estec.esa.int/) will contain the entire set of Cluster high resolution data and other allied products in a standard format and with a complete set of metadata in machine readable form. The data archived are (1) publicly accessible, (2) of the best quality achievable with the given resources, and (3) suitable for science use and publication by both the Cluster and broader scientific community. The CAA to provide user friendly services for searching and accessing these data, e.g. users can save and restore their selections speeding up similar requests. The CAA is continuing to extend and improve the online capabilities of the system, e.g., the CAA products can be downloaded either via a web interface or a machine accessible interface.

  17. Health Occupations Cluster.

    ERIC Educational Resources Information Center

    Walraven, Catherine; And Others

    These instructional materials consist of a series of curriculum worksheets that cover tasks to be mastered by students in health occupations cluster programs. Covered in the curriculum worksheets are diagnostic procedures; observing/recording/reporting/planning; safety; nutrition/elimination; hygiene/personal care/comfort;…

  18. FUEL ROD CLUSTERS

    DOEpatents

    Schultz, A.B.

    1959-08-01

    A cluster of nuclear fuel rods and a tubular casing therefor through which a coolant flows in heat-exchange contact with the fuel rods is described. The fuel rcds are held in the casing by virtue of the compressive force exerted between longitudinal ribs of the fuel rcds and internal ribs of the casing or the internal surfaces thereof.

  19. Clustering in Bubble Suspensions

    NASA Astrophysics Data System (ADS)

    Zenit, Roberto

    2000-11-01

    A monidisperse bubble suspension is studied experimentally for the limit in which the Weber number is small and the Reynolds number is large. For this regime the suspension can be modeled using potential flow theory to describe the dynamics of the interstitial fluid. Complete theoretical descriptions have been composed (Spelt and Sangani, 1998) to model the behavior of these suspensions. Bubble clustering is a natural instability that arises from the potential flow considerations, in which bubbles tend to align in horizontal rafts as they move upwards. The appearance of bubble clusters was recently corroborated experimentally by Zenit et al. (2000), who found that although clusters did appear, their strength was not as strong as the predictions. Experiments involving gravity driven shear flows are used to explain the nature of the clustering observed in these type of flows. Balances of the bubble phase pressure (in terms of a calculated diffusion coefficient) and the Maxwell pressure (from the potential flow description) are presented to predict the stability of the bubble suspension. The predictions are compared with experimental results.

  20. Buckets, Clusters and Dienst

    NASA Technical Reports Server (NTRS)

    Nelson, Michael L.; Maly, Kurt; Shen, Stewart N. T.

    1997-01-01

    In this paper we describe NCSTRL+, a unified, canonical digital library for scientific and technical information (STI). NCSTRL+ is based on the Networked Computer Science Technical Report Library (NCSTRL), a World Wide Web (WWW) accessible digital library (DL) that provides access to over 80 university departments and laboratories. NCSTRL+ implements two new technologies: cluster functionality and publishing "buckets." We have extended the Dienst protocol, the protocol underlying NCSTRL, to provide the ability to "cluster" independent collections into a logically centralized digital library based upon subject category classification, type of organization, and genres of material. The concept of "buckets" provides a mechanism for publishing and managing logically linked entities with multiple data formats. The NCSTRL+ prototype DL contains the holdings of NCSTRL and the NASA Technical Report Server (NTRS). The prototype demonstrates the feasibility of publishing into a multi-cluster DL, searching across clusters, and storing and presenting buckets of information. We show that the overhead for these additional capabilities is minimal to both the author and the user when compared to the equivalent process within NCSTRL.

  1. Curriculum Guide Construction Cluster.

    ERIC Educational Resources Information Center

    Kline, Ken

    As part of a model construction cluster curriculum development project, this guide was developed and implemented in the Beaverton (Oregon) School District. The curriculum guide contains 16 units covering the following topics: introduction to construction jobs; safety and first aid; blueprint readings; basic mathematics; site work; framing; roofing…

  2. Health Occupations Cluster Guide.

    ERIC Educational Resources Information Center

    Oregon State Dept. of Education, Salem.

    Intended to assist the vocational teacher in designing and implementing a cluster program in health occupations, this guide suggests ideas for teaching the specific knowledge and skills that qualify students for entry-level employment in the health occupations field. The knowledge and skills are applicable to 12 occupations: dental assistant;…

  3. PDMS embedded Ag clusters: Coalescence and cluster-matrix interaction

    NASA Astrophysics Data System (ADS)

    Roese, S.; Engemann, D.; Hoffmann, S.; Latussek, K.; Sternemann, C.; Hövel, H.

    2016-05-01

    Polydimethylsiloxane (PDMS) has proven to be a suitable embedding medium for silver clusters to prevent aggregation. In order to investigate the influence of the PDMS on the electronic and local atomic structure of the clusters the measurement of x-ray absorption near edge structure (XANES) spectra for different coverages of silver clusters in PDMS and calculations of corresponding XANES spectra have been performed. The coalescence process and the cluster-PDMS interaction were investigated with XANES.

  4. The Rotation of Galaxy Clusters

    NASA Astrophysics Data System (ADS)

    Tovmassian, H. M.

    2015-09-01

    The method for detection of the galaxy cluster rotation based on the study of distribution of member galaxies with velocities lower and higher than the cluster mean velocity over the cluster image is proposed. The search for rotation is made for flat clusters with a/b > 1.8 and BMI type clusters which are expected to be rotating. For comparison there were studied also round clusters and clusters of NBMI type, the second by brightness galaxy, which does not differ significantly from the cluster cD galaxy. Seventeen out of studied 65 clusters are found to be rotating. It was found that the detection rate is sufficiently high for flat clusters, over 60%, and clusters of BMI type with dominant cD galaxy, ≈ 35% . The obtained results show that clusters were formed from the huge primordial gas clouds and preserved the rotation of the primordial clouds, unless they did not experience mergings with other clusters and groups of galaxies, as a result of which the rotation was prevented.

  5. Femtosecond dynamics of cluster expansion

    NASA Astrophysics Data System (ADS)

    Gao, Xiaohui; Wang, Xiaoming; Shim, Bonggu; Arefiev, Alexey; Tushentsov, Mikhail; Breizman, Boris; Downer, Mike

    2010-03-01

    Noble gas clusters irradiated by intense ultrafast laser expand quickly and become typical plasma in picosecond time scale. During the expansion, the clustered plasma demonstrates unique optical properties such as strong absorption and positive contribution to the refractive index. Here we studied cluster expansion dynamics by fs-time-resolved refractive index and absorption measurements in cluster gas jets after ionization and heating by an intense pump pulse. The refractive index measured by frequency domain interferometry (FDI) shows the transient positive peak of refractive index due to clustered plasma. By separating it from the negative contribution of the monomer plasma, we are able to determine the cluster fraction. The absorption measured by a delayed probe shows the contribution from clusters of various sizes. The plasma resonances in the cluster explain the enhancement of the absorption in our isothermal expanding cluster model. The cluster size distribution can be determined. A complete understanding of the femtosecond dynamics of cluster expansion is essential in the accurate interpretation and control of laser-cluster experiments such as phase-matched harmonic generation in cluster medium.

  6. Cluster Active Archive: Overview

    NASA Astrophysics Data System (ADS)

    Laakso, H.; Perry, C.; McCaffrey, S.; Herment, D.; Allen, A. J.; Harvey, C. C.; Escoubet, C. P.; Gruenberger, C.; Taylor, M. G. G. T.; Turner, R.

    The four-satellite Cluster mission investigates the small-scale structures and physical processes related to interaction between the solar wind and the magnetospheric plasma. The Cluster Active Archive (CAA) (URL: http://caa.estec.esa.int) will contain the entire set of Cluster high-resolution data and other allied products in a standard format and with a complete set of metadata in machine readable format. The total amount of the data files in compressed format is expected to exceed 50 TB. The data archive is publicly accessible and suitable for science use and publication by the world-wide scientific community. The CAA aims to provide user-friendly services for searching and accessing these data and ancillary products. The CAA became operational in February 2006 and as of Summer 2008 has data from most of the Cluster instruments for at least the first 5 years of operations (2001-2005). The coverage and range of products are being continually improved with more than 200 datasets available from each spacecraft, including high-resolution magnetic and electric DC fields and wave spectra; full three-dimensional electron and ion distribution functions from a few eV to hundreds of keV; and various ancillary and browse products to help with spacecraft and event location. The CAA is continuing to extend and improve the online capabilities of the system and the quality of the existing data. It will add new data files for years 2006-2009 and is preparing for the long-term archive with complete coverage after the completion of the Cluster mission.

  7. Genetic variability of watermelon accessions based on microsatellite markers.

    PubMed

    de S Gama, R N C; Santos, C A F; de C S Dias, R

    2013-01-01

    We analyzed the genetic variability of 40 watermelon accessions collected from 8 regions of Northeastern Brazil using microsatellite markers, in order to suggest strategies of conservation and utilization of genetic variability in this species. These accessions are not commercial cultivars. They were sampled in areas of traditional farmers that usually keep their own seeds for future plantings year after year. An UPGMA dendrogram was generated from a distance matrix of the Jaccard coefficient, based on 41 alleles of 13 microsatellite loci. Analysis of molecular variance was made by partitioning between and within geographical regions. The similarity coefficient between accessions ranged from 37 to 96%; the dendrogram gave a co-phenetic value of 0.80. The among population genetic variability was high ( (^)ϕST = 0.319). Specific clusters of accessions sampled in 3 regions of Maranhão were observed while the other 5 regions did not presented specific clusters by regions. We conclude that watermelon genetic variability is not uniformly dispersed in the regions analyzed, indicating that geographical barriers or edaphoclimatic conditions have limited open mating. We suggest sampling a greater number of populations, so regional species diversity will be better represented and preserved in the germplasm bank. PMID:23546958

  8. Choosing the Number of Clusters in K-Means Clustering

    ERIC Educational Resources Information Center

    Steinley, Douglas; Brusco, Michael J.

    2011-01-01

    Steinley (2007) provided a lower bound for the sum-of-squares error criterion function used in K-means clustering. In this article, on the basis of the lower bound, the authors propose a method to distinguish between 1 cluster (i.e., a single distribution) versus more than 1 cluster. Additionally, conditional on indicating there are multiple…

  9. Optimal marker-strategy clinical trial design to detect predictive markers for targeted therapy.

    PubMed

    Zang, Yong; Liu, Suyu; Yuan, Ying

    2016-07-01

    In developing targeted therapy, the marker-strategy design (MSD) provides an important approach to evaluate the predictive marker effect. This design first randomizes patients into non-marker-based or marker-based strategies. Patients allocated to the non-marker-based strategy are then further randomized to receive either the standard or targeted treatments, while patients allocated to the marker-based strategy receive treatments based on their marker statuses. Little research has been done on the statistical properties of the MSD, which has led to some widespread misconceptions and placed clinical researchers at high risk of using inefficient designs. In this article, we show that the commonly used between-strategy comparison has low power to detect the predictive effect and is valid only under a restrictive condition that the randomization ratio within the non-marker-based strategy matches the marker prevalence. We propose a Wald test that is generally valid and also uniformly more powerful than the between-strategy comparison. Based on that, we derive an optimal MSD that maximizes the power to detect the predictive marker effect by choosing the optimal randomization ratios between the two strategies and treatments. Our numerical study shows that using the proposed optimal designs can substantially improve the power of the MSD to detect the predictive marker effect. We use a lung cancer trial to illustrate the proposed optimal designs. PMID:26951724

  10. High-resolution typing by integration of genome sequencing data in a large tuberculosis cluster.

    PubMed

    Schürch, Anita C; Kremer, Kristin; Daviena, Olaf; Kiers, Albert; Boeree, Martin J; Siezen, Roland J; van Soolingen, Dick

    2010-09-01

    To investigate whether genome sequencing yields more useful markers than those currently used to study the epidemiology of tuberculosis, it was applied to three Mycobacterium tuberculosis isolates of the Harlingen outbreak. Our findings suggest that single nucleotide polymorphisms can be used to identify transmission chains in restriction fragment length polymorphism clusters. PMID:20592143

  11. Identification of RAPD and SCAR markers associated with yield traits in the Indian tropical tasar silkworm Antheraea mylitta drury.

    PubMed

    Dutta, Suhrid R; Kar, Prasanta K; Srivastava, Ashok K; Sinha, Manoj K; Shankar, Jai; Ghosh, Ananta K

    2012-12-01

    The tropical tasar silkworm, Antheraea mylitta, is a semi-domesticated vanya silk-producing insect of high economic importance. To date, no molecular marker associated with cocoon and shell weights has been identified in this species. In this report, we identified a randomly amplified polymorphic DNA (RAPD) marker and examined its inheritance, and also developed a stable diagnostic sequence-characterized amplified region (SCAR) marker. Silkworms were divided into groups with high (HCSW) and low (LCSW) cocoon and shell weights, and the F(2) progeny of a cross between these two groups were obtained. DNA from these silkworms was screened by PCR using 34 random primers and the resulting RAPD fragments were used for cluster analysis and discriminant function analysis (DFA). The clustering pattern in a UPGMA-based dendogram and DFA clearly distinguished the HCSW and LCSW groups. Multiple regression analysis identified five markers associated with cocoon and shell weights. The marker OPW16(905 bp) showed the most significant association with cocoon and shell weights, and its inheritance was confirmed in F(2) progeny. Cloning and sequencing of this 905 bp fragment showed 88% identity between its 134 nucleotides and the Bmc-1/Yamato-like retroposon of A. mylitta. This marker was further converted into a diagnostic SCAR marker (SCOPW 16(826 bp)). The SCAR marker developed here may be useful in identifying the right parental stock of tasar silk-worms for high cocoon and shell weights in breeding programs designed to enhance the productivity of tasar silk. PMID:23271934

  12. Animation of the Phoenix Cluster

    NASA Video Gallery

    This animation shows how large numbers of stars form in the Phoenix Cluster. It begins by showing several galaxies in the cluster and hot gas (in red). This hot gas contains more normal matter than...

  13. High-throughput novel microsatellite marker of faba bean via next generation sequencing

    PubMed Central

    2012-01-01

    Background Faba bean (Vicia faba L.) is an important food legume crop, grown for human consumption globally including in China, Turkey, Egypt and Ethiopia. Although genetic gain has been made through conventional selection and breeding efforts, this could be substantially improved through the application of molecular methods. For this, a set of reliable molecular markers representative of the entire genome is required. Results A library with 125,559 putative SSR sequences was constructed and characterized for repeat type and length from a mixed genome of 247 spring and winter sown faba bean genotypes using 454 sequencing. A suit of 28,503 primer pair sequences were designed and 150 were randomly selected for validation. Of these, 94 produced reproducible amplicons that were polymorphic among 32 faba bean genotypes selected from diverse geographical locations. The number of alleles per locus ranged from 2 to 8, the expected heterozygocities ranged from 0.0000 to 1.0000, and the observed heterozygosities ranged from 0.0908 to 0.8410. The validation by UPGMA cluster analysis of 32 genotypes based on Nei's genetic distance, showed high quality and effectiveness of those novel SSR markers developed via next generation sequencing technology. Conclusions Large scale SSR marker development was successfully achieved using next generation sequencing of the V. faba genome. These novel markers are valuable for constructing genetic linkage maps, future QTL mapping, and marker-assisted trait selection in faba bean breeding efforts. PMID:23137291

  14. a Comparison Study of Different Marker Selection Methods for Spectral-Spatial Classification of Hyperspectral Images

    NASA Astrophysics Data System (ADS)

    Akbari, D.; Safari, A. R.; Homayouni, S.; Khazai, S.

    2015-12-01

    An effective approach based on the Minimum Spanning Forest (MSF), grown from automatically selected markers using Support Vector Machines (SVM), has been proposed for spectral-spatial classification of hyperspectral images by Tarabalka et al. This paper aims at improving this approach by using image segmentation to integrate the spatial information into marker selection process. In this study, the markers are extracted from the classification maps, obtained by both SVM and segmentation algorithms, and then are used to build the MSF. The segmentation algorithms are the watershed, expectation maximization (EM) and hierarchical clustering. These algorithms are used in parallel and independently to segment the image. Moreover, the pixels of each class, with the largest population in the classification map, are kept for each region of the segmentation map. Lastly, the most reliable classified pixels are chosen from among the exiting pixels as markers. Two benchmark urban hyperspectral datasets are used for evaluation: Washington DC Mall and Berlin. The results of our experiments indicate that, compared to the original MSF approach, the marker selection using segmentation algorithms leads in more accurate classification maps.

  15. Identification of microsatellite markers in coffee associated with resistance to Meloidogyne exigua.

    PubMed

    Pereira, T B; Setotaw, T A; Santos, D N; Mendes, A N G; Salgado, S M L; Carvalho, G R; Rezende, R M

    2016-01-01

    Meloidogyne species are destructive phytonematodes that result in reduced yields of coffee. The classic test for resistance to Meloidogyne exigua in coffee progenies is both expensive and time-consuming. The use of molecular marker techniques can assist the selection process when it is difficult to measure the phenotype, such as in cases of resistance to nematode infestation. The objective of this study was to identify microsatellite markers associated with resistance to M. exigua in F5 progenies of coffee derived from a cross between Híbrido de Timor 440-10 and Catuaí Amarelo IAC 86. Of the 44 simple sequence repeat (SSR) markers evaluated, 11 showed a polymorphic pattern with a mean number of 4.5 alleles per marker. Clustering analysis classified 82 progenies into three groups related to the response to nematodes and parental genotypes allocated to different groups (resistant and susceptible). SSRCafé 40 allele 2, SSRCafé 15 allele 3, SSRCafé 20 allele 3, and SSRCafé 13 allele 1 were negatively correlated with reproduction factor. In addition, SSRCafé 13 allele 2, SSRCafé 19 allele 3, SSRCafé 40 allele 2, SSRCafé 15 allele 3, and SSRCafé 20 allele 3 were correlated with the root gall index of M. exigua. These SSR markers, which have been validated in this population, represent a potential method to select progenies resistant to nematodes in coffee-breeding programs. PMID:27525876

  16. Mapping of 262 DNA markers into 24 intervals on human chromosome 11

    SciTech Connect

    Tanigami, Akira; Tokino, Takashi; Takiguchi, Shuya; Mori, Masaki; Nakamura, Yusuke ); Glaser, T. ); Park, J.W.; Jones, C. )

    1992-01-01

    The authors have extended the authors mapping effort on human chromosome 11 to encompass a total of 262 DNA markers, which have been mapped into 24 intervals on chromosome 11; 123 of the markers reveal RFLPs. Theses clones are scattered throughout the chromosome, although some clustering occurs in R-positive bands (p15.1, p11.2,q13, and q23.3). Fifty-two of the markers were found to contain DNA sequences conserved in Chinese hamster, and some of these 52 also cross-hybridized with DNA from other mammals and/or chicken. As the length of chromosome 11 is estimated at nearly 130 cM, the average distance between RFLP markers is roughly 1 cM. The large panel of DNA markers on their map should contribute to investigations of hereditary diseases on this chromosome, and it will also provide reagents for constructing either fine-scale linkage and physical maps or contig maps of cosmids or yeast artificial chromosomes.

  17. Combined flow cytometric analysis of surface and intracellular antigens reveals surface molecule markers of human neuropoiesis.

    PubMed

    Turaç, Gizem; Hindley, Christopher J; Thomas, Ria; Davis, Jason A; Deleidi, Michela; Gasser, Thomas; Karaöz, Erdal; Pruszak, Jan

    2013-01-01

    Surface molecule profiles undergo dynamic changes in physiology and pathology, serve as markers of cellular state and phenotype and can be exploited for cell selection strategies and diagnostics. The isolation of well-defined cell subsets is needed for in vivo and in vitro applications in stem cell biology. In this technical report, we present an approach for defining a subset of interest in a mixed cell population by flow cytometric detection of intracellular antigens. We have developed a fully validated protocol that enables the co-detection of cluster of differentiation (CD) surface antigens on fixed, permeabilized neural cell populations defined by intracellular staining. Determining the degree of co-expression of surface marker candidates with intracellular target population markers (nestin, MAP2, doublecortin, TUJ1) on neuroblastoma cell lines (SH-SY5Y, BE(2)-M17) yielded a combinatorial CD49f(-)/CD200(high) surface marker panel. Its application in fluorescence-activated cell sorting (FACS) generated enriched neuronal cultures from differentiated cell suspensions derived from human induced pluripotent stem cells. Our data underlines the feasibility of using the described co-labeling protocol and co-expression analysis for quantitative assays in mammalian neurobiology and for screening approaches to identify much needed surface markers in stem cell biology. PMID:23826393

  18. The Assembly of Galaxy Clusters

    SciTech Connect

    Berrier, Joel C.; Stewart, Kyle R.; Bullock, James S.; Purcell, Chris W.; Barton, Elizabeth J.; Wechsler, Risa H.

    2008-05-16

    We study the formation of fifty-three galaxy cluster-size dark matter halos (M = 10{sup 14.0-14.76} M{sub {circle_dot}}) formed within a pair of cosmological {Lambda}CDM N-body simulations, and track the accretion histories of cluster subhalos with masses large enough to host {approx} 0.1L{sub *} galaxies. By associating subhalos with cluster galaxies, we find the majority of galaxies in clusters experience no 'pre-processing' in the group environment prior to their accretion into the cluster. On average, {approx} 70% of cluster galaxies fall into the cluster potential directly from the field, with no luminous companions in their host halos at the time of accretion; and less than {approx} 12% are accreted as members of groups with five or more galaxies. Moreover, we find that cluster galaxies are significantly less likely to have experienced a merger in the recent past ({approx}< 6 Gyr) than a field halo of the same mass. These results suggest that local, cluster processes like ram-pressure stripping, galaxy harassment, or strangulation play the dominant role in explaining the difference between cluster and field populations at a fixed stellar mass; and that pre-evolution or past merging in the group environment is of secondary importance for setting cluster galaxy properties for most clusters. The accretion times for z = 0 cluster members are quite extended, with {approx} 20% incorporated into the cluster halo more than 7 Gyr ago and {approx} 20% within the last 2 Gyr. By comparing the observed morphological fractions in cluster and field populations, we estimate an approximate time-scale for late-type to early-type transformation within the cluster environment to be {approx} 6 Gyr.

  19. [Cluster analysis in biomedical researches].

    PubMed

    Akopov, A S; Moskovtsev, A A; Dolenko, S A; Savina, G D

    2013-01-01

    Cluster analysis is one of the most popular methods for the analysis of multi-parameter data. The cluster analysis reveals the internal structure of the data, group the separate observations on the degree of their similarity. The review provides a definition of the basic concepts of cluster analysis, and discusses the most popular clustering algorithms: k-means, hierarchical algorithms, Kohonen networks algorithms. Examples are the use of these algorithms in biomedical research. PMID:24640781

  20. The Orion nebula star cluster

    NASA Technical Reports Server (NTRS)

    Panek, R. J.

    1982-01-01

    Photography through filters which suppress nebular light reveal a clustering of faint red stars centered on the Trapezium, this evidences a distinct cluster within the larger OB1 association. Stars within about 20 ft of trapezium comprise the Orion Nebula star cluster are considered. Topics discussed re: (1) extinction by dust grains; (2) photometric peculiarities; (3) spectroscopic peculiarities; (4) young variables; (5) the distribution and motion of gas within the cluster.

  1. Clustering signatures classify directed networks

    NASA Astrophysics Data System (ADS)

    Ahnert, S. E.; Fink, T. M. A.

    2008-09-01

    We use a clustering signature, based on a recently introduced generalization of the clustering coefficient to directed networks, to analyze 16 directed real-world networks of five different types: social networks, genetic transcription networks, word adjacency networks, food webs, and electric circuits. We show that these five classes of networks are cleanly separated in the space of clustering signatures due to the statistical properties of their local neighborhoods, demonstrating the usefulness of clustering signatures as a classifier of directed networks.

  2. Observations of Distant Clusters

    NASA Technical Reports Server (NTRS)

    Donahue, Megan

    2004-01-01

    The is the proceedings and papers supported by the LTSA grant: Homer, D. J.\\& Donahue, M. 2003, in "The Emergence of Cosmic Structure": 13'h Astrophysics Conference Proceedings, Vol. 666,3 1 1-3 14, (AIP). Baumgartner, W. H., Loewenstein, M., Horner, D. J., Mushotzky, R. F. 2003, HEAD- AAS, 35.3503. Homer, D. J. , Donahue, M., Voit G. M. 2003, HEAD-AAS, 35.1309. Nowak, M. A., Smith, B., Donahue, M., Stocke, J. 2003, HEAD-AAS, 35.1316. Scott, D., Borys, C., Chapman, S. C., Donahue, M., Fahlman, G. G., Halpem, M. Newbury, P. 2002, AAS, 128.01. Jones, L. R. et al. 2002, A new era in cosmology, ASP Conference Proceedings, Vol. 283, p. 223 Donahue, M., Daly, R. A., Homer, D. J. 2003, ApJ, 584, 643, Constraints on the Cluster Environments and Hotspot magnetic field strengths for radio sources 3280 and 3254. Donahue, M., et al. 2003, ApJ, 598, 190. The mass, baryonic fraction, and x-ray temperature of the luminous, high-redshift cluster of galaxies MS045 1.6-0305 Perlman, E. S. et al. 2002, ApJS, 140, 256. Smith, B. J., Nowak, M., Donahue, M., Stocke, J. 2003, AJ, 126, 1763. Chandra Observations of the Interacting NGC44 10 Group of Galaxies. Postman, M., Lauer, T. R., Oegerle, W., Donahue, M. 2002, ApJ, 579, 93. The KPNO/deep-range cluster survey I. The catalog and space density of intermediate-redshift clusters. Molnar, S. M., Hughes, J. P., Donahue, M., Joy, M. 2002, ApJ, 573, L91, Chandra Observations of Unresolved X-Ray Sources around Two Clusters of Galaxies. Donahue, M., Mack, J., 2002 NewAR, 46, 155, HST NIcmos and WFPC2 observations of molecular hydrogen and dust around cooling flows. Koekemoer, A. M. et al. 2002 NewAR, 46, 149, Interactions between the A2597 central radio source and dense gas host galaxy. Donahue, M. et al. 2002 ApJ, 569,689, Distant cluster hunting II.

  3. Derivatized gold clusters and antibody-gold cluster conjugates

    DOEpatents

    Hainfeld, James F.; Furuya, Frederic R.

    1994-11-01

    Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be as small as 5.0 nm. Methods and reagents are disclosed in which antibodies, Fab' or F(ab').sub.2 fragments thereof are covalently bound to a stable cluster of gold atoms. The gold clusters may contain 6, 8, 9, 11, 13, 55 or 67 gold atoms in their inner core. The clusters may also contain radioactive gold. The antibody-cluster conjugates are useful in electron microscopy applications as well as in clinical applications that include imaging, diagnosis and therapy.

  4. Derivatized gold clusters and antibody-gold cluster conjugates

    DOEpatents

    Hainfeld, J.F.; Furuya, F.R.

    1994-11-01

    Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be as small as 5.0 nm. Methods and reagents are disclosed in which antibodies, Fab' or F(ab')[sub 2] fragments are covalently bound to a stable cluster of gold atoms. The gold clusters may contain 6, 8, 9, 11, 13, 55 or 67 gold atoms in their inner core. The clusters may also contain radioactive gold. The antibody-cluster conjugates are useful in electron microscopy applications as well as in clinical applications that include imaging, diagnosis and therapy. 7 figs.

  5. Semi-supervised spectral clustering with application to detect population stratification

    PubMed Central

    Liu, Binghui; Shen, Xiaotong; Pan, Wei

    2013-01-01

    In genetic association studies, unaccounted population stratification can cause spurious associations in a discovery process of identifying disease-associated genetic markers. In such a situation, prior information is often available for some subjects' population identities. To leverage the additional information, we propose a semi-supervised clustering approach for detecting population stratification. This approach maintains the advantages of spectral clustering, while is integrated with the additional identity information, leading to sharper clustering performance. To demonstrate utility of our approach, we analyze a whole-genome sequencing dataset from the 1000 Genomes Project, consisting of the genotypes of 607 individuals sampled from three continental groups involving 10 subpopulations. This is compared against a semi-supervised spectral clustering method, in addition to a spectral clustering method, with the known subpopulation information by the Rand index and an adjusted Rand (ARand) index. The numerical results suggest that the proposed method outperforms its competitors in detecting population stratification. PMID:24298278

  6. Connecting Remote Clusters with ATM

    SciTech Connect

    Hu, T.C.; Wyckoff, P.S.

    1998-10-01

    Sandia's entry into utilizing clusters of networked workstations is called Computational Plant or CPlant for short. The design of CPlant uses Ethernet to boot the individual nodes, Myrinet to communicate within a node cluster, and ATM to connect between remote clusters. This SAND document covers the work done to enable the use of ATM on the CPlant nodes in the Fall of 1997.

  7. Adaptive Clustering of Hypermedia Documents.

    ERIC Educational Resources Information Center

    Johnson, Andrew; Fotouhi, Farshad

    1996-01-01

    Discussion of hypermedia systems focuses on a comparison of two types of adaptive algorithm (genetic algorithm and neural network) in clustering hypermedia documents. These clusters allow the user to index into the nodes to find needed information more quickly, since clustering is "personalized" based on the user's paths rather than representing…

  8. Genotypic diversity and virulence markers of Yersinia enterocolitica biotype 1A strains isolated from clinical and non-clinical origins.

    PubMed

    Campioni, Fábio; Falcão, Juliana P

    2014-03-01

    Yersinia enterocolitica biotype 1A (B1A) strains are considered as non-pathogenic; however, some reports have identified some strains as the causal agents of infection. In South America, few studies molecularly characterized the strains of this biotype. This work typed 51 B1A strains isolated from clinical and non-clinical sources from Brazil and Chile by Enterobacterial Repetitive Intergenic Consensus-PCR (ERIC-PCR) to elucidate their genotypic diversity, and verify the distribution of 11 virulence markers by PCR. The strains were divided into two groups, ERIC-A and ERIC-B, clustered independently of their clinical or non-clinical origin. No differences were observed in the frequencies of the virulence markers between clinical and non-clinical strains. However, the genes ystB, hreP and myfA occurred exclusively in the strains of the group ERIC-A. Some clinical and non-clinical strains were clustered in the same genetic group and presented the same number of virulence markers, which might suggest the role of the environment and food as a potential source of infection for humans and animals. The results corroborate with the hypothesis that B1A strains are divided into two main clusters that differ in the frequency of some virulence markers, a fact observed for the first time in South American strains. PMID:23763723

  9. Development of SSR Markers and Assessment of Genetic Diversity in Medicinal Chrysanthemum morifolium Cultivars

    PubMed Central

    Feng, Shangguo; He, Renfeng; Lu, Jiangjie; Jiang, Mengying; Shen, Xiaoxia; Jiang, Yan; Wang, Zhi'an; Wang, Huizhong

    2016-01-01

    Chrysanthemum morifolium, is a well-known flowering plant worldwide, and has a high commercial, floricultural, and medicinal value. In this study, simple-sequence repeat (SSR) markers were generated from EST datasets and were applied to assess the genetic diversity among 32 cultivars. A total of 218 in silico SSR loci were identified from 7300 C. morifolium ESTs retrieved from GenBank. Of all SSR loci, 61.47% of them (134) were hexa-nucleotide repeats, followed by tri-nucleotide repeats (17.89%), di-nucleotide repeats (12.39%), tetra-nucleotide repeats (4.13%), and penta-nucleotide repeats (4.13%). In this study, 17 novel EST-SSR markers were verified. Along with 38 SSR markers reported previously, 55 C. morifolium SSR markers were selected for further genetic diversity analysis. PCR amplification of these EST-SSRs produced 1319 fragments, 1306 of which showed polymorphism. The average polymorphism information content of the SSR primer pairs was 0.972 (0.938–0.993), which showed high genetic diversity among C. morifolium cultivars. Based on SSR markers, 32 C. morifolium cultivars were separated into two main groups by partitioning of the clusters using the unweighted pair group method with arithmetic mean dendrogram, which was further supported by a principal coordinate analysis plot. Phylogenetic relationship among C. morifolium cultivars as revealed by SSR markers was highly consistent with the classification of medicinal C. morifolium populations according to their origin and ecological distribution. Our results demonstrated that SSR markers were highly reproducible and informative, and could be used to evaluate genetic diversity and relationships among medicinal C. morifolium cultivars. PMID:27379163

  10. Development of SSR Markers and Assessment of Genetic Diversity in Medicinal Chrysanthemum morifolium Cultivars.

    PubMed

    Feng, Shangguo; He, Renfeng; Lu, Jiangjie; Jiang, Mengying; Shen, Xiaoxia; Jiang, Yan; Wang, Zhi'an; Wang, Huizhong

    2016-01-01

    Chrysanthemum morifolium, is a well-known flowering plant worldwide, and has a high commercial, floricultural, and medicinal value. In this study, simple-sequence repeat (SSR) markers were generated from EST datasets and were applied to assess the genetic diversity among 32 cultivars. A total of 218 in silico SSR loci were identified from 7300 C. morifolium ESTs retrieved from GenBank. Of all SSR loci, 61.47% of them (134) were hexa-nucleotide repeats, followed by tri-nucleotide repeats (17.89%), di-nucleotide repeats (12.39%), tetra-nucleotide repeats (4.13%), and penta-nucleotide repeats (4.13%). In this study, 17 novel EST-SSR markers were verified. Along with 38 SSR markers reported previously, 55 C. morifolium SSR markers were selected for further genetic diversity analysis. PCR amplification of these EST-SSRs produced 1319 fragments, 1306 of which showed polymorphism. The average polymorphism information content of the SSR primer pairs was 0.972 (0.938-0.993), which showed high genetic diversity among C. morifolium cultivars. Based on SSR markers, 32 C. morifolium cultivars were separated into two main groups by partitioning of the clusters using the unweighted pair group method with arithmetic mean dendrogram, which was further supported by a principal coordinate analysis plot. Phylogenetic relationship among C. morifolium cultivars as revealed by SSR markers was highly consistent with the classification of medicinal C. morifolium populations according to their origin and ecological distribution. Our results demonstrated that SSR markers were highly reproducible and informative, and could be used to evaluate genetic diversity and relationships among medicinal C. morifolium cultivars. PMID:27379163

  11. Prognostic Cell Biological Markers in Cervical Cancer Patients Primarily Treated With (Chemo)radiation: A Systematic Review

    SciTech Connect

    Noordhuis, Maartje G.; Eijsink, Jasper J.H.; Roossink, Frank; Graeff, Pauline de; Pras, Elisabeth; Schuuring, Ed; Wisman, G. Bea A.; Bock, Geertruida H. de; Zee, Ate G.J. van der

    2011-02-01

    The aim of this study was to systematically review the prognostic and predictive significance of cell biological markers in cervical cancer patients primarily treated with (chemo)radiation. A PubMed, Embase, and Cochrane literature search was performed. Studies describing a relation between a cell biological marker and survival in {>=}50 cervical cancer patients primarily treated with (chemo)radiation were selected. Study quality was assessed, and studies with a quality score of 4 or lower were excluded. Cell biological markers were clustered on biological function, and the prognostic and predictive significance of these markers was described. In total, 42 studies concerning 82 cell biological markers were included in this systematic review. In addition to cyclooxygenase-2 (COX-2) and serum squamous cell carcinoma antigen (SCC-ag) levels, markers associated with poor prognosis were involved in epidermal growth factor receptor (EGFR) signaling (EGFR and C-erbB-2) and in angiogenesis and hypoxia (carbonic anhydrase 9 and hypoxia-inducible factor-1{alpha}). Epidermal growth factor receptor and C-erbB-2 were also associated with poor response to (chemo)radiation. In conclusion, EGFR signaling is associated with poor prognosis and response to therapy in cervical cancer patients primarily treated with (chemo)radiation, whereas markers involved in angiogenesis and hypoxia, COX-2, and serum SCC-ag levels are associated with a poor prognosis. Therefore, targeting these pathways in combination with chemoradiation may improve survival in advanced-stage cervical cancer patients.

  12. Additional first-trimester ultrasound markers.

    PubMed

    Sonek, J; Nicolaides, K

    2010-09-01

    The first trimester (11-13 +6 weeks) ultrasound examination is useful for several reasons: determination of an accurate date of confinement, diagnostic purposes, and screening for fetal defects. Nuchal translucency measurement combined with maternal serum markers (free b-human chorionic gonadotropin and pregnancy-associated plasma protein A) is the mainstay of first-trimester screening for chromosomal defects. However, over the past decade additional ultrasound markers have been developed that improve the performance of this type of screening. The novel markers include evaluation of the nasal bone, fronto-maxillary angle measurement, and Doppler evaluations of the blood flow across the tricuspid valve and in the ductus venosus. PMID:20638573

  13. Multiplexed microsatellite markers for seven Metarhizium species.

    PubMed

    Mayerhofer, Johanna; Lutz, Andy; Widmer, Franco; Rehner, Stephen A; Leuchtmann, Adrian; Enkerli, Jürg

    2015-11-01

    Cross-species transferability of 41 previously published simple sequence repeat (SSR) markers was assessed for 11 species of the entomopathogenic fungus Metarhizium. A collection of 65 Metarhizium strains including all 54 used in a recent phylogenetic revision of the genus were characterized. Between 15 and 34 polymorphic SSR markers produced scorable PCR amplicons in seven species, including M. anisopliae, M. brunneum, M. guizhouense, M. lepidiotae, M. majus, M. pingshaense, and M. robertsii. To provide genotyping tools for concurrent analysis of these seven species fifteen markers grouped in five multiplex pools were selected based on high allelic diversity and easy scorability of SSR chromatograms. PMID:26407949

  14. Salivary Markers for Periodontal and General Diseases

    PubMed Central

    Podzimek, Stepan; Vondrackova, Lucie; Duskova, Jana; Janatova, Tatjana; Broukal, Zdenek

    2016-01-01

    The determination of biomarkers in saliva is becoming an important part of laboratory diagnostics and the prediction of not only periodontal, but also other tissue and organ diseases. Biomarkers in saliva (e.g., enzymes, protein markers, or oxidative stress markers) can be used for activity determination and for periodontal disease prognosis. Saliva also contains many markers which can predict the risk of certain diseases (e.g., diabetes mellitus, cardiovascular, oncology, endocrinology, and psychiatric diseases). The study of salivary components proteomics clearly shows the relationship of periodontal diseases and diseases of distant systems, organs, or tissues. PMID:27143814

  15. Quantitative Methylation Analysis of the PCDHB Gene Cluster.

    PubMed

    Banelli, Barbara; Romani, Massimo

    2015-01-01

    Long Range Epigenetic Silencing (LRES) is a repressed chromatin state of large chromosomal regions caused by DNA hypermethylation and histone modifications and is commonly observed in cancer. At 5q31 a LRES region of 800 kb includes three multi-gene clusters (PCDHA@, PCDHB@, and PCDHG@, respectively). Multiple experimental evidences have led to consider the PCDHB cluster as a DNA methylation marker of aggressiveness in neuroblastoma, second most common solid tumor in childhood. Because of its potential involvement not only in neuroblastoma but also in other malignancies, an easy and fast assay to screen the DNA methylation content of the PCDHB cluster might be useful for the precise stratification of the patients into risk groups and hence for choosing the most appropriate therapeutic protocol. Accordingly, we have developed a simple and cost-effective Pyrosequencing(®) assay to evaluate the methylation level of 17 genes in the protocadherin B cluster (PCDHB@). The rationale behind this Pyrosequencing assay can in principle be applied to analyze the DNA methylation level of any gene cluster with high homologies for screening purposes. PMID:26103900

  16. Gas deficiency in cluster galaxies - A comparison of nine clusters

    NASA Technical Reports Server (NTRS)

    Giovanelli, R.; Haynes, M. P.

    1985-01-01

    The available 21 cm line data in the literature for galaxies in nine clusters is combined with new high-sensitivity observations of 51 galaxies in five of the nine clusters in order to test for discriminating circumstances between those clusters which show H I deficiency among their spiral population and those which do not. An H I deficiency for the complete cluster sample is derived employing a comparison sample of galaxies chosen from the Catalog of Isolated Galaxies. The deficiency and its radial dependence is summarized for each cluster and a composite. A comparison of the environments in different clusters leads to the conclusion that the occurrence of H I deficiency is correlated with the presence of a hot X-ray intracluster medium, and that an ongoing interaction process is active through the cores of X-ray clusters.

  17. Clusterization in Ternary Fission

    NASA Astrophysics Data System (ADS)

    Kamanin, D. V.; Pyatkov, Y. V.

    This lecture notes are devoted to the new kind of ternary decay of low excited heavy nuclei called by us "collinear cluster tri-partition" (CCT) due to the features of the effect observed, namely, decay partners fly away almost collinearly and at least one of them has magic nucleon composition. At the early stage of our work the process of "true ternary fission" (fission of the nucleus into three fragments of comparable masses) was considered to be undiscovered for low excited heavy nuclei. Another possible prototype—three body cluster radioactivity—was also unknown. The most close to the CCT phenomenon, at least cinematically, stands so called "polar emission", but only very light ions (up to isotopes of Be) were observed so far.

  18. Swirling granular solidlike clusters

    NASA Astrophysics Data System (ADS)

    Scherer, Michael A.; Kötter, Karsten; Markus, Mario; Goles, Eric; Rehberg, Ingo

    2000-04-01

    Experiments and three-dimensional numerical simulations are presented to elucidate the dynamics of granular material in a cylindrical dish driven by a horizontal, periodic motion. The following phenomena are obtained both in the experiments and in the simulations: First, for large particle numbers N the particles describe hypocycloidal trajectories. In this state the particles are embedded in a solidlike cluster (``pancake'') which counter-rotates with respect to the external driving (reptation). Self-organization within the cluster occurs such that the probability distribution of the particles consists of concentric rings. Second, the system undergoes phase transitions. These can be identified by changes of the quantity dEkin/dN (Ekin is the mean kinetic energy) between zero (rotation), positive (reptation), and negative values (appearance of the totality of concentric rings).

  19. Massive cold cloud clusters

    NASA Astrophysics Data System (ADS)

    Toth, L. Viktor; Marton, Gabor; Zahorecz, Sarolta

    2015-08-01

    The all-sky Planck catalogue of Galactic Cold Clumps (PGCC, Planck 2015 results XXVIII 2015) allows an almost unbiased study of the early phases of star-formation in our Galaxy. Several thousand of the clumps have also distance estimates allowing a mass, and density determination. The nature of Planck clumps varies from IRDCs to tiny nearby cold clouds with masses ranging from one to several tens of thousands solar masses. Some of the clumps are embedded in GMCs, others are isolated. Some are close or even very close to OB associations, while others lay far from any UV luminous objects.The small scale clustering of these objects was studied with the improved Minimum Spanning Tree method of Cartwright & Whitworth identifying groups in 3D space. As a result also massive cold cloud clusters were identified. We analyse the MST structures, and discuss their relation to ongoing and future massive star formation.

  20. Fractal polyzirconosiloxane cluster coatings

    SciTech Connect

    Sugama, T.

    1992-08-01

    Fractal polyzirconosiloxane (PZS) cluster films were prepared through the hydrolysis-polycondensation-pyrolysis synthesis of two-step HCl acid-NaOH base catalyzed sol precursors consisting of N-[3-(triethoxysilyl)propyl]-4,5-dihydroimidazole, Zr(OC{sub 3}H{sub 7}){sub 4}, methanol, and water. When amorphous PZSs were applied to aluminum as protective coatings against NaCl-induced corrosion, the effective film was that derived from the sol having a pH near the isoelectric point in the positive zeta potential region. The following four factors played an important role in assembling the protective PZS coating films: (1) a proper rate of condensation, (2) a moderate ratio of Si-O-Si to Si-O-Zr linkages formed in the PZS network, (3) hydrophobic characteristics, and (4) a specific microstructural geometry, in which large fractal clusters were linked together.

  1. Fractal polyzirconosiloxane cluster coatings

    SciTech Connect

    Sugama, T.

    1992-01-01

    Fractal polyzirconosiloxane (PZS) cluster films were prepared through the hydrolysis-polycondensation-pyrolysis synthesis of two-step HCl acid-NaOH base catalyzed sol precursors consisting of N-(3-(triethoxysilyl)propyl)-4,5-dihydroimidazole, Zr(OC{sub 3}H{sub 7}){sub 4}, methanol, and water. When amorphous PZSs were applied to aluminum as protective coatings against NaCl-induced corrosion, the effective film was that derived from the sol having a pH near the isoelectric point in the positive zeta potential region. The following four factors played an important role in assembling the protective PZS coating films: (1) a proper rate of condensation, (2) a moderate ratio of Si-O-Si to Si-O-Zr linkages formed in the PZS network, (3) hydrophobic characteristics, and (4) a specific microstructural geometry, in which large fractal clusters were linked together.

  2. Hydrated hydride anion clusters

    NASA Astrophysics Data System (ADS)

    Lee, Han Myoung; Kim, Dongwook; Singh, N. Jiten; Kołaski, Maciej; Kim, Kwang S.

    2007-10-01

    On the basis of density functional theory (DFT) and high level ab initio theory, we report the structures, binding energies, thermodynamic quantities, IR spectra, and electronic properties of the hydride anion hydrated by up to six water molecules. Ground state DFT molecular dynamics simulations (based on the Born-Oppenheimer potential surface) show that as the temperature increases, the surface-bound hydride anion changes to the internally bound structure. Car-Parrinello molecular dynamics simulations are also carried out for the spectral analysis of the monohydrated hydride. Excited-state ab initio molecular dynamics simulations show that the photoinduced charge-transfer-to-solvent phenomena are accompanied by the formation of the excess electron-water clusters and the detachment of the H radical from the clusters. The dynamics of the detachment process of a hydrogen radical upon the excitation is discussed.

  3. Layers in Crater Cluster

    NASA Technical Reports Server (NTRS)

    2003-01-01

    MGS MOC Release No. MOC2-431, 24 July 2003

    This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows a cluster of old, small impact craters near 36.3oN, 281.9oW. The group of craters was probably formed by secondary impacts following a much larger impact that occurred some distance away; the material that created these craters would have been the ejecta from the larger crater, rather than meteoroids from outer space. The craters cluster is considered to be relatively old because none of the craters have ejecta blankets any more, and each was filled, or partially filled, with layered material that was later eroded to form the terraced mounds found in their floors. This picture is illuminated from the lower left.

  4. Cosmology, Clusters and Calorimeters

    NASA Technical Reports Server (NTRS)

    Figueroa-Feliciano, Enectali

    2005-01-01

    I will review the current state of Cosmology with Clusters and discuss the application of microcalorimeter arrays to this field. With the launch of Astro-E2 this summer and a slew of new missions being developed, microcalorimeters are the next big thing in x-ray astronomy. I will cover the basics and not-so-basic concepts of microcalorimeter designs and look at the future to see where this technology will go.

  5. Cluster galaxies die hard

    NASA Astrophysics Data System (ADS)

    Weinmann, Simone M.; Kauffmann, Guinevere; von der Linden, Anja; De Lucia, Gabriella

    2010-08-01

    We investigate how the specific star formation rates of galaxies of different masses depend on cluster-centric radius and on the central/satellite dichotomy in both field and cluster environments. Recent data from a variety of sources, including the cluster catalogue of von der Linden et al., are compared to the semi-analytic models of De Lucia & Blaizot. We find that these models predict too many passive satellite galaxies in clusters, too few passive central galaxies with low stellar masses and too many passive central galaxies with high masses. We then outline a series of modifications to the model necessary to solve these problems: (a) instead of instantaneous stripping of the external gas reservoir after a galaxy becomes a satellite, the gas supply is assumed to decrease at the same rate that the surrounding halo loses mass due to tidal stripping and (b) the active galactic nuclei (AGN) feedback efficiency is lowered to bring the fraction of massive passive centrals in better agreement with the data. We also allow for radio mode AGN feedback in satellite galaxies. (c) We assume that satellite galaxies residing in host haloes with masses below 1012h-1Msolar do not undergo any stripping. We highlight the fact that in low-mass galaxies, the external reservoir is composed primarily of gas that has been expelled from the galactic disc by supernovae-driven winds. This gas must remain available as a future reservoir for star formation, even in satellite galaxies. Finally, we present a simple recipe for the stripping of gas and dark matter in satellites that can be used in models where subhalo evolution is not followed in detail.

  6. Embedded Clusters in Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Lada, Charles J.; Lada, Elizabeth A.

    Stellar clusters are born embedded within giant molecular clouds (GMCs) and during their formation and early evolution are often only visible at infrared wavelengths, being heavily obscured by dust. Over the past 15 years advances in infrared detection capabilities have enabled the first systematic studies of embedded clusters in galactic molecular clouds. In this article we review the current state of empirical knowledge concerning these extremely young protocluster systems. From a survey of the literature we compile the first extensive catalog of galactic embedded clusters. We use the catalog to construct the mass function and estimate the birthrate for embedded clusters within 2 kpc of the sun. We find that the embedded cluster birthrate exceeds that of visible open clusters by an order of magnitude or more indicating a high infant mortality rate for protocluster systems. Less than 4-7% of embedded clusters survive emergence from molecular clouds to become bound clusters of Pleiades age. The vast majority (90%) of stars that form in embedded clusters form in rich clusters of 100 or more members with masses in excess of 50 M⊙. Moreover, observations of nearby cloud complexes indicate that embedded clusters account for a significant (70-90%) fraction of all stars formed in GMCs. We review the role of embedded clusters in investigating the nature of the initial mass function (IMF) that, in one nearby example, has been measured over the entire range of stellar and substellar mass, from OB stars to substellar objects near the deuterium burning limit. We also review the role embedded clusters play in the investigation of circumstellar disk evolution and the important constraints they provide for understanding the origin of planetary systems. Finally, we discuss current ideas concerning the origin and dynamical evolution of embedded clusters and the implications for the formation of bound open clusters.

  7. Use of molecular markers to compare Fusarium verticillioides pathogenic strains isolated from plants and humans.

    PubMed

    Chang, S C; Macêdo, D P C; Souza-Motta, C M; Oliveira, N T

    2013-01-01

    Fusarium verticillioides is a pathogen of agriculturally important crops, especially maize. It is considered one of the most important pathogens responsible for fumonisin contamination of food products, which causes severe, chronic, and acute intoxication in humans and animals. Moreover, it is recognized as a cause of localized infections in immunocompetent patients and disseminated infections among severely immunosuppressed patients. Several molecular tools have been used to analyze the intraspecific variability of fungi. The objective of this study was to use molecular markers to compare pathogenic isolates of F. verticillioides and isolates of the same species obtained from clinical samples of patients with Fusarium mycoses. The molecular markers that we used were inter-simple sequence repeat markers (primers GTG5 and GACA4), intron splice site primer (primer EI1), random amplified polymorphic DNA marker (primer OPW-6), and restriction fragment length polymorphism-internal transcribed spacer (ITS) from rDNA. From the data obtained, clusters were generated based on the UPGMA clustering method. The amplification products obtained using primers ITS4 and ITS5 and loci ITS1-5.8-ITS2 of the rDNA yielded fragments of approximately 600 bp for all the isolates. Digestion of the ITS region fragment using restriction enzymes such as EcoRI, DraI, BshI, AluI, HaeIII, HinfI, MspI, and PstI did not permit differentiation among pathogenic and clinical isolates. The inter-simple sequence repeat, intron splice site primer, and random amplified polymorphic DNA markers presented high genetic homogeneity among clinical isolates in contrast to the high variability found among the phytopathogenic isolates of F. verticillioides. PMID:24065642

  8. Astrophysics of galaxy clusters

    NASA Astrophysics Data System (ADS)

    Ettori, Stefano

    2016-07-01

    As the nodes of the cosmic web, clusters of galaxies trace the large-scale distribution of matter in the Universe. They are thus privileged sites in which to investigate the complex physics of structure formation. However, the complete story of how these structures grow, and how they dissipate the gravitational and non-thermal components of their energy budget over cosmic time, is still beyond our grasp. Most of the baryons gravitationally bound to the cluster's halo is in the form of a diffuse, hot, metal-enriched plasma that radiates primarily in the X-ray band. X-ray observations of the evolving cluster population provide a unique opportunity to address such fundamental open questions as: How do hot diffuse baryons accrete and dynamically evolve in dark matter potentials? How and when was the energy that we observe in the ICM generated and distributed? Where and when are heavy elements produced and how are they circulated? We will present the ongoing activities to define the strategy on how an X-ray observatory with large collecting area and an unprecedented combination of high spectral and angular resolution, such as Athena, can address these questions.

  9. Progestins and cardiovascular risk markers.

    PubMed

    Sitruk-Ware, R

    2000-01-01

    Several risks are attributed to progestins as a class-effect; however, the progestins used in hormone replacement therapy (HRT) have varying pharmacologic properties and do not induce the same side effects. Natural progesterone (P) and some of its derivatives, such as the 19-norprogesterones, do not exert any androgenic effect and, hence, have no negative effect on the lipids. On the other hand, the 19-nortestosterone derivatives and even some 17-hydroxyprogesterones have a partial androgenic effect, which may explain some of the negative effects observed on surrogate markers of cardiovascular risk. The relevance of the lipid changes induced by sex steroids has been questioned, and studies in the female cynomolgous monkey have not shown a direct relationship to atherosclerosis. Results suggest that estrogens (E) have antiatherogenic effects and that P does not reverse the beneficial effect of estradiol. Also, sex hormones modulate the vasomotor response of the main arteries. E preserves the normal endothelium-mediated dilation of coronary arteries, and P does not reverse this potential cardioprotective mechanism. In the same animal model, the addition of cyclic or continuous medroxyprogesterone acetate (MPA) to E inhibited vasodilatation by 50%, while nomegestrol acetate did not diminish the E-induced vasodilatation. Not all progestins act similarly on vasomotion or affect cardiovascular risk factors in the same way. Progestins, such as MPA or norethisterone acetate (NETA), exert a partial detrimental effect on the beneficial actions of estrogens with regard to lipid changes, atheroma development, or vasomotion. In contrast, progesterone itself does not have this inhibitory effect on lipid changes and vascular reactivity in animal models or on exercise-induced myocardial ischemia in humans. Nonandrogenic molecules of P itself and of derivatives, such as 19-norprogesterones, would appear neutral on the vessels. Several ongoing randomized controlled trials of HRT are

  10. Stormy weather in galaxy clusters

    PubMed

    Burns

    1998-04-17

    Recent x-ray, optical, and radio observations coupled with particle and gas dynamics numerical simulations reveal an unexpectedly complex environment within clusters of galaxies, driven by ongoing accretion of matter from large-scale supercluster filaments. Mergers between clusters and continuous infall of dark matter and baryons from the cluster periphery produce long-lived "stormy weather" within the gaseous cluster atmosphere-shocks, turbulence, and winds of more than 1000 kilometers per second. This weather may be responsible for shaping a rich variety of extended radio sources, which in turn act as "barometers" and "anemometers" of cluster weather. PMID:9545210

  11. Cluster headache after orbital exenteration.

    PubMed

    Evers, S; Sörös, P; Brilla, R; Gerding, H; Husstedt, I W

    1997-10-01

    A 37-year-old man developed an ipsilateral headache which fulfilled the criteria for cluster headache after orbital extenteration because of a traumatic lesion of the bulb. The headache could be treated successfully by drugs usually applied in the therapy of cluster headache. Six similar cases of cluster headache after orbital exenteration could be identified in the literature suggesting that the eye itself is not necessarily part of the pathogenesis of cluster headache. We hypothesize that orbital exenteration can cause cluster headache by lesions of sympathetic structures. Possibly, these mechanisms are similar to those of sympathetic reflex dystrophy (Sudeck-Leriche syndrome) causing pain of the limbs. PMID:9350391

  12. Multiscale hierarchical support vector clustering

    NASA Astrophysics Data System (ADS)

    Hansen, Michael Saas; Holm, David Alberg; Sjöstrand, Karl; Ley, Carsten Dan; Rowland, Ian John; Larsen, Rasmus

    2008-03-01

    Clustering is the preferred choice of method in many applications, and support vector clustering (SVC) has proven efficient for clustering noisy and high-dimensional data sets. A method for multiscale support vector clustering is demonstrated, using the recently emerged method for fast calculation of the entire regularization path of the support vector domain description. The method is illustrated on artificially generated examples, and applied for detecting blood vessels from high resolution time series of magnetic resonance imaging data. The obtained results are robust while the need for parameter estimation is reduced, compared to support vector clustering.

  13. Potential markers of preeclampsia – a review

    PubMed Central

    Grill, Simon; Rusterholz, Corinne; Zanetti-Dällenbach, Rosanna; Tercanli, Sevgi; Holzgreve, Wolfgang; Hahn, Sinuhe; Lapaire, Olav

    2009-01-01

    Preeclampsia is a leading cause of maternal and fetal/neonatal mortality and morbidity worldwide. The early identification of patients with an increased risk for preeclampsia is therefore one of the most important goals in obstetrics. The availability of highly sensitive and specific physiologic and biochemical markers would allow not only the detection of patients at risk but also permit a close surveillance, an exact diagnosis, timely intervention (e.g. lung maturation), as well as simplified recruitment for future studies looking at therapeutic medications and additional prospective markers. Today, several markers may offer the potential to be used, most likely in a combinatory analysis, as predictors or diagnostic tools. We present here the current knowledge on the biology of preeclampsia and review several biochemical markers which may be used to monitor preeclampsia in a future, that, we hope, is not to distant from today. PMID:19602262

  14. Characterizing Safflower Germplasm with AFLP Molecular Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Characterization of safflower (Carthamus tinctorius L.) germplasm with molecular markers is needed to enhance germplasm management and utilization. Amplified Fragment Length Polymorphism (AFLP) analysis was completed in safflower using two selective primer pairs resulting in 102 unambiguous polymor...

  15. MOLECULAR MARKER ANALYSIS OF DEARS SAMPLES

    EPA Science Inventory

    Source apportionment based on organic molecular markers provides a promising approach for meeting the Detroit Exposure and Aerosol Research Study (DEARS) objective of comparing source contributions between community air monitoring stations and various neighborhoods. Source appor...

  16. (ISEA) MOLECULAR MARKER ANALYSIS OF DEARS SAMPLES

    EPA Science Inventory

    Source apportionment based on organic molecular markers provides a promising approach for meeting the Detroit Exposure and Aerosol Research Study (DEARS) objective of comparing source contributions between community air monitoring stations and various neighborhoods. Source appor...

  17. DNA marker technology for wildlife conservation

    PubMed Central

    Arif, Ibrahim A.; Khan, Haseeb A.; Bahkali, Ali H.; Al Homaidan, Ali A.; Al Farhan, Ahmad H.; Al Sadoon, Mohammad; Shobrak, Mohammad

    2011-01-01

    Use of molecular markers for identification of protected species offers a greater promise in the field of conservation biology. The information on genetic diversity of wildlife is necessary to ascertain the genetically deteriorated populations so that better management plans can be established for their conservation. Accurate classification of these threatened species allows understanding of the species biology and identification of distinct populations that should be managed with utmost care. Molecular markers are versatile tools for identification of populations with genetic crisis by comparing genetic diversities that in turn helps to resolve taxonomic uncertainties and to establish management units within species. The genetic marker analysis also provides sensitive and useful tools for prevention of illegal hunting and poaching and for more effective implementation of the laws for protection of the endangered species. This review summarizes various tools of DNA markers technology for application in molecular diversity analysis with special emphasis on wildlife conservation. PMID:23961128

  18. Confirmation of Clematis hybrids using molecular markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The hybrid origin of two progeny from reciprocal crosses of Clematis tubulosa and C. brevicaudata was investigated using molecular markers generated by randomly amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and single nucleotide polymorphisms (SNPs). Morphologi...

  19. Stellar Snowflake Cluster

    NASA Technical Reports Server (NTRS)

    2005-01-01

    [figure removed for brevity, see original site] Figure 1 Stellar Snowflake Cluster Combined Image [figure removed for brevity, see original site] Figure 2 Infrared Array CameraFigure 3 Multiband Imaging Photometer

    Newborn stars, hidden behind thick dust, are revealed in this image of a section of the Christmas Tree cluster from NASA's Spitzer Space Telescope, created in joint effort between Spitzer's infrared array camera and multiband imaging photometer instruments.

    The newly revealed infant stars appear as pink and red specks toward the center of the combined image (fig. 1). The stars appear to have formed in regularly spaced intervals along linear structures in a configuration that resembles the spokes of a wheel or the pattern of a snowflake. Hence, astronomers have nicknamed this the 'Snowflake' cluster.

    Star-forming clouds like this one are dynamic and evolving structures. Since the stars trace the straight line pattern of spokes of a wheel, scientists believe that these are newborn stars, or 'protostars.' At a mere 100,000 years old, these infant structures have yet to 'crawl' away from their location of birth. Over time, the natural drifting motions of each star will break this order, and the snowflake design will be no more.

    While most of the visible-light stars that give the Christmas Tree cluster its name and triangular shape do not shine brightly in Spitzer's infrared eyes, all of the stars forming from this dusty cloud are considered part of the cluster.

    Like a dusty cosmic finger pointing up to the newborn clusters, Spitzer also illuminates the optically dark and dense Cone nebula, the tip of which can be seen towards the bottom left corner of each image.

    This combined image shows the presence of organic molecules mixed with dust as wisps of green, which have been illuminated by nearby star formation. The larger yellowish dots neighboring the baby red stars in the Snowflake Cluster are massive stellar infants forming

  20. Detection of immunocytological markers in photomicroscopic images

    NASA Astrophysics Data System (ADS)

    Friedrich, David; zur Jacobsmühlen, Joschka; Braunschweig, Till; Bell, André; Chaisaowong, Kraisorn; Knüchel-Clarke, Ruth; Aach, Til

    2012-03-01

    Early detection of cervical cancer can be achieved through visual analysis of cell anomalies. The established PAP smear achieves a sensitivity of 50-90%, most false negative results are caused by mistakes in the preparation of the specimen or reader variability in the subjective, visual investigation. Since cervical cancer is caused by human papillomavirus (HPV), the detection of HPV-infected cells opens new perspectives for screening of precancerous abnormalities. Immunocytochemical preparation marks HPV-positive cells in brush smears of the cervix with high sensitivity and specificity. The goal of this work is the automated detection of all marker-positive cells in microscopic images of a sample slide stained with an immunocytochemical marker. A color separation technique is used to estimate the concentrations of the immunocytochemical marker stain as well as of the counterstain used to color the nuclei. Segmentation methods based on Otsu's threshold selection method and Mean Shift are adapted to the task of segmenting marker-positive cells and their nuclei. The best detection performance of single marker-positive cells was achieved with the adapted thresholding method with a sensitivity of 95.9%. The contours differed by a modified Hausdorff Distance (MHD) of 2.8 μm. Nuclei of single marker positive cells were detected with a sensitivity of 95.9% and MHD = 1.02 μm.

  1. Convex Clustering: An Attractive Alternative to Hierarchical Clustering

    PubMed Central

    Chen, Gary K.; Chi, Eric C.; Ranola, John Michael O.; Lange, Kenneth

    2015-01-01

    The primary goal in cluster analysis is to discover natural groupings of objects. The field of cluster analysis is crowded with diverse methods that make special assumptions about data and address different scientific aims. Despite its shortcomings in accuracy, hierarchical clustering is the dominant clustering method in bioinformatics. Biologists find the trees constructed by hierarchical clustering visually appealing and in tune with their evolutionary perspective. Hierarchical clustering operates on multiple scales simultaneously. This is essential, for instance, in transcriptome data, where one may be interested in making qualitative inferences about how lower-order relationships like gene modules lead to higher-order relationships like pathways or biological processes. The recently developed method of convex clustering preserves the visual appeal of hierarchical clustering while ameliorating its propensity to make false inferences in the presence of outliers and noise. The solution paths generated by convex clustering reveal relationships between clusters that are hidden by static methods such as k-means clustering. The current paper derives and tests a novel proximal distance algorithm for minimizing the objective function of convex clustering. The algorithm separates parameters, accommodates missing data, and supports prior information on relationships. Our program CONVEXCLUSTER incorporating the algorithm is implemented on ATI and nVidia graphics processing units (GPUs) for maximal speed. Several biological examples illustrate the strengths of convex clustering and the ability of the proximal distance algorithm to handle high-dimensional problems. CONVEXCLUSTER can be freely downloaded from the UCLA Human Genetics web site at http://www.genetics.ucla.edu/software/ PMID:25965340

  2. Analysis of genetic stability of in vitro propagated potato microtubers using DNA markers.

    PubMed

    Tiwari, Jagesh K; Chandel, Poonam; Gupta, Shruti; Gopal, Jai; Singh, B P; Bhardwaj, Vinay

    2013-10-01

    The genetic stability of in vitro propagated potato microtubers was assessed using random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR), simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers. Microtubers were developed through in vitro from potato microplants using standardized protocols. The microtubers were conserved for 1 year under three different culture media and consequently microplants were regenerated for the DNA analyses. During the study, a total of 38 (10 RAPD, 11 ISSR, 12 SSR and 5 AFLP) primers produced a total of 407 (58 RAPD, 56 ISSR, 96 SSR and 197 AFLP) clear, distinct and reproducible amplicons. Cluster analysis revealed 100 % genetic similarity among the mother plant and its derivatives within the clusters by SSR, ISSR and RAPD analyses, whereas AFLP analysis revealed from 85 to 100 % genetic similarity. Dendrogram analysis based on the Jaccard's coefficient classified the genotypes into five clusters (I-V), each cluster consisting of mother plant and its derivatives. Principal component analysis (PCA) also plotted mother plant and its genotypes of each cluster together. Based on our results, it is concluded that AFLP is the best method followed by SSR, ISSR and RAPD to detect genetic stability of in vitro conserved potato microtubers. The in vitro conservation medium (T2) is a safe method for conservation of potato microtubers to produce true-to-type plans. PMID:24431528

  3. Genetic fidelity and variability of micropropagated cassava plants (Manihot esculenta Crantz) evaluated using ISSR markers.

    PubMed

    Vidal, Á M; Vieira, L J; Ferreira, C F; Souza, F V D; Souza, A S; Ledo, C A S

    2015-01-01

    Molecular markers are efficient for assessing the genetic fidelity of various species of plants after in vitro culture. In this study, we evaluated the genetic fidelity and variability of micropropagated cassava plants (Manihot esculenta Crantz) using inter-simple sequence repeat markers. Twenty-two cassava accessions from the Embrapa Cassava & Fruits Germplasm Bank were used. For each accession, DNA was extracted from a plant maintained in the field and from 3 plants grown in vitro. For DNA amplification, 27 inter-simple sequence repeat primers were used, of which 24 generated 175 bands; 100 of those bands were polymorphic and were used to study genetic variability among accessions of cassava plants maintained in the field. Based on the genetic distance matrix calculated using the arithmetic complement of the Jaccard's index, genotypes were clustered using the unweighted pair group method using arithmetic averages. The number of bands per primer was 2-13, with an average of 7.3. For most micropropagated accessions, the fidelity study showed no genetic variation between plants of the same accessions maintained in the field and those maintained in vitro, confirming the high genetic fidelity of the micropropagated plants. However, genetic variability was observed among different accessions grown in the field, and clustering based on the dissimilarity matrix revealed 7 groups. Inter-simple sequence repeat markers were efficient for detecting the genetic homogeneity of cassava plants derived from meristem culture, demonstrating the reliability of this propagation system. PMID:26214457

  4. Genetic diversity analysis of okra (Abelmoschus esculentus L.) by inter-simple sequence repeat (ISSR) markers.

    PubMed

    Yuan, C Y; Zhang, C; Wang, P; Hu, S; Chang, H P; Xiao, W J; Lu, X T; Jiang, S B; Ye, J Z; Guo, X H

    2014-01-01

    Okra (Abelmoschus esculentus L.) is not only a nutrient-rich vegetable but also an important medicinal herb. Inter-simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and differentiation of 24 okra genotypes. In this study, the PCR products were separated by electrophoresis on 8% nondenaturing polyacrylamide gel and visualized by silver staining. The 22 ISSR primers produced 289 amplified DNA fragments, and 145 (50%) fragments were polymorphic. The 289 markers were used to construct the dendrogram based on the unweighted pair-group method with arithmetic average (UPGMA) cluster analysis. The dendrogram indicated that 24 okras were clustered into 4 geographically distinct groups. The average polymorphism information content (PIC) was 0.531929, which showed that the majority of primers were informative. The high values of allele frequency, genetic diversity, and heterozygosity showed that primer-sample combinations produced measurable fragments. The mean distances ranged from 0.045455 to 0.454545. The dendrogram indicated that the ISSR markers succeeded in distinguishing most of the 24 varieties in relation to their genetic backgrounds and geographical origins. PMID:24841648

  5. Genetic diversity in the germplasm of black pepper determined by EST-SSR markers.

    PubMed

    Wu, B D; Fan, R; Hu, L S; Wu, H S; Hao, C Y

    2016-01-01

    This study aimed to assess genetic diversity in the germplasm of black pepper from around the world using SSR markers from EST. In total, 13 markers were selected and successfully amplified the target loci across the black pepper germplasm. All the EST-SSR markers showed high levels of polymorphisms with an average polymorphism information content of 0.93. The genetic similarity coefficients among all accessions ranged from 0.724 to 1.000, with an average of 0.867. These results indicated that black pepper germplasms possess a complex genetic background and high genetic diversity. Based on a cluster analysis, 148 black pepper germplasms were grouped in two major clades: the Neotropics and the Asian tropics. Peperomia pellucida was grouped separately and distantly from all other accessions. These results generally agreed with the genetic and geographic distances. However, the Asian tropics clade did not cluster according to their geographic origins. In addition, compared with the American accessions, the Asian wild accessions and cultivated accessions grouped together, indicating a close genetic relationship. This verified the origin of black pepper. The newly developed EST-SSRs are highly valuable resources for the conservation of black pepper germplasm diversity and for black pepper breeding. PMID:27050963

  6. Measuring Cluster Relaxedness

    SciTech Connect

    Moreland, Blythe; /Michigan U. /SLAC

    2012-08-24

    When is a dark matter halo 'relaxed'? In our efforts to understand the structure of the universe, dark matter simulations have provided essential grounds for theoretical predictions. These simulations provide a wealth of ways of parameterizing and measuring the features of astronomical objects. It is these measurements on which we base comparisons of our world and our attempts to re-create it. One of the essential questions dark matter simulations help address is how dark matter halos evolve. How does one characterize different states of that evolution? The focus of this project is identifying cluster relaxedness and how it relates to the internal structure of the halo. A dark matter simulation consists of an N-body simulation which takes an initial set of positions and velocities of the dark matter particles and evolves them under the influence of gravity [6]. Though scientists have so far not been able to detect dark matter particles, the information from these simulations is still valuable especially given the relationship between dark matter halos and galaxy clusters. Galaxies sit within dark matter halos and recent evidence points to filaments of dark matter forming the framework on which galaxy clusters grow [7]. A dark matter halo is a collapsed group of gravitationally bound dark matter particles. Subsets of bound particles form subhalos or substructures. The dark matter simulation is carried out over time - with decreasing redshift (z) or increasing scale factor (a = 1/1+z ). (Thus, z = 0 or a = 1.0 is present-day.) The merger history of a halo can be represented pictorally by a merger tree. A major merger event occurs when a structure joins the main halo with the mass ratio between it and the main halo being above a certain threshold. These events mark important points in the halo's evolution. And it is at these events that one hopes, and perhaps is more likely, to relate measures of relaxedness to this mass accretion. Cluster relaxedness is not a well

  7. The Ages of Globular Clusters

    NASA Astrophysics Data System (ADS)

    McNamara, D. H.

    2001-03-01

    We examine the luminosity levels of the main-sequence turnoffs, MTOv, and horizontal branches, Mv(HB), in 16 globular clusters. An entirely new approach of inferring the luminosity levels by utilizing high-amplitude δ Scuti variables (HADS) is introduced. When the MTOv values are compared with theoretical values inferred from models, we find all 16 clusters (metal-strong to metal-poor) are coeval with an average age of ~11.3 Gyr. A considerable scatter of Mv(HB) values of clusters at similar [Fe/H] values is found. A trend for clusters with blue horizontal branches to have brighter Mv(HB) than clusters with blue-red horizontal branches is suggested by the data. The Mv(HB) values appear to depend on another or other parameters in addition to the [Fe/H] values. In spite of this problem, we derive an equation relating Mv(HB) values of globular clusters to their [Fe/H] values. We also derive an equation relating the MTOv values of clusters to their [Fe/H] values. Both of these equations can be utilized to find cluster distances. The distance modulus of the LMC is found to be 18.66 from the VTO values of three LMC globular clusters; RR Lyrae stars in seven globular clusters yield 18.61, and RR Lyrae stars in the LMC bar yield 18.64.

  8. GPU-based Multilevel Clustering.

    PubMed

    Chiosa, Iurie; Kolb, Andreas

    2010-04-01

    The processing power of parallel co-processors like the Graphics Processing Unit (GPU) are dramatically increasing. However, up until now only a few approaches have been presented to utilize this kind of hardware for mesh clustering purposes. In this paper we introduce a Multilevel clustering technique designed as a parallel algorithm and solely implemented on the GPU. Our formulation uses the spatial coherence present in the cluster optimization and hierarchical cluster merging to significantly reduce the number of comparisons in both parts . Our approach provides a fast, high quality and complete clustering analysis. Furthermore, based on the original concept we present a generalization of the method to data clustering. All advantages of the meshbased techniques smoothly carry over to the generalized clustering approach. Additionally, this approach solves the problem of the missing topological information inherent to general data clustering and leads to a Local Neighbors k-means algorithm. We evaluate both techniques by applying them to Centroidal Voronoi Diagram (CVD) based clustering. Compared to classical approaches, our techniques generate results with at least the same clustering quality. Our technique proves to scale very well, currently being limited only by the available amount of graphics memory. PMID:20421676

  9. Photoionization of argon clusters

    SciTech Connect

    Dehmer, Patricia M.; Pratt, Stephen T.

    1982-01-01

    Argon clusters were produced in a free supersonic molecular beam expansion of pure argon at room temperature and the photoionization efficiency curves of the trimer through hexamer were measured in the wavelength regions from threshold to 700 Â. A study of the Ar⁺3 photoionization efficiency curve as a function of nozzle stagnation pressure shows that fragmentation of heavier clusters can dominate the spectrum, even near threshold, and even when the nozzle conditions are such that the Ar⁺4 intensity is only a small fraction of the Ar⁺3 intensity. The Ar⁺3 photoionization efficiency curve, obtained using nozzle stagnation conditions such that no heavier ions were detected, exhibits several broad peaks near threshold which show similarities to bands of the dimer. At high nozzle stagnation pressures, the photoionization efficiency curves for Ar⁺3 to Ar⁺6 are nearly identical due to the effects of fragmentation. These spectra exhibit two very broad features which are similar to features observed in the solid. The threshold regions for all the positive ions show extremely gradual onsets, making it difficult to determine the appearance potentials accurately. The appearance potentials for Ar⁺2 and Ar⁺3 are 855.0±1.5 and 865.0±1.5 Â, respectively, yielding a value of 0.18±0.05 eV for the dissociation energy of Ar⁺3. The appearance potentials for the heavier clusters Ar⁺4 through Ar⁺6 are all approximately 870±2 Â.

  10. Velocity correlations of galaxy clusters

    NASA Technical Reports Server (NTRS)

    Cen, Renyue; Bahcall, Neta A.; Gramann, Mirt

    1994-01-01

    We determine the velocity correlation function, pairwise peculiar velocity difference, and rms pairwise peculiar velocity dispersion of rich clusters of galaxies, as a function of pair separation, for three cosmological models: Omega = 1 and Omega = 0.3 cold dark matter (CDM), and Omega = 0.3 primeval baryonic isocurvature (PBI) models (all flat and Cosmic Background Explorer (COBE)-normalized). We find that close cluster pairs, with separation r is less than or equal to 10/h Mpc, exhibit strong attractive peculiar velocities in all models; the cluster pairwise velocities depend sensitively on the model. The mean pairwise attractive velocity of clusters on 5/h Mpc scale ranges from approximately 1700 km/s for Omega = 1 CDM to approximately 1000 km/s for PBI to approximately 700 km/s for Omega = 0.3 CDM. The small-scale pairwise velocities depend also on cluster mass: richer, more massive clusters exhibit stronger attractive velocities than less massive clusters. On large scales, from approximately 20 to 200/h Mpc, the cluster peculiar velocities are increasingly dominated by bulk and random motions; they are independent of cluster mass. The cluster velocity correlation function is negative on small scales for Omega = 1 and Omega = 0.3 CDM, indicating strong pairwise motion relative to bulk motion on small scales; PBI exhibits relatively larger bulk motions. The cluster velocity correlation function is positive on very large scales, from r approximately 10/h Mpc to r approximately 200/h Mpc, for all models. These positive correlations, which decrease monotonically with scale, indicate significant bulk motions of clusters up to approximately 200/h Mpc. The strong dependence of the cluster velocity functions on models, especially at small separations, makes them useful tools in constraining cosmological models when compared with observations.

  11. Molecular Characterization of Cultivated Bromeliad Accessions with Inter-Simple Sequence Repeat (ISSR) Markers

    PubMed Central

    Zhang, Fei; Ge, Yaying; Wang, Weiyong; Yu, Xinying; Shen, Xiaolan; Liu, Jianxin; Liu, Xiaojing; Tian, Danqing; Shen, Fuquan; Yu, Yongming

    2012-01-01

    Bromeliads are of great economic importance in flower production; however little information is available with respect to genetic characterization of cultivated bromeliads thus far. In the present study, a selection of cultivated bromeliads was characterized via inter-simple sequence repeat (ISSR) markers with an emphasis on genetic diversity and population structure. Twelve ISSR primers produced 342 bands, of which 287 (~84%) were polymorphic, with polymorphic bands per primer ranging from 17 to 34. The Jaccard’s similarity ranged from 0.08 to 0.89 and averaged ~0.30 for the investigated bromeliads. The Bayesian-based approach, together with the un-weighted paired group method with arithmetic average (UPGMA)-based clustering and the principal coordinate analysis (PCoA), distinctly grouped the bromeliads from Neoregelia, Guzmania, and Vriesea into three separately clusters, well corresponding with their botanical classifications; whereas the bromeliads of Aechmea other than the recently selected hybrids were not well assigned to a cluster. Additionally, ISSR marker was proven efficient for the identification of hybrids and bud sports of cultivated bromeliads. The findings achieved herein will further our knowledge about the genetic variability within cultivated bromeliads and therefore facilitate breeding for new varieties of cultivated bromeliads in future as well. PMID:22754348

  12. Reticulate evolution of the Daphnia pulex complex as revealed by nuclear markers.

    PubMed

    Vergilino, Roland; Markova, Silvia; Ventura, Marc; Manca, Marina; Dufresne, France

    2011-03-01

    The study of species complexes is of particular interest to understand how evolutionary young species maintain genomic integrity. The Daphnia pulex complex has been intensively studied as it includes species that dominate freshwater environments in the Northern hemisphere and as it is the sole North American complex that shows transitions to obligate parthenogenesis. Past studies using mitochondrial markers have revealed the presence of 10 distinct lineages in the complex. This study is the first to examine genetic relationships among seven species of the complex at nuclear markers (nine microsatellite loci and one protein-coding gene). Clones belonging to the seven species of the Daphnia pulex complex were characterized at the mitochondrial NADH dehydrogenase (ND5) gene and at the Lactate dehydrogenase (LDH) locus. K-means, principal coordinate analyses and phylogenetic network analyses on the microsatellite data all separated European D. pulicaria, D. tenebrosa, North American D. pulex, D. pulicaria and their hybrids into distinct clusters. The hybrid cluster was composed of diploid and polyploid hybrids with D. pulex mitochondria and some clones with D. pulicaria mitochondria. By contrast, the phylogeny of the D. pulex complex using Rab4 was not well resolved but still showed clusters consisting mostly of D. pulex alleles and others of D. pulicaria alleles. Incomplete lineage sorting and hybridization may obscure genetic relationships at this locus. This study shows that hybridization and introgression have played an important role in the evolution of this complex. PMID:21294799

  13. Molecular characterization of cultivated bromeliad accessions with Inter-Simple Sequence Repeat (ISSR) Markers.

    PubMed

    Zhang, Fei; Ge, Yaying; Wang, Weiyong; Yu, Xinying; Shen, Xiaolan; Liu, Jianxin; Liu, Xiaojing; Tian, Danqing; Shen, Fuquan; Yu, Yongming

    2012-01-01

    Bromeliads are of great economic importance in flower production; however little information is available with respect to genetic characterization of cultivated bromeliads thus far. In the present study, a selection of cultivated bromeliads was characterized via inter-simple sequence repeat (ISSR) markers with an emphasis on genetic diversity and population structure. Twelve ISSR primers produced 342 bands, of which 287 (~84%) were polymorphic, with polymorphic bands per primer ranging from 17 to 34. The Jaccard's similarity ranged from 0.08 to 0.89 and averaged ~0.30 for the investigated bromeliads. The Bayesian-based approach, together with the un-weighted paired group method with arithmetic average (UPGMA)-based clustering and the principal coordinate analysis (PCoA), distinctly grouped the bromeliads from Neoregelia, Guzmania, and Vriesea into three separately clusters, well corresponding with their botanical classifications; whereas the bromeliads of Aechmea other than the recently selected hybrids were not well assigned to a cluster. Additionally, ISSR marker was proven efficient for the identification of hybrids and bud sports of cultivated bromeliads. The findings achieved herein will further our knowledge about the genetic variability within cultivated bromeliads and therefore facilitate breeding for new varieties of cultivated bromeliads in future as well. PMID:22754348

  14. Are Earthquake Magnitudes Clustered?

    SciTech Connect

    Davidsen, Joern; Green, Adam

    2011-03-11

    The question of earthquake predictability is a long-standing and important challenge. Recent results [Phys. Rev. Lett. 98, 098501 (2007); ibid.100, 038501 (2008)] have suggested that earthquake magnitudes are clustered, thus indicating that they are not independent in contrast to what is typically assumed. Here, we present evidence that the observed magnitude correlations are to a large extent, if not entirely, an artifact due to the incompleteness of earthquake catalogs and the well-known modified Omori law. The latter leads to variations in the frequency-magnitude distribution if the distribution is constrained to those earthquakes that are close in space and time to the directly following event.

  15. Poxvirus Orthologous Clusters (POCs).

    PubMed

    Ehlers, Angelika; Osborne, John; Slack, Stephanie; Roper, Rachel L; Upton, Chris

    2002-11-01

    Poxvirus Orthologous Clusters (POCs) is a JAVA client-server application which accesses an updated database containing all complete poxvirus genomes; it automatically groups orthologous genes into families based on BLASTP scores for assessment by a human database curator. POCs has a user-friendly interface permitting complex SQL queries to retrieve interesting groups of DNA and protein sequences as well as gene families for subsequent interrogation by a variety of integrated tools: BLASTP, BLASTX, TBLASTN, Jalview (multiple alignment), Dotlet (Dotplot), Laj (local alignment), and NAP (nucleotide to amino acid alignment). PMID:12424130

  16. Properties of The Brightest Cluster Galaxy and Its Host Cluster

    NASA Astrophysics Data System (ADS)

    Katayama, H.; Hayashida, K.; Takahara, F.

    2001-09-01

    We investigate the relation between the brightest cluster galaxy (BCG) and its host cluster. A BCG is a bright and massive elliptical galaxy in a cluster of galaxies. The luminosity of a BCG is 10 times larger than that of normal field galaxy and the mass of a BCG is about 1013Msolar which corresponds to that of galaxy group. In order to explain the origin of BCGs, the following three models are proposed: (1) star formation from cooling flow. In this model, intracluster gas gradually condenses at the center of the cluster and forms the BCG. (2) ``Galactic cannibalism'' or the accretion of smaller galaxies. In this model, dynamical friction accounts for the formation of the BCG. These two models predict the BCG evolves with the evolution of cluster. (3) Galaxy merging in the early history of the formation of the cluster. In this model, the property of BCGs is determined no later than cluster collapse. In any model, the formation of BCGs is related to the collapse and formation of its host cluster. The relation between the BCG and its host cluster was studied by Edge (1991). Edge (1991) found that the optical luminosity of the BCG is positively correlated with the X-ray luminosity and temperature of its host cluster. Edge (1991) concludes that these correlations indicate that the BCG responds to the overall cluster properties. In order to investigate the other relation between the BCG and its host cluster, we analyzed ROSAT archival data and compared the displacement between the X-ray peak and the BCG with the Z parameter of the fundamental relation found by Fujita and Takahara (1999). It is found that the displacement is larger with decreasing Z. Furthermore, the large Z clusters tend to have a regular X-ray profile, which implies a relaxed system. The fundamental parameter Z depends mainly on the virial density ρvir, and is considered to be related to the formation epoch of the cluster, i.e., large Z clusters are old clusters and small Z clusters are young

  17. Modes of clustered star formation

    NASA Astrophysics Data System (ADS)

    Pfalzner, S.; Kaczmarek, T.; Olczak, C.

    2012-09-01

    Context. The recent realization that most stars form in clusters, immediately raises the question of whether star and planet formation are influenced by the cluster environment. The stellar density in the most prevalent clusters is the key factor here. Whether dominant modes of clustered star formation exist is a fundamental question. Using near-neighbour searches in young clusters, Bressert and collaborators claim this not to be the case. They conclude that - at least in the solar neighbourhood - star formation is continuous from isolated to densely clustered environments and that the environment plays a minor role in star and planet formation. Aims: We investigate under which conditions near-neighbour searches in young clusters can distinguish between different modes of clustered star formation. Methods: Model star clusters with different memberships and density distributions are set up and near-neighbour searches are performed. We investigate the influence of the combination of different cluster modes, observational biases, and types of diagnostic on the results. Results: We find that the specific cluster density profile, the relative sample sizes, the limitations of the observation, and the choice of diagnostic method decide, whether modelled modes of clustered star formation are detected by near-neighbour searches. For density distributions that are centrally concentrated but span a wide density range (for example, King profiles), separate cluster modes are only detectable under ideal conditions (sample selection, completeness) if the mean density of the individual clusters differs by at least a factor of ~65. Introducing a central cut-off can lead to an underestimate of the mean density by more than a factor of ten especially in high density regions. The environmental effect on star and planet formation is similarly underestimated for half of the population in dense systems. Conclusions: Local surface-density distributions are a very useful tool for single

  18. RNA-Seq identifies SNP markers for growth traits in rainbow trout.

    PubMed

    Salem, Mohamed; Vallejo, Roger L; Leeds, Timothy D; Palti, Yniv; Liu, Sixin; Sabbagh, Annas; Rexroad, Caird E; Yao, Jianbo

    2012-01-01

    Fast growth is an important and highly desired trait, which affects the profitability of food animal production, with feed costs accounting for the largest proportion of production costs. Traditional phenotype-based selection is typically used to select for growth traits; however, genetic improvement is slow over generations. Single nucleotide polymorphisms (SNPs) explain 90% of the genetic differences between individuals; therefore, they are most suitable for genetic evaluation and strategies that employ molecular genetics for selective breeding. SNPs found within or near a coding sequence are of particular interest because they are more likely to alter the biological function of a protein. We aimed to use SNPs to identify markers and genes associated with genetic variation in growth. RNA-Seq whole-transcriptome analysis of pooled cDNA samples from a population of rainbow trout selected for improved growth versus unselected genetic cohorts (10 fish from 1 full-sib family each) identified SNP markers associated with growth-rate. The allelic imbalances (the ratio between the allele frequencies of the fast growing sample and that of the slow growing sample) were considered at scores >5.0 as an amplification and <0.2 as loss of heterozygosity. A subset of SNPs (n = 54) were validated and evaluated for association with growth traits in 778 individuals of a three-generation parent/offspring panel representing 40 families. Twenty-two SNP markers and one mitochondrial haplotype were significantly associated with growth traits. Polymorphism of 48 of the markers was confirmed in other commercially important aquaculture stocks. Many markers were clustered into genes of metabolic energy production pathways and are suitable candidates for genetic selection. The study demonstrates that RNA-Seq at low sequence coverage of divergent populations is a fast and effective means of identifying SNPs, with allelic imbalances between phenotypes. This technique is suitable for marker

  19. Electronic Principles Governing the Stability and Reactivity of Ligated Metal and Silicon Encapsulated Transition Metal Clusters

    NASA Astrophysics Data System (ADS)

    Abreu, Marissa Baddick

    A thorough understanding of the underlying electronic principles guiding the stability and reactivity of clusters has direct implications for the identification of stable clusters for incorporation into clusters-assembled materials with tunable properties. This work explores the electronic principles governing the stability and reactivity of two types of clusters: ligated metal clusters and silicon encapsulated transition metal clusters. In the first case, the reactivity of iodine-protected aluminum clusters, Al13Ix - (x=0-4) and Al14Iy- (y=0-5), with the protic species methanol was studied. The symmetrical ground states of Al13Ix- showed no reactivity with methanol but reactivity was achieved in a higher energy isomer of Al 13I2- with iodines on adjacent aluminum atoms -- complementary Lewis acid-base active sites were induced on the opposite side of the cluster capable of breaking the O-H bond in methanol. Al 14Iy- (y=2-5) react with methanol, but only at the ligated adatom site. Reaction of methanol with Al14 - and Al14I- showed that ligation of the adatom was necessary for the reaction to occur there -- revealing the concept of a ligand-activated adatom. In the second case, the study focused heavily on CrSi12, a silicon encapsulated transition metal cluster whose stability and the reason for that stability has been debated heavily in the literature. Calculations of the energetic properties of CrSi n (n=6-16) revealed both CrSi12 and CrSi14 to have enhanced stability relative to other clusters; however CrSi12 lacks all the traditional markers of a magic cluster. Molecular orbital analysis of each of these clusters showed the CNFEG model to be inadequate in describing their stability. Because the 3dz2 orbital of Cr is unfilled in CrSi12, this cluster has only 16 effective valence electrons, meaning that the 18-electron rule is not applicable. The moderate stability of CrSi 12 can be accounted for by the crystal-field splitting of the 3d orbitals, which pushes the

  20. Decaying neutrinos in galaxy clusters

    NASA Technical Reports Server (NTRS)

    Melott, Adrian L.; Splinter, Randall J.; Persic, Massimo; Salucci, Paolo

    1994-01-01

    Davidsen et al. (1991) have argued that the failure to detect UV photons from the dark matter (DM) in cluster A665 excludes the decaying neutrino hypothesis. Sciama et al. (1993) argued that because of high central concentration the DM in that cluster must be baryonic. We study the DM profile in clusters of galaxies simulated using the Harrison-Zel'dovich spectrum of density fluctuations, and an amplitude previously derived from numerical simulations (Melott 1984b; Anninos et al. 1991) and in agreement with microwave background fluctuations (Smoot et al. 1992). We find that with this amplitude normalization cluster neutrino DM densities are comparable to observed cluster DM values. We conclude that given this normalization, the cluster DM should be at least largely composed of neutrinos. The constraint of Davidsen et al. can be somewhat weakened by the presence of baryonic DM; but it cannot be eliminated given our assumptions.

  1. Textures and clusters. [of galaxies

    NASA Technical Reports Server (NTRS)

    Bartlett, James G.; Gooding, Andrew K.; Spergel, David N.

    1993-01-01

    We discuss the properties of galaxy clusters expected in a texture-seeded, CDM-dominated, Omega = 1 universe. Assuming that the textures are spherical, we use the spherical collapse model to compute the cluster velocity dispersion (or temperature) distribution function. For objects of mass 10 exp 11 to 10 exp 15 solar masses, we find v varies as M super gamma with gamma of about 0.25. An unbiased (b = 1) texture model predicts too many high-velocity dispersion clusters. A biased texture model appears to be compatible with cluster properties inferred from optical and X-ray observations. In the texture model, the cluster velocity distribution functio does not evolve rapidly; thus, the model predicts the existence of rich clusters at moderate redshift (about 1-2).

  2. Practical considerations for imputation of untyped markers in admixed populations.

    PubMed

    Shriner, Daniel; Adeyemo, Adebowale; Chen, Guanjie; Rotimi, Charles N

    2010-04-01

    Imputation of genotypes for markers untyped in a study sample has become a standard approach to increase genome coverage in genome-wide association studies at practically zero cost. Most methods for imputing missing genotypes extend previously described algorithms for inferring haplotype phase. These algorithms generally fall into three classes based on the underlying model for estimating the conditional distribution of haplotype frequencies: a cluster-based model, a multinomial model, or a population genetics-based model. We compared BEAGLE, PLINK, and MACH, representing the three classes of models, respectively, with specific attention to measures of imputation success and selection of the reference panel for an admixed study sample of African Americans. Based on analysis of chromosome 22 and after calibration to a fixed level of 90% concordance between experimentally determined and imputed genotypes, MACH yielded the largest absolute number of successfully imputed markers and the largest gain in coverage of the variation captured by HapMap reference panels. Following the common practice of performing imputation once, the Yoruba in Ibadan, Nigeria (YRI) reference panel outperformed other HapMap reference panels, including (1) African ancestry from Southwest USA (ASW) data, (2) an unweighted combination of the Northern and Western Europe (CEU) and YRI data into a single reference panel, and (3) a combination of the CEU and YRI data into a single reference panel with weights matching estimates of admixture proportions. For our admixed study sample, the optimal strategy involved imputing twice with the HapMap CEU and YRI reference panels separately and then merging the data sets. PMID:19918757

  3. Somatic markers, working memory, and decision making.

    PubMed

    Hinson, John M; Jameson, Tina L; Whitney, Paul

    2002-12-01

    The somatic marker hypothesis formulated by Damasio (e.g., 1994; Damasio, Tranel, & Damasio, 1991) argues that affective reactions ordinarily guide and simplify decision making. Although originally intended to explain decision-making deficits in people with specific frontal lobe damage, the hypothesis also applies to decision-making problems in populations without brain injury. Subsequently, the gambling task was developed by Bechara (Bechara, Damasio, Damasio, & Anderson, 1994) as a diagnostic test of decision-making deficit in neurological populations. More recently, the gambling task has been used to explore implications of the somatic marker hypothesis, as well as to study suboptimal decision making in a variety of domains. We examined relations among gambling task decision making, working memory (WM) load, and somatic markers in a modified version of the gambling task. Increased WM load produced by secondary tasks led to poorer gambling performance. Declines in gambling performance were associated with the absence of the affective reactions that anticipate choice outcomes and guide future decision making. Our experiments provide evidence that WM processes contribute to the development of somatic markers. If WM functioning is taxed, somatic markers may not develop, and decision making may thereby suffer. PMID:12641178

  4. The SMART CLUSTER METHOD - adaptive earthquake cluster analysis and declustering

    NASA Astrophysics Data System (ADS)

    Schaefer, Andreas; Daniell, James; Wenzel, Friedemann

    2016-04-01

    Earthquake declustering is an essential part of almost any statistical analysis of spatial and temporal properties of seismic activity with usual applications comprising of probabilistic seismic hazard assessments (PSHAs) and earthquake prediction methods. The nature of earthquake clusters and subsequent declustering of earthquake catalogues plays a crucial role in determining the magnitude-dependent earthquake return period and its respective spatial variation. Various methods have been developed to address this issue from other researchers. These have differing ranges of complexity ranging from rather simple statistical window methods to complex epidemic models. This study introduces the smart cluster method (SCM), a new methodology to identify earthquake clusters, which uses an adaptive point process for spatio-temporal identification. Hereby, an adaptive search algorithm for data point clusters is adopted. It uses the earthquake density in the spatio-temporal neighbourhood of each event to adjust the search properties. The identified clusters are subsequently analysed to determine directional anisotropy, focussing on a strong correlation along the rupture plane and adjusts its search space with respect to directional properties. In the case of rapid subsequent ruptures like the 1992 Landers sequence or the 2010/2011 Darfield-Christchurch events, an adaptive classification procedure is applied to disassemble subsequent ruptures which may have been grouped into an individual cluster using near-field searches, support vector machines and temporal splitting. The steering parameters of the search behaviour are linked to local earthquake properties like magnitude of completeness, earthquake density and Gutenberg-Richter parameters. The method is capable of identifying and classifying earthquake clusters in space and time. It is tested and validated using earthquake data from California and New Zealand. As a result of the cluster identification process, each event in

  5. Consensus mapping and identification of markers for marker-assisted selection of Wsm2 in wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A recently identified Wheat streak mosaic virus (WSMV) resistance gene Wsm2 confers a high level of resistance. Objective of this study was to identify closely linked DNA markers for Wsm2 for use in marker-assisted selection (MAS) in wheat. Two segregating populations (CO960293-2/’TAM 111’ and CO96...

  6. Immersed boundary method with non-uniform distribution of Lagrangian markers for a non-uniform Eulerian mesh

    NASA Astrophysics Data System (ADS)

    Akiki, G.; Balachandar, S.

    2016-02-01

    This study presents a technique to incorporate spheres in a channel flow that uses a non-uniform Eulerian grid using immersed boundary methods with direct forcing. An efficient algorithm is presented which distributes the Lagrangian markers non-uniformly to match the fluid grid and keep the number of markers optimized. Also a novel method to calculate the area weights of the Lagrangian markers is given. It is observed that even the best available algorithms for uniform distribution of markers on a sphere result in a finite error. Using vector spherical harmonics, this error is quantified and reduced to machine precision. A series of simulations of a stationary and moving sphere in a periodic channel at Reynolds number range of 1-100 are presented. Results for a sphere in an ambient shear flow in close proximity of a wall are also shown, where the present non-uniform distribution offers an order of magnitude reduction over uniform distribution of Lagrangian markers. Simulations of a random cluster of 640 monodisperse spherical particles show a 77% reduction in Lagrangian markers with an error of 0.135% in computing the total drag.

  7. 30 CFR 816.11 - Signs and markers.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 3 2011-07-01 2011-07-01 false Signs and markers. 816.11 Section 816.11... § 816.11 Signs and markers. (a) Specifications. Signs and markers required under this part shall— (1) Be...) Conform to local ordinances and codes. (b) Duration of maintenance. Signs and markers shall be...

  8. 30 CFR 816.11 - Signs and markers.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 3 2013-07-01 2013-07-01 false Signs and markers. 816.11 Section 816.11... § 816.11 Signs and markers. (a) Specifications. Signs and markers required under this part shall— (1) Be...) Conform to local ordinances and codes. (b) Duration of maintenance. Signs and markers shall be...

  9. 30 CFR 816.11 - Signs and markers.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 3 2014-07-01 2014-07-01 false Signs and markers. 816.11 Section 816.11... § 816.11 Signs and markers. (a) Specifications. Signs and markers required under this part shall— (1) Be...) Conform to local ordinances and codes. (b) Duration of maintenance. Signs and markers shall be...

  10. 30 CFR 816.11 - Signs and markers.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 3 2012-07-01 2012-07-01 false Signs and markers. 816.11 Section 816.11... § 816.11 Signs and markers. (a) Specifications. Signs and markers required under this part shall— (1) Be...) Conform to local ordinances and codes. (b) Duration of maintenance. Signs and markers shall be...

  11. 30 CFR 816.11 - Signs and markers.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 3 2010-07-01 2010-07-01 false Signs and markers. 816.11 Section 816.11... § 816.11 Signs and markers. (a) Specifications. Signs and markers required under this part shall— (1) Be...) Conform to local ordinances and codes. (b) Duration of maintenance. Signs and markers shall be...

  12. Genetic diversity in cultivated carioca common beans based on molecular marker analysis

    PubMed Central

    Küpper Cardoso Perseguini, Juliana Morini; Chioratto, Alisson Fernando; Zucchi, Maria Imaculada; Colombo, Carlos Augusto; Carbonell, Sérgio Augusto Moraes; Costa Mondego, Jorge Mauricio; Gazaffi, Rodrigo; Franco Garcia, Antonio Augusto; de Campos, Tatiana; de Souza, Anete Pereira; Rubiano, Luciana Benchimol

    2011-01-01

    A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats – SSRs and amplified fragment length polymorphisms – AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger’s modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm. PMID:21637550

  13. Needles: Toward Large-Scale Genomic Prediction with Marker-by-Environment Interaction.

    PubMed

    De Coninck, Arne; De Baets, Bernard; Kourounis, Drosos; Verbosio, Fabio; Schenk, Olaf; Maenhout, Steven; Fostier, Jan

    2016-05-01

    Genomic prediction relies on genotypic marker information to predict the agronomic performance of future hybrid breeds based on trial records. Because the effect of markers may vary substantially under the influence of different environmental conditions, marker-by-environment interaction effects have to be taken into account. However, this may lead to a dramatic increase in the computational resources needed for analyzing large-scale trial data. A high-performance computing solution, called Needles, is presented for handling such data sets. Needles is tailored to the particular properties of the underlying algebraic framework by exploiting a sparse matrix formalism where suited and by utilizing distributed computing techniques to enable the use of a dedicated computing cluster. It is demonstrated that large-scale analyses can be performed within reasonable time frames with this framework. Moreover, by analyzing simulated trial data, it is shown that the effects of markers with a high environmental interaction can be predicted more accurately when more records per environment are available in the training data. The availability of such data and their analysis with Needles also may lead to the discovery of highly contributing QTL in specific environmental conditions. Such a framework thus opens the path for plant breeders to select crops based on these QTL, resulting in hybrid lines with optimized agronomic performance in specific environmental conditions. PMID:26936924

  14. Isolation of Bacteroides from fish and human fecal samples for identification of unique molecular markers.

    PubMed

    Kabiri, Leila; Alum, Absar; Rock, Channah; McLain, Jean E; Abbaszadegan, Morteza

    2013-12-01

    Bacteroides molecular markers have been used to identify human fecal contamination in natural waters, but recent work in our laboratory confirmed cross-amplification of several human-specific Bacteroides spp. assays with fecal DNA from fish. For identification of unique molecular markers, Bacteroides from human (n = 4) and fish (n = 7) fecal samples were cultured and their identities were further confirmed using Rapid ID 32A API strips. The 16S rDNA from multiple isolates from each sample was PCR amplified, cloned, and sequenced to identify unique markers for development of more stringent human-specific assays. In human feces, Bacteroides vulgatus was the dominant species (75% of isolates), whereas in tilapia feces, Bacteroides eggerthii was dominant (66%). Bacteroides from grass carp, channel catfish, and blue catfish may include Bacteroides uniformis, Bacteroides ovatus, or Bacteroides stercoris. Phylogenic analyses of the 16S rRNA gene sequences showed distinct Bacteroides groupings from each fish species, while human sequences clustered with known B. vulgatus. None of the fish isolates showed significant similarity to Bacteroides sequences currently deposited in NCBI (National Center for Biotechnology Information). This study expands the current sequence database of cultured fish Bacteroides. Such data are essential for identification of unique molecular markers in human Bacteroides that can be utilized in differentiating fish and human fecal contamination in water samples. PMID:24313449

  15. Development of simple sequence repeat (SSR) markers of sesame (Sesamum indicum) from a genome survey.

    PubMed

    Wei, Xin; Wang, Linhai; Zhang, Yanxin; Qi, Xiaoqiong; Wang, Xiaoling; Ding, Xia; Zhang, Jing; Zhang, Xiurong

    2014-01-01

    Sesame (Sesamum indicum), an important oil crop, is widely grown in tropical and subtropical regions. It provides part of the daily edible oil allowance for almost half of the world's population. A limited number of co-dominant markers has been developed and applied in sesame genetic diversity and germplasm identity studies. Here we report for the first time a whole genome survey used to develop simple sequence repeat (SSR) markers and to detect the genetic diversity of sesame germplasm. From the initial assembled sesame genome, 23,438 SSRs (≥5 repeats) were identified. The most common repeat motif was dinucleotide with a frequency of 84.24%, followed by 13.53% trinucleotide, 1.65% tetranucleotide, 0.3% pentanucleotide and 0.28% hexanucleotide motifs. From 1500 designed and synthesised primer pairs, 218 polymorphic SSRs were developed and used to screen 31 sesame accessions that from 12 countries. STRUCTURE and phylogenetic analyses indicated that all sesame accessions could be divided into two groups: one mainly from China and another from other countries. Cluster analysis classified Chinese major sesame varieties into three groups. These novel SSR markers are a useful tool for genetic linkage map construction, genetic diversity detection, and marker-assisted selective sesame breeding. PMID:24759074

  16. Active matter clusters at interfaces.

    NASA Astrophysics Data System (ADS)

    Copenhagen, Katherine; Gopinathan, Ajay

    2016-03-01

    Collective and directed motility or swarming is an emergent phenomenon displayed by many self-organized assemblies of active biological matter such as clusters of embryonic cells during tissue development, cancerous cells during tumor formation and metastasis, colonies of bacteria in a biofilm, or even flocks of birds and schools of fish at the macro-scale. Such clusters typically encounter very heterogeneous environments. What happens when a cluster encounters an interface between two different environments has implications for its function and fate. Here we study this problem by using a mathematical model of a cluster that treats it as a single cohesive unit that moves in two dimensions by exerting a force/torque per unit area whose magnitude depends on the nature of the local environment. We find that low speed (overdamped) clusters encountering an interface with a moderate difference in properties can lead to refraction or even total internal reflection of the cluster. For large speeds (underdamped), where inertia dominates, the clusters show more complex behaviors crossing the interface multiple times and deviating from the predictable refraction and reflection for the low velocity clusters. We then present an extreme limit of the model in the absence of rotational damping where clusters can become stuck spiraling along the interface or move in large circular trajectories after leaving the interface. Our results show a wide range of behaviors that occur when collectively moving active biological matter moves across interfaces and these insights can be used to control motion by patterning environments.

  17. Digging Deep in Pandora's Cluster

    NASA Astrophysics Data System (ADS)

    Blakeslee, John P.; Alamo-Martinez, Karla; Toloba, Elisa; Barro, Guillermo; Peng, Eric W.

    2015-01-01

    Abell 2744, the first and nearest (z=0.31) of the Hubble Frontier Fields, is extraordinarily rich in the number and variety of galaxies it contains. Nicknamed "Pandora's Cluster," it exhibits multiple peaks in the dark matter, X-ray, and galaxy density distributions, suggesting an ongoing collision of several massive clusters. The exceptional depth of the Hubble Frontier Field imaging now makes it possible to throw open Pandora's cluster and peer deep inside. To do this, we first model and remove the stellar light of the cluster galaxies; underneath we find not only distant background galaxies, but (like the Hope that lay at the bottom of Pandora's box) a large population of globular star clusters and compact cluster members within Abell 2744 itself. Our earlier work on the massive lensing cluster Abell 1689 (Alamo-Martinez et al. 2013) revealed the largest known population of globular clusters, with a spatial profile intermediate between the galaxy light and the dark matter. Abell 2744 is similarly massive, but far less regular in its density distribution; we examine what implications this has for the copious globular clusters coursing through its multiple cores.

  18. Lattice QCD clusters at Fermilab

    SciTech Connect

    Holmgren, D.; Mackenzie, Paul B.; Singh, Anitoj; Simone, Jim; /Fermilab

    2004-12-01

    As part of the DOE SciDAC ''National Infrastructure for Lattice Gauge Computing'' project, Fermilab builds and operates production clusters for lattice QCD simulations. This paper will describe these clusters. The design of lattice QCD clusters requires careful attention to balancing memory bandwidth, floating point throughput, and network performance. We will discuss our investigations of various commodity processors, including Pentium 4E, Xeon, Opteron, and PPC970. We will also discuss our early experiences with the emerging Infiniband and PCI Express architectures. Finally, we will present our predictions and plans for future clusters.

  19. Constrained Clustering With Imperfect Oracles.

    PubMed

    Zhu, Xiatian; Loy, Chen Change; Gong, Shaogang

    2016-06-01

    While clustering is usually an unsupervised operation, there are circumstances where we have access to prior belief that pairs of samples should (or should not) be assigned with the same cluster. Constrained clustering aims to exploit this prior belief as constraint (or weak supervision) to influence the cluster formation so as to obtain a data structure more closely resembling human perception. Two important issues remain open: 1) how to exploit sparse constraints effectively and 2) how to handle ill-conditioned/noisy constraints generated by imperfect oracles. In this paper, we present a novel pairwise similarity measure framework to address the above issues. Specifically, in contrast to existing constrained clustering approaches that blindly rely on all features for constraint propagation, our approach searches for neighborhoods driven by discriminative feature selection for more effective constraint diffusion. Crucially, we formulate a novel approach to handling the noisy constraint problem, which has been unrealistically ignored in the constrained clustering literature. Extensive comparative results show that our method is superior to the state-of-the-art constrained clustering approaches and can generally benefit existing pairwise similarity-based data clustering algorithms, such as spectral clustering and affinity propagation. PMID:25622327

  20. Genetic relationships of ethnic minorities in Southwest China revealed by microsatellite markers.

    PubMed

    Lin, Hongbin; Fan, Hao; Zhang, Feng; Huang, Xiaoqin; Lin, Keqin; Shi, Lei; Hu, Songnian; Chu, Jiayou; Wang, Duen-Mei

    2010-01-01

    Population migrations in Southwest and South China have played an important role in the formation of East Asian populations and led to a high degree of cultural diversity among ethnic minorities living in these areas. To explore the genetic relationships of these ethnic minorities, we systematically surveyed the variation of 10 autosomal STR markers of 1,538 individuals from 30 populations of 25 ethnic minorities, of which the majority were chosen from Southwest China, especially Yunnan Province. With genotyped data of the markers, we constructed phylogenies of these populations with both D(A) and D(C) measures and performed a principal component analysis, as well as a clustering analysis by structure. Results showed that we successfully recovered the genetic structure of analyzed populations formed by historical migrations. Aggregation patterns of these populations accord well with their linguistic affiliations, suggesting that deciphering of genetic relationships does in fact offer clues for study of ethnic differentiation. PMID:20360948

  1. Genetic diversity analysis of sweet kernel apricot in China based on SSR and ISSR markers.

    PubMed

    Liu, M P; Du, H Y; Zhu, G P; Fu, D L; Tana, W Y

    2015-01-01

    Simple sequence repeat (SSR) and inter-simple sequence repeat (ISSR) markers were used to evaluate genetic diversity among 22 sweet kernel apricot accessions and 12 cultivars in China to provide information on how to improve the utilization of kernel apricot germplasms. The results showed that 10 pairs of SSR primers screened from 40 primer pairs amplified 43 allelic variants, all of which were polymorphic (100%), and 9 ISSR primers selected from 100 primers amplified 67 allelic variants with 50 polymorphic bands (74.63%). There was a relatively distant genetic relationship between the 34 samples, where their genetic similarity coefficient was between 0.62 and 0.99. The UPGMA dendrogram constructed using combined data of the two marker systems separated the genotypes into three main clusters. PMID:26345904

  2. Study of rust resistance genes in wheat germplasm with DNA markers

    PubMed Central

    Haque, Asma; Shaheen, Tayyaba; Gulzar, Tahsin; Rahman, Mahmood ur; Jalal, Fatima; Sattar, Summera; Ehsan, Beenish; Iqbal, Zafar; Younas, Muhammad

    2014-01-01

    Wheat is a vital dietary component for human health and widely consumed in the world. Wheat rusts are dangerous pathogens and contribute serious threat to its production. In present study, PCR-Based DNA Markers were employed to check the rust resistance genes among 20 wheat genotypes and 22 markers were amplified. NTSYS-pc 2.2 was used to calculate genetic diversity and Nei and Li's coefficients ranged from 0.55 to 0.95. Cluster analysis was obtained using UPGMA (Unweighted Pair Group Method of Arithmetic Average) algorithm. Maximum no. of genes (23) was amplified from TW-760010 genotype whereas minimum no of genes (14) were amplified from TW-76005 genotype. The data gained from present study open up new ways to produce new varieties by breeding rust resistant germplasm to avoid the economic and food loss and varieties with improved characteristics. PMID:25097381

  3. Sox17-Mediated Maintenance of Fetal Intra-Aortic Hematopoietic Cell Clusters

    PubMed Central

    Osawa, Mitsujiro; Uemura, Mami; Kishikawa, Yoko; Anani, Maha; Harada, Kaho; Takagi, Haruna; Saito, Kiyoka; Kanai-Azuma, Masami; Kanai, Yoshiakira; Iwama, Atsushi

    2014-01-01

    During mouse development, definitive hematopoiesis is first detected around embryonic day 10.5 (E10.5) in the aorta-gonad-mesonephros (AGM) region, which exhibits intra-aortic cell clusters. These clusters are known to contain hematopoietic stem cells (HSCs). On the other hand, it is not clear how the cells in such clusters maintain their HSC phenotype and how they are triggered to differentiate. Here we found that an endodermal transcription factor marker, Sox17, and other F-group (SoxF) proteins, Sox7 and Sox18, were expressed in E10.5 intra-aortic cell clusters. Forced expression of any of these SoxF proteins, particularly Sox17, in E10.5 AGM CD45low c-Kithigh cells, which are the major component of intra-aortic clusters, led to consistent formation of cell clusters in vitro during several passages of cocultures with stromal cells. Cluster-forming cells with constitutive Sox17 expression retained long-term bone marrow reconstitution activity in vivo. Notably, shutdown of exogenously introduced Sox17 gene expression resulted in immediate hematopoietic differentiation. These results indicate that SoxF proteins, especially Sox17, contribute to the maintenance of cell clusters containing HSCs in the midgestation AGM region. Furthermore, SoxF proteins play a pivotal role in controlling the HSC fate decision between indefinite self-renewal and differentiation during fetal hematopoiesis. PMID:24662049

  4. Coarse Point Cloud Registration by Egi Matching of Voxel Clusters

    NASA Astrophysics Data System (ADS)

    Wang, Jinhu; Lindenbergh, Roderik; Shen, Yueqian; Menenti, Massimo

    2016-06-01

    Laser scanning samples the surface geometry of objects efficiently and records versatile information as point clouds. However, often more scans are required to fully cover a scene. Therefore, a registration step is required that transforms the different scans into a common coordinate system. The registration of point clouds is usually conducted in two steps, i.e. coarse registration followed by fine registration. In this study an automatic marker-free coarse registration method for pair-wise scans is presented. First the two input point clouds are re-sampled as voxels and dimensionality features of the voxels are determined by principal component analysis (PCA). Then voxel cells with the same dimensionality are clustered. Next, the Extended Gaussian Image (EGI) descriptor of those voxel clusters are constructed using significant eigenvectors of each voxel in the cluster. Correspondences between clusters in source and target data are obtained according to the similarity between their EGI descriptors. The random sampling consensus (RANSAC) algorithm is employed to remove outlying correspondences until a coarse alignment is obtained. If necessary, a fine registration is performed in a final step. This new method is illustrated on scan data sampling two indoor scenarios. The results of the tests are evaluated by computing the point to point distance between the two input point clouds. The presented two tests resulted in mean distances of 7.6 mm and 9.5 mm respectively, which are adequate for fine registration.

  5. On the Quality of Velocity Interpolation Schemes for Marker-In-Cell Methods on 3-D Staggered Grids

    NASA Astrophysics Data System (ADS)

    Kaus, B.; Pusok, A. E.; Popov, A.

    2015-12-01

    The marker-in-cell method is generally considered to be a flexible and robust method to model advection of heterogenous non-diffusive properties (i.e. rock type or composition) in geodynamic problems or incompressible Stokes problems. In this method, Lagrangian points carrying compositional information are advected with the ambient velocity field on an immobile, Eulerian grid. However, velocity interpolation from grid points to marker locations is often performed without preserving the zero divergence of the velocity field at the interpolated locations (i.e. non-conservative). Such interpolation schemes can induce non-physical clustering of markers when strong velocity gradients are present (Jenny et al., 2001) and this may, eventually, result in empty grid cells, a serious numerical violation of the marker-in-cell method. Solutions to this problem include: using larger mesh resolutions and/or marker densities, or repeatedly controlling the marker distribution (i.e. inject/delete), but which does not have an established physical background. To remedy this at low computational costs, Jenny et al. (2001) and Meyer and Jenny (2004) proposed a simple, conservative velocity interpolation (CVI) scheme for 2-D staggered grid, while Wang et al. (2015) extended the formulation to 3-D finite element methods. Here, we follow up with these studies and report on the quality of velocity interpolation methods for 2-D and 3-D staggered grids. We adapt the formulations from both Jenny et al. (2001) and Wang et al. (2015) for use on 3-D staggered grids, where the velocity components have different node locations as compared to finite element, where they share the same node location. We test the different interpolation schemes (CVI and non-CVI) in combination with different advection schemes (Euler, RK2 and RK4) and with/out marker control on Stokes problems with strong velocity gradients, which are discretized using a finite difference method. We show that a conservative formulation

  6. Cutaneous markers of coronary artery disease.

    PubMed

    Dwivedi, Shridhar; Jhamb, Rajat

    2010-09-26

    Coronary artery disease (CAD) is rapidly increasing in prevalence across the world and particularly in south Asians at a relatively younger age. As atherosclerosis starts in early childhood, the process of risk evaluation must start quite early. The present review addresses the issue of cutaneous markers associated with atherosclerosis, and the strengths and weaknesses of the markers in identifying early coronary atherosclerosis. A diligent search for such clinical markers, namely xanthelasma, xanthoma, arcus juvenilis, acanthosis nigricans, skin tags, ear lobe crease, nicotine stains, premature graying in smokers, hyperpigmented hands in betel quid sellers, central obesity, and signs of peripheral vascular disease may prove to be a rewarding exercise in identifying asymptomatic CAD in high risk individuals. PMID:21160602

  7. Markers of metastatic carcinoma of breast origin.

    PubMed

    Gown, Allen M; Fulton, Regan S; Kandalaft, Patricia L

    2016-01-01

    This review summarizes the three major breast-associated markers that can be of assistance in evaluating metastatic carcinomas for which a breast primary diagnosis is entertained. These markers include gross cystic disease fluid protein-15 (GCDFP-15), mammaglobin, and GATA3. The first two are cytoplasmic markers that show comparable sensitivities for breast cancer, although relatively few of the published studies have employed the same antibodies against the target molecule, making direct comparisons challenging. GATA3 is a nuclear transcription factor that shows superior sensitivity to GCDFP-15 and mammaglobin. However, the specificity of GATA3 can pose challenges, inasmuch as carcinomas of the bladder and other sites can show significant levels of positivity. Determination of the optimal panel of antibodies employed in a given clinical setting will thus depend on the non-breast tumours included in the differential diagnosis. PMID:26768031

  8. Trophoblastic markers in women using intrauterine contraception.

    PubMed

    Ylikorkala, O; Siljander, M; Huhtaniemi, I; Kauppila, A; Seppälä, M

    1980-03-01

    Serum levels of human chorionic gonadotropin (hCG) and pregnancy-specific beta 1-glycoprotein (PSBG) were measured in 214 women using Copper-T200 intrauterine devices (CIUDs). In a cross-sectional study the samples were taken between the 25th and 35th cycle days, 1 sample per cycle. Either trophoblastic marker was detectable in 8 women (3.7%), hCG in 3 (1.4%), PSBG in 7 (3.3%), and both markers together in (0.9%). Normal menstruation-like bleeding ensued in all but 1 woman whose bleeding was delayed by 5 days. Our results suggest that the intrauterine contraceptive device (IUD) prevents pregnancy mainly before significant amounts of trophoblastic products are secreted. Still, the incidence of subclinical abortion based on the demonstration of trophoblastic markers in serum was 7 to 10 times higher than that of established pregnancy in women using a CIUD. PMID:6965779

  9. Genetic Relationships of Aglaonema Species and Cultivars Inferred from AFLP Markers

    PubMed Central

    CHEN, JIANJUN; DEVANAND, PACHANOOR S.; NORMAN, DAVID J.; HENNY, RICHARD J.; CHAO, CHIH‐CHENG T.

    2004-01-01

    • Background and Aims Aglaonema is an important ornamental foliage plant genus, but genetic relationships among its species and cultivars have not been reported. This study analysed genetic relatedness of 54 cultivars derived from nine species using amplified fragment length polymorphism (AFLP) markers. • Methods Initially, 48 EcoRI + 2/MseI + 3 primer set combinations were screened, from which six primer sets that showed clear scoreable and highly polymorphic fragments were selected and used for AFLP reactions. AFLP fragments were scored and entered into a binary data matrix as discrete variables. Jaccard’s coefficient of similarity was calculated for all pair‐wise comparisons among the 54 cultivars, and a dendrogram was constructed by the unweighted pair‐group method using the arithmetic average (UPGMA). • Key Results The number of AFLP fragments generated per primer set ranged from 59 to 112 with fragment sizes varying from 50 to 565 bp. A total of 449 AFLP fragments was detected, of which 314 were polymorphic (70 %). All cultivars were clearly differentiated by their AFLP fingerprints. The 54 cultivars were divided into seven clusters; cultivars within each cluster generally share similar morphological characteristics. Cluster I contains 35 cultivars, most of them are interspecific hybrids developed mainly from A. commutatum, A. crispum or A. nitidum. However, Jaccard’s similarity coefficients among these hybrids are 0·84 or higher, suggesting that these popular hybrid cultivars are genetically much closer than previously thought. This genetic similarity may imply that A. nitidum and A. crispum are likely progenitors of A. commutatum. • Conclusions Results of this study demonstrate the efficiency and ease of using AFLP markers for investigating genetic relationships of ornamental foliage plants, a group usually propagated vegetatively. The AFLP markers developed will help future Aglaonema cultivar identification, germplasm conservation and

  10. Postpartum Circulating Markers of Inflammation and the Systemic Acute-Phase Response After Early-Onset Preeclampsia.

    PubMed

    van Rijn, Bas B; Bruinse, Hein W; Veerbeek, Jan H; Post Uiterweer, Emiel D; Koenen, Steven V; van der Bom, Johanna G; Rijkers, Ger T; Roest, Mark; Franx, Arie

    2016-02-01

    Preeclampsia is an inflammatory-mediated hypertensive disorder of pregnancy and seems to be an early indicator of increased cardiovascular risk, but mechanisms underlying this association are unclear. In this study, we identified levels of circulating inflammatory markers and dynamic changes in the systemic acute-phase response in 44 women with a history of severe early-onset preeclampsia, compared with 29 controls with only uneventful pregnancies at 1.5 to 3.5 years postpartum. Models used were in vivo seasonal influenza vaccination and in vitro whole-blood culture with T-cell stimulants and the toll-like receptor-4 ligand lipopolysaccharide. Outcome measures were C-reactive protein, interleukin-6 (IL-6), IL-18, fibrinogen, myeloperoxidase, and a panel of 13 cytokines representative of the innate and adaptive inflammatory response, in addition to established cardiovascular markers. The in vivo acute-phase response was higher for women with previous preeclampsia than that for controls without such a history, although only significant for C-reactive protein (P=0.04). Preeclampsia was associated with higher IL-1β (P<0.05) and IL-8 (P<0.01) responses to T-cell activation. Hierarchical clustering revealed 2 distinct inflammatory clusters associated with previous preeclampsia: an adaptive response cluster associated with increased C-reactive protein and IL-6 before and after vaccination, increased weight, and low high-density lipoprotein cholesterol; and a toll-like receptor-4 mediated the cluster associated with increased IL-18 before and after vaccination but not associated with other cardiovascular markers. Furthermore, we found interactions between previous preeclampsia, common TLR4 gene variants, and the IL-18 response to vaccination. In conclusion, preeclampsia is associated with alterations in the inflammatory response postpartum mostly independent of other established cardiovascular risk markers. PMID:26711734

  11. Microsatellite marker diversity in common bean (Phaseolus vulgaris L.).

    PubMed

    Blair, M W; Giraldo, M C; Buendía, H F; Tovar, E; Duque, M C; Beebe, S E

    2006-06-01

    A diversity survey was used to estimate allelic diversity and heterozygosity of 129 microsatellite markers in a panel of 44 common bean (Phaseolus vulgaris L.) genotypes that have been used as parents of mapping populations. Two types of microsatellites were evaluated, based respectively on gene coding and genomic sequences. Genetic diversity was evaluated by estimating the polymorphism information content (PIC), as well as the distribution and range of alleles sizes. Gene-based microsatellites proved to be less polymorphic than genomic microsatellites in terms of both number of alleles (6.0 vs. 9.2) and PIC values (0.446 vs. 0.594) while greater size differences between the largest and the smallest allele were observed for the genomic microsatellites than for the gene-based microsatellites (31.4 vs. 19.1 bp). Markers that showed a high number of alleles were identified with a maximum of 28 alleles for the marker BMd1. The microsatellites were useful for distinguishing Andean and Mesoamerican genotypes, for uncovering the races within each genepool and for separating wild accessions from cultivars. Greater polymorphism and race structure was found within the Andean gene pool than within the Mesoamerican gene pool and polymorphism rate between genotypes was consistent with genepool and race identity. Comparisons between Andean genotypes had higher polymorphism (53.0%) on average than comparisons among Mesoamerican genotypes (33.4%). Within the Mesoamerican parental combinations, the intra-racial combinations between Mesoamerica and Durango or Jalisco race genotypes showed higher average rates of polymorphism (37.5%) than the within-race combinations between Mesoamerica race genotypes (31.7%). In multiple correspondance analysis we found two principal clusters of genotypes corresponding to the Mesoamerican and Andean gene pools and subgroups representing specific races especially for the Nueva Granada and Peru races of the Andean gene pool. Intra population diversity

  12. Liver fibrosis markers in alcoholic liver disease

    PubMed Central

    Chrostek, Lech; Panasiuk, Anatol

    2014-01-01

    Alcohol is one of the main factors of liver damage. The evaluation of the degree of liver fibrosis is of great value for therapeutic decision making in patients with alcoholic liver disease (ALD). Staging of liver fibrosis is essential to define prognosis and management of the disease. Liver biopsy is a gold standard as it has high sensitivity and specificity in fibrosis diagnostics. Taking into account the limitations of liver biopsy, there is an exigency to introduce non-invasive serum markers for fibrosis that would be able to replace liver biopsy. Ideal serum markers should be specific for the liver, easy to perform and independent to inflammation and fibrosis in other organs. Serum markers of hepatic fibrosis are divided into direct and indirect. Indirect markers reflect alterations in hepatic function, direct markers reflect extracellular matrix turnover. These markers should correlate with dynamic changes in fibrogenesis and fibrosis resolution. The assessment of the degree of liver fibrosis in alcoholic liver disease has diagnostic and prognostic implications, therefore noninvasive assessment of fibrosis remains important. There are only a few studies evaluating the diagnostic and prognostic values of noninvasive biomarkers of fibrosis in patients with ALD. Several noninvasive laboratory tests have been used to assess liver fibrosis in patients with alcoholic liver disease, including the hyaluronic acid, FibroTest, FibrometerA, Hepascore, Forns and APRI indexes, FIB4, an algorithm combining Prothrombin index (PI), α-2 macroglobulin and hyaluronic acid. Among these tests, Fibrotest, FibrometerA and Hepascore demonstrated excellent diagnostic accuracy in identifying advanced fibrosis and cirrhosis, and additionally, Fibrotest was independently associated with survival. Therefore, the use of biomarkers may reduce the need for liver biopsy and permit an earlier treatment of alcoholic patients. PMID:25009372

  13. [Study of genetic markers of duodenal ulcer].

    PubMed

    Tsimmerman, Ia S; Onosova, E A; Tsimmerman, I Ia

    1989-05-01

    The results of determination of various hereditary predisposition markers in peptic ulcer are given: in the population, in patients with duodenal ulcer and in their siblings (risk group). Of importance for revealing subjects with hereditary predisposition to duodenal ulcer are the clinico-genealogical analysis, determination of the blood group, especially in simultaneous determination of a "secretory status" ("status of non-secretion" of the ABH blood system agglutinogen in the saliva), increase in the mass of parietal cells and, to some extent, of the distinguishing features of dermatoglyphics (in combination with the above markers). Determination of taste sensitivity to phenylthiocarbamide is non-informative. PMID:2770215

  14. Cell Surface Markers in HTLV-1 Pathogenesis

    PubMed Central

    Kress, Andrea K.; Grassmann, Ralph; Fleckenstein, Bernhard

    2011-01-01

    The phenotype of HTLV-1-transformed CD4+ T lymphocytes largely depends on defined viral effector molecules such as the viral oncoprotein Tax. In this review, we exemplify the expression pattern of characteristic lineage markers, costimulatory receptors and ligands of the tumor necrosis factor superfamily, cytokine receptors, and adhesion molecules on HTLV-1-transformed cells. These molecules may provide survival signals for the transformed cells. Expression of characteristic surface markers might therefore contribute to persistence of HTLV-1-transformed lymphocytes and to the development of HTLV-1-associated disease. PMID:21994790

  15. Home care safety markers: a scoping review.

    PubMed

    Macdonald, Marilyn; Lang, Ariella; Storch, Jan; Stevenson, Lynn; Donaldson, Susan; Barber, Tanya; Iaboni, Kristine

    2013-01-01

    Safety in home care is a new research frontier, and one in which demand for services continues to rise. A scoping review of the home care literature on chronic obstructive pulmonary disease and congestive heart failure was thus completed to identify safety markers that could serve to develop our understanding of safety in this sector. Results generated seven safety markers: (a) Home alone; (b) A fixed agenda in a foreign language; (c) Strangers in the home; (d) The butcher, the baker, the candlestick maker; (e) Medication mania; (f) Out of pocket: The cost of caring at home; and (g) My health for yours: Declining caregiver health. PMID:23679662

  16. Analyzing geographic clustered response

    SciTech Connect

    Merrill, D.W.; Selvin, S.; Mohr, M.S.

    1991-08-01

    In the study of geographic disease clusters, an alternative to traditional methods based on rates is to analyze case locations on a transformed map in which population density is everywhere equal. Although the analyst's task is thereby simplified, the specification of the density equalizing map projection (DEMP) itself is not simple and continues to be the subject of considerable research. Here a new DEMP algorithm is described, which avoids some of the difficulties of earlier approaches. The new algorithm (a) avoids illegal overlapping of transformed polygons; (b) finds the unique solution that minimizes map distortion; (c) provides constant magnification over each map polygon; (d) defines a continuous transformation over the entire map domain; (e) defines an inverse transformation; (f) can accept optional constraints such as fixed boundaries; and (g) can use commercially supported minimization software. Work is continuing to improve computing efficiency and improve the algorithm. 21 refs., 15 figs., 2 tabs.

  17. Biological Cluster Mass Spectrometry

    PubMed Central

    Winograd, Nicholas; Garrison, Barbara J.

    2010-01-01

    This article reviews the new physics and new applications of secondary ion mass spectrometry using cluster ion probes. These probes, particularly C60, exhibit enhanced molecular desorption with improved sensitivity owing to the unique nature of the energy-deposition process. In addition, these projectiles are capable of eroding molecular solids while retaining the molecular specificity of mass spectrometry. When the beams are microfocused to a spot on the sample, bioimaging experiments in two and three dimensions are feasible. We describe emerging theoretical models that allow the energy-deposition process to be understood on an atomic and molecular basis. Moreover, experiments on model systems are described that allow protocols for imaging on biological materials to be implemented. Finally, we present recent applications of imaging to biological tissue and single cells to illustrate the future directions of this methodology. PMID:20055679

  18. Clustered engine study

    NASA Technical Reports Server (NTRS)

    Shepard, Kyle; Sager, Paul; Kusunoki, Sid; Porter, John; Campion, AL; Mouritzan, Gunnar; Glunt, George; Vegter, George; Koontz, Rob

    1993-01-01

    Several topics are presented in viewgraph form which together encompass the preliminary assessment of nuclear thermal rocket engine clustering. The study objectives, schedule, flow, and groundrules are covered. This is followed by the NASA groundrules mission and our interpretation of the associated operational scenario. The NASA reference vehicle is illustrated, then the four propulsion system options are examined. Each propulsion system's preliminary design, fluid systems, operating characteristics, thrust structure, dimensions, and mass properties are detailed as well as the associated key propulsion system/vehicle interfaces. A brief series of systems analysis is also covered including: thrust vector control requirements, engine out possibilities, propulsion system failure modes, surviving system requirements, and technology requirements. An assessment of vehicle/propulsion system impacts due to the lessons learned are presented.

  19. Ionized cluster beam deposition

    NASA Technical Reports Server (NTRS)

    Kirkpatrick, A. R.

    1983-01-01

    Ionized Cluster Beam (ICB) deposition, a new technique originated by Takagi of Kyoto University in Japan, offers a number of unique capabilities for thin film metallization as well as for deposition of active semiconductor materials. ICB allows average energy per deposited atom to be controlled and involves impact kinetics which result in high diffusion energies of atoms on the growth surface. To a greater degree than in other techniques, ICB involves quantitative process parameters which can be utilized to strongly control the characteristics of films being deposited. In the ICB deposition process, material to be deposited is vaporized into a vacuum chamber from a confinement crucible at high temperature. Crucible nozzle configuration and operating temperature are such that emerging vapor undergoes supercondensation following adiabatic expansion through the nozzle.

  20. Cross-Clustering: A Partial Clustering Algorithm with Automatic Estimation of the Number of Clusters

    PubMed Central

    Tellaroli, Paola; Bazzi, Marco; Donato, Michele; Brazzale, Alessandra R.; Drăghici, Sorin

    2016-01-01

    Four of the most common limitations of the many available clustering methods are: i) the lack of a proper strategy to deal with outliers; ii) the need for a good a priori estimate of the number of clusters to obtain reasonable results; iii) the lack of a method able to detect when partitioning of a specific data set is not appropriate; and iv) the dependence of the result on the initialization. Here we propose Cross-clustering (CC), a partial clustering algorithm that overcomes these four limitations by combining the principles of two well established hierarchical clustering algorithms: Ward’s minimum variance and Complete-linkage. We validated CC by comparing it with a number of existing clustering methods, including Ward’s and Complete-linkage. We show on both simulated and real datasets, that CC performs better than the other methods in terms of: the identification of the correct number of clusters, the identification of outliers, and the determination of real cluster memberships. We used CC to cluster samples in order to identify disease subtypes, and on gene profiles, in order to determine groups of genes with the same behavior. Results obtained on a non-biological dataset show that the method is general enough to be successfully used in such diverse applications. The algorithm has been implemented in the statistical language R and is freely available from the CRAN contributed packages repository. PMID:27015427

  1. De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery

    PubMed Central

    Lu, Xingrong; Zhu, Peng; Duan, Anqin; Tan, Zhengzhun; Huang, Jian; Li, Hui; Chen, Mingtan; Liang, Xianwei

    2016-01-01

    The Chinese swamp buffalo (Bubalis bubalis) is vital to the lives of small farmers and has tremendous economic importance. However, a lack of genomic information has hampered research on augmenting marker assisted breeding programs in this species. Thus, a high-throughput transcriptomic sequencing of B. bubalis was conducted to generate transcriptomic sequence dataset for gene discovery and molecular marker development. Illumina paired-end sequencing generated a total of 54,109,173 raw reads. After trimming, de novo assembly was performed, which yielded 86,017 unigenes, with an average length of 972.41 bp, an N50 of 1,505 bp, and an average GC content of 49.92%. A total of 62,337 unigenes were successfully annotated. Among the annotated unigenes, 27,025 (43.35%) and 23,232 (37.27%) unigenes showed significant similarity to known proteins in NCBI non-redundant protein and Swiss-Prot databases (E-value < 1.0E-5), respectively. Of these annotated unigenes, 14,439 and 15,813 unigenes were assigned to the Gene Ontology (GO) categories and EuKaryotic Ortholog Group (KOG) cluster, respectively. In addition, a total of 14,167 unigenes were assigned to 331 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, 17,401 simple sequence repeats (SSRs) were identified as potential molecular markers. One hundred and fifteen primer pairs were randomly selected for amplification to detect polymorphisms. The results revealed that 110 primer pairs (95.65%) yielded PCR amplicons and 69 primer pairs (60.00%) presented polymorphisms in 35 individual buffaloes. A phylogenetic analysis showed that the five swamp buffalo populations were clustered together, whereas two river buffalo breeds clustered separately. In the present study, the Illumina RNA-seq technology was utilized to perform transcriptome analysis and SSR marker discovery in the swamp buffalo without using a reference genome. Our findings will enrich the current SSR markers resources and help spearhead molecular

  2. Genetic Characterization of Turkish Snake Melon (Cucumis melo L. subsp. melo flexuosus Group) Accessions Revealed by SSR Markers.

    PubMed

    Solmaz, Ilknur; Kacar, Yildiz Aka; Simsek, Ozhan; Sari, Nebahat

    2016-08-01

    Snake melon is an important cucurbit crop especially in the Southeastern and the Mediterranean region of Turkey. It is consumed as fresh or pickled. The production is mainly done with the local landraces in the country. Turkey is one of the secondary diversification centers of melon and possesses valuable genetic resources which have different morphological characteristics in case of snake melon. Genetic diversity of snake melon genotypes collected from different regions of Turkey and reference genotypes obtained from World Melon Gene Bank in Avignon-France was examined using 13 simple sequence repeat (SSR) markers. A total of 69 alleles were detected, with an average of 5.31 alleles per locus. The polymorphism information content of SSR markers ranged from 0.19 to 0.57 (average 0.38). Based on cluster analysis, two major groups were defined. The first major group included only one accession (61), while the rest of all accessions grouped in the second major group and separated into different sub-clusters. Based on SSR markers, cluster analysis indicated that considerably high genetic variability exists among the examined accessions; however, Turkish snake melon accessions were grouped together with the reference snake melon accessions. PMID:27193591

  3. Development and characterization of microsatellite markers for Morus spp. and assessment of their transferability to other closely related species

    PubMed Central

    2013-01-01

    into distinct clusters. Conclusion We report a total of 188 genomic and genic SSR markers in Morus alba L. A large proportion of these markers (164) were polymorphic both among mulberry species and genotypes. A substantial number of these markers (149) were also transferable to other related species like Ficus, Fig and Jackfruit. The extent of polymorphism revealed and the ability to detect heterozygosity among the cross pollinated mulberry species and genotypes render these markers an invaluable genomic resource that can be utilized in assessing molecular diversity as well as in QTL mapping and subsequently mulberry crop improvement through MAS. PMID:24289047

  4. Potential Start Codon Targeted (SCoT) and Inter-retrotransposon Amplified Polymorphism (IRAP) Markers for Evaluation of Genetic Diversity and Conservation of Wild Pistacia Species Population.

    PubMed

    Sorkheh, Karim; Amirbakhtiar, Nazanin; Ercisli, Sezai

    2016-08-01

    Wild pistachio species is important species in forests regions Iran and provide protection wind and soil erosion. Even though cultivation and utilization of Pistacia are fully exploited, the evolutionary history of the Pistacia genus and the relationships among the species and accessions is still not well understood. Two molecular marker strategies, SCoT and IRAP markers were analyzed for assessment of 50 accessions of this species accumulated from diverse geographical areas of Iran. A thorough of 115 bands were amplified using eight IRAP primers, of which 104 (90.4 %) have been polymorphic, and 246 polymorphic bands (68.7 %) had been located in 358 bands amplified by way of forty-four SCoT primers. Average PIC for IRAP and SCoT markers became 0.32 and 0.48, respectively. This is exposed that SCoT markers have been extra informative than IRAP for the assessment of variety among pistachio accessions. Primarily based on the two extraordinary molecular markers, cluster evaluation revealed that the 50 accessions taken for the evaluation may be divided into three distinct clusters. Those results recommend that the performance of SCoT and IRAP markers was highly the equal in fingerprinting of accessions. The results affirmed a low genetic differentiation among populations, indicating the opportunity of gene drift most of the studied populations. These findings might render striking information in breeding management strategies for genetic conservation and cultivar improvement. PMID:27056191

  5. Information Clustering Based on Fuzzy Multisets.

    ERIC Educational Resources Information Center

    Miyamoto, Sadaaki

    2003-01-01

    Proposes a fuzzy multiset model for information clustering with application to information retrieval on the World Wide Web. Highlights include search engines; term clustering; document clustering; algorithms for calculating cluster centers; theoretical properties concerning clustering algorithms; and examples to show how the algorithms work.…

  6. Antibody-gold cluster conjugates

    DOEpatents

    Hainfeld, J.F.

    1988-06-28

    Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be about 5.0 nm. Methods and reagents are disclosed in which antibodies or Fab' fragments thereof are covalently bound to a stable cluster of gold atoms. 2 figs.

  7. Two generalizations of Kohonen clustering

    NASA Technical Reports Server (NTRS)

    Bezdek, James C.; Pal, Nikhil R.; Tsao, Eric C. K.

    1993-01-01

    The relationship between the sequential hard c-means (SHCM), learning vector quantization (LVQ), and fuzzy c-means (FCM) clustering algorithms is discussed. LVQ and SHCM suffer from several major problems. For example, they depend heavily on initialization. If the initial values of the cluster centers are outside the convex hull of the input data, such algorithms, even if they terminate, may not produce meaningful results in terms of prototypes for cluster representation. This is due in part to the fact that they update only the winning prototype for every input vector. The impact and interaction of these two families with Kohonen's self-organizing feature mapping (SOFM), which is not a clustering method, but which often leads ideas to clustering algorithms is discussed. Then two generalizations of LVQ that are explicitly designed as clustering algorithms are presented; these algorithms are referred to as generalized LVQ = GLVQ; and fuzzy LVQ = FLVQ. Learning rules are derived to optimize an objective function whose goal is to produce 'good clusters'. GLVQ/FLVQ (may) update every node in the clustering net for each input vector. Neither GLVQ nor FLVQ depends upon a choice for the update neighborhood or learning rate distribution - these are taken care of automatically. Segmentation of a gray tone image is used as a typical application of these algorithms to illustrate the performance of GLVQ/FLVQ.

  8. Active matter clusters at interfaces

    NASA Astrophysics Data System (ADS)

    Copenhagen, Katherine; Gopinathan, Ajay

    Collective and directed motility or swarming is an emergent phenomenon displayed by many self-organized assemblies of active biological matter such as clusters of embryonic cells during tissue development and flocks of birds. Such clusters typically encounter very heterogeneous environments. What happens when a cluster encounters an interface between two different environments has implications for its function and fate. Here we study this problem by using a mathematical model of a cluster that treats it as a single cohesive unit whose movement depends on the nature of the local environment. We find that low speed clusters which exert forces but no active torques, encountering an interface with a moderate difference in properties can lead to refraction or even total internal reflection of the cluster. For large speeds and clusters with active torques, they show more complex behaviors crossing the interface multiple times, becoming trapped at the interface and deviating from the predictable refraction and reflection of the low velocity clusters. Our results show a wide range of behaviors that occur when collectively moving active biological matter moves across interfaces and these insights can be used to control motion by patterning environments.

  9. Cluster highlights in magnetospheric physics

    NASA Astrophysics Data System (ADS)

    Escoubet, C. Philippe; Laakso, Harri; Taylor, Matthew; Goldstein, Mevlyn; Hapgood, Mike; Masson, Arnaud; Volpp, Juergen; Sieg, Detlef

    The Cluster mission has been operated successfully for 14 years. As the first science mission comprising four identical spacecraft, Cluster has faced many challenges during its lifetime: its long selection process together with SOHO, the failure of the first Ariane V launch, its fast rebuilt, and the launch on two Soyuz rockets in 2000. The separation of the Cluster spacecraft was changed more than 25 times from a few kilometers up to 36000 km to address the various scientific objectives; the smallest distance achieved between two Cluster spacecraft was 4 km, about 50 times smaller than planned at the beginning of the mission. The main goal of the Cluster mission is to study in three dimensions small-scale plasma structures in key plasma regions of Earth’s geospace environment: solar wind and bow shock, magnetopause, polar cusps, magnetotail, plasmasphere and auroral zone. We will present science highlights obtained such as ripples on the bow shock, 3D current measurements and Kelvin-Helmholtz waves at the magnetopause, bifurcated current sheet in the magnetotail, and first measurement of the electron pressure tensor near a site of magnetic reconnection. In addition, we highlight Cluster results on understanding the impact of Coronal Mass Ejections (CME) on the Earth's environment. We will also present the distribution of data through the Cluster Science Data System (CSDS), and the Cluster Archive. Those systems were implemented to provide, for the first time for a plasma physics mission, a permanent and public archive of all the high resolution data from all instruments.

  10. Multidimensional model of cluster radioactivity

    NASA Astrophysics Data System (ADS)

    Denisov, V. Yu.

    2013-10-01

    The cluster decays 228Th→208Pb+20O, 232U→208Pb+24Ne, 236Pu→208Pb+28Mg, and 242Cm→208Pb+34Si are considered in the framework of the multidimensional cluster-preformation model. The macroscopic potential-energy surface related to the interaction between the cluster and the residue nucleus is evaluated in the framework of the nonlocal ℏ4 extended Thomas-Fermi approach with Skyrme and Coulomb forces. The shell correction to the macroscopic potential energy is also taken into account. The dynamical surface deformations of both the cluster and the residue nucleus are taken into consideration at the barrier penetration path. The heights of saddle points related to deformed nuclear shapes are lower than the barrier height between the spherical cluster and residue nuclei; therefore the dynamical deformations of nuclei increase the barrier penetrability and reduce the half-life of cluster decay. The shell-correction contribution into the potential energy between cluster and residue nucleus is important for both the potential landscape and the half-life evaluation. The experimental values of cluster-decay half-lives are well reproduced in the model.

  11. Destruction of giant cluster-like vesicles by an ultrasonically activated device

    NASA Astrophysics Data System (ADS)

    Yahagi, Ryosuke; Yoshida, Kenji; Zhang, Yiting; Ebata, Masahiko; Toyota, Taro; Yamaguchi, Tadashi; Hayashi, Hideki

    2016-07-01

    In this paper, we propose a technically simple method of destroying a tissue marker composed of giant cluster-like vesicles (GCVs) to facilitate laparoscopic surgeries; the method releases various biological tracers contained in GCVs. An ultrasonically activated device (USAD) emitting 55.5 kHz ultrasound was employed for this purpose. Optical microscopy and fluorospectrophotometry revealed the destruction of GCVs after ultrasound irradiation when the blade tip was set 1.0 mm or closer to, but not directly in contact with, a GCV-containing cell. This means that USAD could be safely used for destroying this GCV tissue marker in clinical settings.

  12. Theoretical Studies on Cluster Compounds

    NASA Astrophysics Data System (ADS)

    Lin, Zhenyang

    Available from UMI in association with The British Library. Requires signed TDF. The Thesis describes some theoretical studies on ligated and bare clusters. Chapter 1 gives a review of the two theoretical models, Tensor Surface Harmonic Theory (TSH) and Jellium Model, accounting for the electronic structures of ligated and bare clusters. The Polyhedral Skeletal Electron Pair Theory (PSEPT), which correlates the structures and electron counts (total number of valence electrons) of main group and transition metal ligated clusters, is briefly described. A structural jellium model is developed in Chapter 2 which accounts for the electronic structures of clusters using a crystal-field perturbation. The zero-order potential we derive is of central-field form, depends on the geometry of the cluster, and has a well-defined relationship to the full nuclear-electron potential. Qualitative arguments suggest that this potential produces different energy level orderings for clusters with a nucleus with large positive charge at the centre of the cluster. Analysis of the effects of the non-spherical perturbation on the spherical jellium shell structures leads to the conclusion that for a cluster with a closed shell electronic structure a high symmetry arrangement which is approximately or precisely close packed will be preferred. It also provides a basis for rationalising those structures of clusters with incomplete shell electronic configurations. In Chapter 3, the geometric conclusions derived in the structural jellium model are developed in more detail. The group theoretical consequences of the Tensor Surface Harmonic Theory are developed in Chapter 4 for (ML_2) _{rm n}, (ML_4) _{rm n} and (ML_5 ) _{rm n} clusters where either the xz and yz or x^2 -y^2 and xy components to L_sp{rm d}{pi } and L_sp{rm d} {delta} do not contribute equally to the bonding. The closed shell requirements for such clusters are defined and the orbital symmetry constraints pertaining to the

  13. Cluster beam analysis via photoionization

    SciTech Connect

    Grover, J.R. ); Herron, W.J.; Coolbaugh, M.T.; Peifer, W.R.; Garvey, J.F. )

    1991-08-22

    A photoionization method for quantitatively analyzing the neutral products of free jet expansions is described. The basic principle is to measure the yield of an ion characterization of each component cluster at a photon energy just below that at which production of the same ion from larger clusters can be detected. Since there is then no problem with fragmentation, the beam density of each neutral cluster can be measured in the presence of larger clusters. Although these measurements must be done in the test ions' onset regions where their yields are often quite small, the technique is made highly practicable by the large intensities of widely tunable vacuum-ultraviolet synchrotron light now available at electron storage rings. As an example, the method is applied to the analysis of cluster beams collimated from the free jet expansion of a 200:1 ammonia-chlorobenzene mixture.

  14. Single System Image Cluster Management

    2004-02-13

    Cluster computing has quickly proven itself to be a capable workhorse for a wide variety of production computing tasks; however, setting up and maintaining a cluster still requires significantly more effort than administrating just a single machine. As computing hardware descreases in price and cluster sizes grow, it is becoming increasingly important to manage clusters cleverly so that a system administration effort can "scale" as well. To ease the task of mananging many machines, administratorsmore » often deploy an environment that is homogeneous across all nodes of a cluster, and maintain a snapshot of the filesystem as a 'master image'. However due to operational, behavioral, and physical constraints, many nodes often require numerous deviations from the master image in order to operate as desired.« less

  15. Decaying neutrinos in galaxy clusters

    NASA Technical Reports Server (NTRS)

    Melott, Adrian L.; Splinter, Randall J.; Persic, Massimo; Salucci, Paolo

    1993-01-01

    The DM profile in clusters of galaxies was studied and simulated using the Harrison-Zel'dovich spectrum of density fluctuations, and an amplitude previously derived from numerical simulations and in agreement with microwave background fluctuations. Neutrino DM densities, with this amplitude normalization cluster, are comparable to observed cluster DM values. It was concluded that given this normalization, the cluster DM should be al least largely composed of neutrinos. The constraint of Davidson et al., who argued that the failure to detect uv photons from the dark matter (DM) in cluster A665 excludes the decaying neutrino hypothesis, could be somewhat weakened by the presence of baryonic DM; but it cannot be eliminated given our assumptions.

  16. SACS: Spitzer Archival Cluster Survey

    NASA Astrophysics Data System (ADS)

    Stern, Daniel

    Emerging from the cosmic web, galaxy clusters are the most massive gravitationally bound structures in the universe. Thought to have begun their assembly at z > 2, clusters provide insights into the growth of large-scale structure as well as the physics that drives galaxy evolution. Understanding how and when the most massive galaxies assemble their stellar mass, stop forming stars, and acquire their observed morphologies in these environments remain outstanding questions. The redshift range 1.3 < z < 2 is a key epoch in this respect: elliptical galaxies start to become the dominant population in cluster cores, and star formation in spiral galaxies is being quenched. Until recently, however, this redshift range was essentially unreachable with available instrumentation, with clusters at these redshifts exceedingly challenging to identify from either ground-based optical/nearinfrared imaging or from X-ray surveys. Mid-infrared (MIR) imaging with the IRAC camera on board of the Spitzer Space Telescope has changed the landscape. High-redshift clusters are easily identified in the MIR due to a combination of the unique colors of distant galaxies and a negative k-correction in the 3-5 μm range which makes such galaxies bright. Even 90-sec observations with Spitzer/IRAC, a depth which essentially all extragalactic observations in the archive achieve, is sufficient to robustly detect overdensities of L* galaxies out to z~2. Here we request funding to embark on a ambitious scientific program, the “SACS: Spitzer Archival Cluster Survey”, a comprehensive search for the most distant galaxy clusters in all Spitzer/IRAC extragalactic pointings available in the archive. With the SACS we aim to discover ~2000 of 1.3 < z < 2.5 clusters, thus provide the ultimate catalog for high-redshift MIR selected clusters: a lasting legacy for Spitzer. The study we propose will increase by more than a factor of 10 the number of high-redshift clusters discovered by all previous surveys

  17. Protonated water clusters in TPC's

    NASA Astrophysics Data System (ADS)

    Kaya, Yunus; Kalkan, Yalçın; Veenhof, Rob

    2016-07-01

    Water vapour is added to the ALICE TPC gas to enhance its stability. These polar molecules create large protonated water clusters around a H+ core. In this context, the reactions H3O+(H2O)n-1 +H2 O →H3O+(H2O)n (n=1-9) were studied in the gas phase. Structures for these clusters are suggested and the most stable structures for each cluster size are shown. The thermodynamic parameters Δ Hn-1,n0,Δ Gn-1,n0,Δ Sn-1,n0 and equilibrium constants Kn-1,n for the reaction were calculated to determine the size of the water clusters. The results are close to experimental data found in the literature. Protonated water clusters at stp have a size of 6-9 which corresponds to a mass of 127.1 - 181.2 g / mole.

  18. Versatile cluster based photoelectron spectrometer

    SciTech Connect

    Knappenberger, K. L. Jr.; Jones, C. E. Jr.; Sobhy, M. A.; Castleman, A. W. Jr.

    2006-12-15

    A recently constructed cluster based photoelectron spectrometer is described. This instrumentation is unique in that it enables the kinetic energy analysis of electrons ejected from both anions and neutral clusters. This capability permits the investigation of discrete electronic levels in all charge states (anionic, neutral, and cationic). A laser vaporization plasma reactor cluster source affixed with a sublimation cell is employed to produce a variety of metal clusters, and the resulting cluster distributions are analyzed with time-of-flight mass spectrometry. The corresponding electronic structure is analyzed with a 'magnetic bottle' photoelectron spectrometer. Examples of instrument performance operating in both anion photodetachment and neutral multiphoton ionization (MPI) modes are provided. In the case of neutral MPI, the corresponding product distribution is collected with a Wiley-McLaren [Rev. Sci. Instrum. 26, 1150 (1955)] mass spectrometer mounted perpendicular to the magnetic bottle photoelectron spectrometer.

  19. Seven poor clusters of galaxies

    NASA Technical Reports Server (NTRS)

    Beers, T. C.; Geller, M. J.; Huchra, J. P.; Latham, D. W.; Davis, R. J.

    1984-01-01

    The measurement of 83 new redshifts from galaxies in the region of seven of the poor clusters of galaxies identified by Morgan et al (1975) and Albert et al (1977) has been followed by an estimation of cluster masses through the application of both the virial theorem and the projected mas method. For each system, these two estimates are consistent. For the two clusters with highest X-ray luminosities, the line-of-sight velocity dispersions are about 700 km/sec, while for the five other clusters, the dispersions are of the order of less than about 370 km/sec. The D or cD galaxy in each poor cluster is at the kinematic center of each system.

  20. Transcriptomic markers meet the real world: finding diagnostic signatures of corticosteroid treatment in commercial beef samples

    PubMed Central

    2012-01-01

    Background The use of growth-promoters in beef cattle, despite the EU ban, remains a frequent practice. The use of transcriptomic markers has already proposed to identify indirect evidence of anabolic hormone treatment. So far, such approach has been tested in experimentally treated animals. Here, for the first time commercial samples were analyzed. Results Quantitative determination of Dexamethasone (DEX) residues in the urine collected at the slaughterhouse was performed by Liquid Chromatography-Mass Spectrometry (LC-MS). DNA-microarray technology was used to obtain transcriptomic profiles of skeletal muscle in commercial samples and negative controls. LC-MS confirmed the presence of low level of DEX residues in the urine of the commercial samples suspect for histological classification. Principal Component Analysis (PCA) on microarray data identified two clusters of samples. One cluster included negative controls and a subset of commercial samples, while a second cluster included part of the specimens collected at the slaughterhouse together with positives for corticosteroid treatment based on thymus histology and LC-MS. Functional analysis of the differentially expressed genes (3961) between the two groups provided further evidence that animals clustering with positive samples might have been treated with corticosteroids. These suspect samples could be reliably classified with a specific classification tool (Prediction Analysis of Microarray) using just two genes. Conclusions Despite broad variation observed in gene expression profiles, the present study showed that DNA-microarrays can be used to find transcriptomic signatures of putative anabolic treatments and that gene expression markers could represent a useful screening tool. PMID:23110699

  1. Development of microsatellite markers by transcriptome sequencing in two species of Amorphophallus (Araceae)

    PubMed Central

    2013-01-01

    Background Amorphophallus is a genus of perennial plants widely distributed in the tropics or subtropics of West Africa and South Asia. Its corms contain a high level of water-soluble glucomannan; therefore, it has long been used as a medicinal herb and food source. Genetic studies of Amorphophallus have been hindered by a lack of genetic markers. A large number of molecular markers are required for genetic diversity study and improving disease resistance in Amorphophallus. Here, we report large scale of transcriptome sequencing of two species: Amorphophallus konjac and Amorphophallus bulbifer using deep sequencing technology, and microsatellite (SSR) markers were identified based on these transcriptome sequences. Results cDNAs of A. konjac and A. bulbifer were sequenced using Illumina HiSeq™ 2000 sequencing technology. A total of 135,822 non-redundant unigenes were assembled from about 9.66 gigabases, and 19,596 SSRs were identified in 16,027 non-redundant unigenes. Di-nucleotide SSRs were the most abundant motif (61.6%), followed by tri- (30.3%), tetra- (5.6%), penta- (1.5%), and hexa-nucleotides (1%) repeats. The top di- and tri-nucleotide repeat motifs included AG/CT (45.2%) and AGG/CCT (7.1%), respectively. A total of 10,754 primer pairs were designed for marker development. Of these, 320 primers were synthesized and used for validation of amplification and assessment of polymorphisms in 25 individual plants. The total of 275 primer pairs yielded PCR amplification products, of which 205 were polymorphic. The number of alleles ranged from 2 to 14 and the polymorphism information content valued ranged from 0.10 to 0.90. Genetic diversity analysis was done using 177 highly polymorphic SSR markers. A phenogram based on Jaccard’s similarity coefficients was constructed, which showed a distinct cluster of 25 Amorphophallus individuals. Conclusion A total of 10,754 SSR markers have been identified in Amorphophallus using transcriptome sequencing. One hundred and

  2. Evaluation of Pakistan wheat germplasms for stripe rust resistance using molecular markers.

    PubMed

    Sobia, Tabassum; Muhammad, Ashraf; Chen, XianMing

    2010-09-01

    sequence repeat (SSR) and sequence tagged site (STS) markers were used to determine the presence and absence of some important stripe rust resistance genes, such as Yr5, Yr8, Yr9, Yr15 and Yr18. Of the 60 cultivars analyzed, 17% of cultivars showed a RGAP marker band for Yr9 and 12% of cultivars exhibited the Yr18 marker band. No marker band was detected for Yr5, Yr8 and Yr15, indicating a likely absence of these genes in the tested Pakistan wheat cultivars. Cluster analysis based on molecular and stripe rust reaction data is useful in identifying considerable genetic diversity among Pakistan wheat cultivars. The resistant germplasms identified with 22 RGAP markers and from the resistance evaluations should be useful in developing new wheat cultivars with stripe rust resistance. PMID:21104373

  3. Comprehension of Discourse Markers and Reading Comprehension

    ERIC Educational Resources Information Center

    Khatib, Mohamad

    2011-01-01

    According to many research findings, the presence of discourse markers (DMs) enhances readers' comprehension of the texts they read. However, there is a paucity of research on the relationship between knowledge of DMs and reading comprehension (RC) and the present study explores the relationship between them. Knowledge of DMs is measured through…

  4. Associations between STR autosomal markers and longevity.

    PubMed

    Bediaga, N G; Aznar, J M; Elcoroaristizabal, X; Albóniga, O; Gómez-Busto, F; Artaza Artabe, I; Rocandio, Ana; de Pancorbo, M M

    2015-10-01

    Life span is a complex and multifactorial trait, which is shaped by genetic, epigenetic, environmental, and stochastic factors. The possibility that highly hypervariable short tandem repeats (STRs) associated with longevity has been largely explored by comparing the genotypic pools of long lived and younger individuals, but results so far have been contradictory. In view of these contradictory findings, the present study aims to investigate whether HUMTHO1 and HUMCSF1PO STRs, previously associated with longevity, exert a role as a modulator of life expectancy, as well as to assess the extent to which other autosomal STR markers are associated with human longevity in population from northern Spain. To that end, 21 autosomal microsatellite markers have been studied in 304 nonagenarian individuals (more than 90 years old) and 516 younger controls of European descent. Our results do not confirm the association found in previous studies between longevity and THO1 and CSF1PO loci. However, significant association between longevity and autosomal STR markers D12S391, D22S1045, and DS441 was observed. Even more, when we compared allelic frequency distribution of the 21 STR markers between cases and controls, we found that 6 out of the 21 STRs studied showed different allelic frequencies, thus suggesting that the genomic portrait of the human longevity is far complex and probably shaped by a high number of genomic loci. PMID:26335621

  5. Structuring Conversation: Discourse Markers in Cervantes's "Entremeses"

    ERIC Educational Resources Information Center

    King, Jeremy

    2011-01-01

    Due to the recent shift in the linguistic pragmatics literature from the analysis of isolated speech acts to the focus on phenomena which affect the global meaning of a message, discourse markers (DMs) have become a frequent research topic. Despite their popularity, the evolution and development of these forms is often neglected in investigations…

  6. Functions of Discourse Markers in Japanese.

    ERIC Educational Resources Information Center

    Fujita, Yasuko

    2001-01-01

    Through an examination of the discourse markers "ano" and "sono" in Japanese (commonly characterized as demonstrative adjectives but which cannot be used interchangeably in a context), this paper explores how these linguistic devices function in conversation found in Japanese writings. The focus of this analysis is the mental and social functions…

  7. A Pilot Study of Hungarian Discourse Markers

    ERIC Educational Resources Information Center

    Der, Csilla Ilona; Marko, Alexandra

    2010-01-01

    This study is the first attempt at detecting formal and positional characteristics of single-word simple discourse markers in a spontaneous speech sample of Hungarian. In the first part of the research, theoretical claims made in the relevant literature were tested. The data did not confirm or only partially confirmed the claims that Hungarian…

  8. Discourse Markers as Indicators of Register.

    ERIC Educational Resources Information Center

    Brizuela, Maquela; Andersen, Elaine; Stallings, Lynne

    1999-01-01

    Explores the ability of children to use discourse markers (DMs) as indicators of register, examining the distribution of various DMs in the role-play speech of Spanish-dominant bilingual elementary students as they played with puppets representing several characters with different social relationships. Children used DMs to specifically mark…

  9. Quantitative PCR marker genes for endometrial adenocarcinoma.

    PubMed

    Kölbl, Alexandra C; Victor, Lisa-Marie; Birk, Amelie E; Jeschke, Udo; Andergassen, Ulrich

    2016-09-01

    Endometrial adenocarcinoma is a common malignancy in women worldwide, with formation of remote metastasis occurring following oncological treatment. Circulating tumor cells (CTCs) are regarded to be the origin of haematogenous metastasis formation. The present study aimed to identify suitable marker genes using a quantitative polymerase chain reaction (qPCR) approach to detect CTCs from blood samples of patients with endometrial carcinoma. Therefore, RNA was isolated from endometrial adenocarcinoma cell lines and from healthy endometrial tissue and reverse transcribed to cDNA, which was then used in qPCR on a number of marker genes. Cytokeratin 19 and claudin 4 were identified as suitable marker genes for CTCs in endometrial adenocarcinoma, due to their high expression in the majority of the cell lines investigated. The expression values of the genes examined varied widely between the different cell lines, which is similar to the variation in the patient samples. Therefore, the necessity for a set of genes for CTC detection and not one single marker gene is demonstrated. qPCR is a fast, cost‑efficient and easy to perform technique, which may be used in the detection of CTCs. Investigation of the occurrence of CTCs in cancer patients would aid in the prevention of metastasis and thereby refine treatment. PMID:27431566

  10. Structural assessment of backcrossing using microsatellite markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Backcrossing, coupled with marker or gene assisted selection, can be used to introgress a specific gene or chromosomal region from one population into another. The objective of this study was to assess the genomic structure of cattle produced by backcrossing for loci that are unlinked to a locus tha...

  11. Linguistic Markers of Inference Generation While Reading

    ERIC Educational Resources Information Center

    Clinton, Virginia; Carlson, Sarah E.; Seipel, Ben

    2016-01-01

    Words can be informative linguistic markers of psychological constructs. The purpose of this study is to examine associations between word use and the process of making meaningful connections to a text while reading (i.e., inference generation). To achieve this purpose, think-aloud data from third-fifth grade students (N = 218) reading narrative…

  12. New softwares for automated microsatellite marker development.

    PubMed

    Martins, Wellington; de Sousa, Daniel; Proite, Karina; Guimarães, Patrícia; Moretzsohn, Marcio; Bertioli, David

    2006-01-01

    Microsatellites are repeated small sequence motifs that are highly polymorphic and abundant in the genomes of eukaryotes. Often they are the molecular markers of choice. To aid the development of microsatellite markers we have developed a module that integrates a program for the detection of microsatellites (TROLL), with the sequence assembly and analysis software, the Staden Package. The module has easily adjustable parameters for microsatellite lengths and base pair quality control. Starting with large datasets of unassembled sequence data in the form of chromatograms and/or text data, it enables the creation of a compact database consisting of the processed and assembled microsatellite containing sequences. For the final phase of primer design, we developed a program that accepts the multi-sequence 'experiment file' format as input and produces a list of primer pairs for amplification of microsatellite markers. The program can take into account the quality values of consensus bases, improving success rate of primer pairs in PCR. The software is freely available and simple to install in both Windows and Unix-based operating systems. Here we demonstrate the software by developing primer pairs for 427 new candidate markers for peanut. PMID:16493138

  13. A visible dominant marker for insect transgenesis.

    PubMed

    Osanai-Futahashi, Mizuko; Ohde, Takahiro; Hirata, Junya; Uchino, Keiro; Futahashi, Ryo; Tamura, Toshiki; Niimi, Teruyuki; Sezutsu, Hideki

    2012-01-01

    Transgenesis of most insects currently relies on fluorescence markers. Here we establish a transformation marker system causing phenotypes visible to the naked eye due to changes in the color of melanin pigments, which are widespread in animals. Ubiquitous overexpression of arylalkylamine-N-acetyl transferase in the silkworm, Bombyx mori, changes the color of newly hatched first-instar larvae from black to a distinctive light brown color, and can be used as a molecular marker by directly connecting to baculovirus immediate early 1 gene promoter. Suppression of black pigmentation by Bm-arylalkylamine-N-acetyl transferase can be observed throughout the larval stages and in adult animals. Alternatively, overexpression in another gene, B. mori β-alanyl-dopamine synthetase (Bm-ebony), changes the larval body color of older instars, although first-instar larvae had normal dark coloration. We further show that ectopic Bm-arylalkylamine-N-acetyl transferase expression lightens coloration in ladybird beetle Harmonia axyridis and fruit fly Drosophila melanogaster, highlighting the potential usefulness of this marker for transgenesis in diverse insect taxa. PMID:23250425

  14. Multiplexed microsatellite markers for seven Metarhizium species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cross-species transferability of 41 previously published simple sequence repeat (SSR) markers was assessed for 11 species of the entomopathogenic fungus Metarhizium. A collection of 65 Metarhizium isolates including all 54 used in a recent phylogenetic revision of the genus were characterized. Betwe...

  15. Discourse Markers in Chinese Conversational Narrative

    ERIC Educational Resources Information Center

    Xiao, Yang

    2010-01-01

    This study examines the indexicality of discourse markers (DMs) in Chinese conversational narrative. Drawing upon theoretical and methodological principles related to narrative dimensions (Ochs & Capps, 2001), narrative desires (Ochs, 1997, 2004), and narrative positioning (Bamberg, 1997), this work proposes an integrated analytical framework for…

  16. Considerations For Optimizing Microbiome Analysis Using a Marker Gene.

    PubMed

    de la Cuesta-Zuluaga, Jacobo; Escobar, Juan S

    2016-01-01

    Next-generation sequencing technologies have found a widespread use in the study of host-microbe interactions due to the increase in their throughput and their ever-decreasing costs. The analysis of human-associated microbial communities using a marker gene, particularly the 16S rRNA, has been greatly benefited from these technologies - the human gut microbiome research being a remarkable example of such analysis that has greatly expanded our understanding of microbe-mediated human health and disease, metabolism, and food absorption. 16S studies go through a series of in vitro and in silico steps that can greatly influence their outcomes. However, the lack of a standardized workflow has led to uncertainties regarding the transparency and reproducibility of gut microbiome studies. We, here, discuss the most common challenges in the archetypical 16S rRNA workflow, including the extraction of total DNA, its use as template in PCR with primers that amplify specific hypervariable regions of the gene, amplicon sequencing, the denoising and removal of low-quality reads, the detection and removal of chimeric sequences, the clustering of high-quality sequences into operational taxonomic units, and their taxonomic classification. We recommend the essential technical information that should be conveyed in publications for reproducibility of results and encourage non-experts to include procedures and available tools that mitigate most of the problems encountered in microbiome analysis. PMID:27551678

  17. Considerations For Optimizing Microbiome Analysis Using a Marker Gene

    PubMed Central

    de la Cuesta-Zuluaga, Jacobo; Escobar, Juan S.

    2016-01-01

    Next-generation sequencing technologies have found a widespread use in the study of host–microbe interactions due to the increase in their throughput and their ever-decreasing costs. The analysis of human-associated microbial communities using a marker gene, particularly the 16S rRNA, has been greatly benefited from these technologies – the human gut microbiome research being a remarkable example of such analysis that has greatly expanded our understanding of microbe-mediated human health and disease, metabolism, and food absorption. 16S studies go through a series of in vitro and in silico steps that can greatly influence their outcomes. However, the lack of a standardized workflow has led to uncertainties regarding the transparency and reproducibility of gut microbiome studies. We, here, discuss the most common challenges in the archetypical 16S rRNA workflow, including the extraction of total DNA, its use as template in PCR with primers that amplify specific hypervariable regions of the gene, amplicon sequencing, the denoising and removal of low-quality reads, the detection and removal of chimeric sequences, the clustering of high-quality sequences into operational taxonomic units, and their taxonomic classification. We recommend the essential technical information that should be conveyed in publications for reproducibility of results and encourage non-experts to include procedures and available tools that mitigate most of the problems encountered in microbiome analysis. PMID:27551678

  18. Mapping the chromosome 16 cadherin gene cluster to a minimal deleted region in ductal breast cancer.

    PubMed

    Chalmers, I J; Aubele, M; Hartmann, E; Braungart, E; Werner, M; Höfler, H; Atkinson, M J

    2001-04-01

    The cadherin family of cell adhesion molecules has been implicated in tumor metastasis and progression. Eight family members have been mapped to the long arm of chromosome 16. Using radiation hybrid mapping, we have located six of these genes within a cluster at 16q21-q22.1. In invasive lobular carcinoma of the breast frequent LOH and accompanying mutation affect the CDH1 gene, which is a member of this chromosome 16 gene cluster. CDH1 LOH also occurs in invasive ductal carcinoma, but in the absence of gene mutation. The proximity of other cadherin genes to 16q22.1 suggests that they may be affected by LOH in invasive ductal carcinomas. Using the mapping data, microsatellite markers were selected which span regions of chromosome 16 containing the cadherin genes. In breast cancer tissues, a high rate of allelic loss was found over the gene cluster region, with CDH1 being the most frequently lost marker. In invasive ductal carcinoma a minimal deleted region was identified within part of the chromosome 16 cadherin gene cluster. This provides strong evidence for the existence of a second 16q22 suppressor gene locus within the cadherin cluster. PMID:11343777

  19. Clusterization and quadrupole deformation in nuclei

    SciTech Connect

    Cseh, J.; Algora, A.; Antonenko, N. V.; Jolos, R. V.; Scheid, W.; Darai, J.; Hess, P. O.

    2006-04-26

    We study the interrelation of the clusterization and quadrupole deformation of atomic nuclei, by applying cluster models. Both the energetic stability and the exclusion principle is investigated. Special attention is paid to the relative orientations of deformed clusters.

  20. Microsatellite markers reveal population structure and low gene flow among collections of Bactrocera cucurbitae (Diptera: Tephritidae) in Asia.

    PubMed

    Wu, Yi; Li, Yunlong; Ruiz-Arce, Raul; McPheron, Bruce A; Wu, Jiajiao; Li, Zhihong

    2011-06-01

    The melon fruit fly, Bactrocera cucurbitae (Coquillett) (Diptera: Tephritidae), is widespread agricultural pest, and it is known to have the potential to establish invasive populations in various tropical and subtropical areas. Despite the economic risk associated with a putative stable presence of this fly, the population genetics of this pest have remained relatively unexplored in Asia, the main area for distribution of this pest. The goals for this study were to employ nuclear markers to examine geographic collections for population genetic structure and quantify the extent of gene flow within these Southeast Asian and Chinese populations. To achieve these goals, we used 12 polymorphic microsatellite markers. A low level of genetic diversity was found among collections from China and higher levels were seen in Southeast Asia collections. Three genetically distinct groups, Southeast Asia, southwest China, and southeast China, were recovered by Bayesian model-based clustering methods, the phylogenetic reconstruction and the principal coordinate analysis. The Mantel test clearly shows geographical distance contributed in the genetic structuring of B. cucurbitae's populations. No recent bottlenecks for any of the populations examined. The results of clustering, migration analyses, and Mantel test, strongly suggest that the regional structure observed may be due to geographical factors such as mountains, rivers, and islands. We found a high rate of migration in some sites from the southwest China region (cluster 1) and the southeast China region (cluster 2), suggesting that China-Guangdong-Guangzhou (GZ) may be the center of melon fruit fly in the southeast China region. PMID:21735930

  1. Mesenchymal progenitor cell markers in human articular cartilage: normal distribution and changes in osteoarthritis

    PubMed Central

    Grogan, Shawn P; Miyaki, Shigeru; Asahara, Hiroshi; D'Lima, Darryl D; Lotz, Martin K

    2009-01-01

    Introduction Recent findings suggest that articular cartilage contains mesenchymal progenitor cells. The aim of this study was to examine the distribution of stem cell markers (Notch-1, Stro-1 and VCAM-1) and of molecules that modulate progenitor differentiation (Notch-1 and Sox9) in normal adult human articular cartilage and in osteoarthritis (OA) cartilage. Methods Expression of the markers was analyzed by immunohistochemistry (IHC) and flow cytometry. Hoechst 33342 dye was used to identify and sort the cartilage side population (SP). Multilineage differentiation assays including chondrogenesis, osteogenesis and adipogenesis were performed on SP and non-SP (NSP) cells. Results A surprisingly high number (>45%) of cells were positive for Notch-1, Stro-1 and VCAM-1 throughout normal cartilage. Expression of these markers was higher in the superficial zone (SZ) of normal cartilage as compared to the middle zone (MZ) and deep zone (DZ). Non-fibrillated OA cartilage SZ showed reduced Notch-1 and Sox9 staining frequency, while Notch-1, Stro-1 and VCAM-1 positive cells were increased in the MZ. Most cells in OA clusters were positive for each molecule tested. The frequency of SP cells in cartilage was 0.14 ± 0.05% and no difference was found between normal and OA. SP cells displayed chondrogenic and osteogenic but not adipogenic differentiation potential. Conclusions These results show a surprisingly high number of cells that express putative progenitor cell markers in human cartilage. In contrast, the percentage of SP cells is much lower and within the range of expected stem cell frequency. Thus, markers such as Notch-1, Stro-1 or VCAM-1 may not be useful to identify progenitors in cartilage. Instead, their increased expression in OA cartilage implicates involvement in the abnormal cell activation and differentiation process characteristic of OA. PMID:19500336

  2. Partial sequencing of the bottle gourd genome reveals markers useful for phylogenetic analysis and breeding

    PubMed Central

    2011-01-01

    Background Bottle gourd [Lagenaria siceraria (Mol.) Standl.] is an important cucurbit crop worldwide. Archaeological research indicates that bottle gourd was domesticated more than 10,000 years ago, making it one of the earliest plants cultivated by man. In spite of its widespread importance and long history of cultivation almost nothing has been known about the genome of this species thus far. Results We report here the partial sequencing of bottle gourd genome using the 454 GS-FLX Titanium sequencing platform. A total of 150,253 sequence reads, which were assembled into 3,994 contigs and 82,522 singletons were generated. The total length of the non-redundant singletons/assemblies is 32 Mb, theoretically covering ~ 10% of the bottle gourd genome. Functional annotation of the sequences revealed a broad range of functional types, covering all the three top-level ontologies. Comparison of the gene sequences between bottle gourd and the model cucurbit cucumber (Cucumis sativus) revealed a 90% sequence similarity on average. Using the sequence information, 4395 microsatellite-containing sequences were identified and 400 SSR markers were developed, of which 94% amplified bands of anticipated sizes. Transferability of these markers to four other cucurbit species showed obvious decline with increasing phylogenetic distance. From analyzing polymorphisms of a subset of 14 SSR markers assayed on 44 representative China bottle gourd varieties/landraces, a principal coordinates (PCo) analysis output and a UPGMA-based dendrogram were constructed. Bottle gourd accessions tended to group by fruit shape rather than geographic origin, although in certain subclades the lines from the same or close origin did tend to cluster. Conclusions This work provides an initial basis for genome characterization, gene isolation and comparative genomics analysis in bottle gourd. The SSR markers developed would facilitate marker assisted breeding schemes for efficient introduction of desired

  3. Plug cluster module demonstration

    NASA Technical Reports Server (NTRS)

    Rousar, D. C.

    1978-01-01

    The low pressure, film cooled rocket engine design concept developed during two previous ALRC programs was re-evaluated for application as a module for a plug cluster engine capable of performing space shuttle OTV missions. The nominal engine mixture ratio was 5.5 and the engine life requirements were 1200 thermal cycles and 10 hours total operating life. The program consisted of pretest analysis; engine tests, performed using residual components; and posttest analysis. The pretest analysis indicated that operation of the operation of the film cooled engine at O/F = 5.5 was feasible. During the engine tests, steady state wall temperature and performance measurement were obtained over a range of film cooling flow rates, and the durability of the engine was demonstrated by firing the test engine 1220 times at a nominal performance ranging from 430 - 432 seconds. The performance of the test engine was limited by film coolant sleeve damage which had occurred during previous testing. The post-test analyses indicated that the nominal performance level can be increased to 436 seconds.

  4. Dust cluster explosion

    SciTech Connect

    Saxena, Vikrant; Avinash, K.; Sen, A.

    2012-09-15

    A model for the dust cluster explosion where micron/sub-micron sized particles are accelerated at the expense of plasma thermal energy, in the afterglow phase of a complex plasma discharge is proposed. The model is tested by molecular dynamics simulations of dust particles in a confining potential. The nature of the explosion (caused by switching off the discharge) and the concomitant dust acceleration is found to depend critically on the pressure of the background neutral gas. At low gas pressure, the explosion is due to unshielded Coulomb repulsion between dust particles and yields maximum acceleration, while in the high pressure regime it is due to shielded Yukawa repulsion and yields much feebler acceleration. These results are in agreement with experimental findings. Our simulations also confirm a recently proposed electrostatic (ES) isothermal scaling relation, P{sub E}{proportional_to}V{sub d}{sup -2} (where P{sub E} is the ES pressure of the dust particles and V{sub d} is the confining volume).

  5. Novae in globular clusters

    SciTech Connect

    Kato, Mariko; Hachisu, Izumi; Henze, Martin

    2013-12-10

    We present the first light-curve analysis of Population II novae that appeared in M31 globular clusters. Our light-curve models, based on the optically thick wind theory, reproduce well both the X-ray turn-on and turnoff times with the white dwarf (WD) mass of about 1.2 M {sub ☉} for M31N 2007-06b in Bol 111 and about 1.37 M {sub ☉} for M31N 2010-10f in Bol 126. The transient supersoft X-ray source CXO J004345 in Bol 194 is highly likely a nova remnant of 1.2-1.3 M {sub ☉} WD. These WD masses are quite consistent with the temperatures deduced from X-ray spectra. We also present the dependence of nova light curves on the metallicity in the range from [Fe/H] = 0.4 to –2.7. Whereas strong optically thick winds are accelerated in Galactic disk novae owing to a large Fe opacity peak, only weak winds occur in Population II novae with low Fe abundance. Thus, nova light curves are systematically slow in low Fe environment. For an extremely low Fe abundance normal nova outbursts may not occur unless the WD is very massive. We encourage V or y filter observation rather than R as well as high cadence X-ray monitorings to open quantitative studies of extragalactic novae.

  6. Neuromodulation in cluster headache.

    PubMed

    Fontaine, Denys; Vandersteen, Clair; Magis, Delphine; Lanteri-Minet, Michel

    2015-01-01

    Medically refractory chronic cluster headache (CH) is a severely disabling headache condition for which several surgical procedures have been proposed as a prophylactic treatment. None of them have been evaluated in controlled conditions, only open studies and case series being available. Destructive procedures (radiofrequency lesioning, radiosurgery, section) and microvascular decompression of the trigeminal nerve or the sphenopalatine ganglion (SPG) have induced short-term improvement which did not maintain on long term in most of the patients. They carried a high risk of complications, including severe sensory loss and neuropathic pain, and consequently should not be proposed in first intention.Deep brain stimulation (DBS), targeting the presumed CH generator in the retro-hypothalamic region or fibers connecting it, decreased the attack frequency >50 in 60 % of the 52 patients reported. Complications were infrequent: gaze disturbances, autonomic disturbances, and intracranial hemorrhage (2).Occipital nerve stimulation (ONS) was efficient (decrease of attack frequency >50 %) in about 70 % of the 60 patients reported, with a low risk of complications (essentially hardware related). Considering their respective risks, ONS should be proposed first and DBS only in case of ONS failure.New on-demand chronically implanted SPG stimulation seemed to be efficient to abort CH attacks in a pilot controlled trial, but its long-term safety needs to be further studied. PMID:25411142

  7. The Extended Virgo Cluster Catalog

    NASA Astrophysics Data System (ADS)

    Kim, Suk; Rey, Soo-Chang; Jerjen, Helmut; Lisker, Thorsten; Sung, Eon-Chang; Lee, Youngdae; Chung, Jiwon; Pak, Mina; Yi, Wonhyeong; Lee, Woong

    2014-12-01

    We present a new catalog of galaxies in the wider region of the Virgo cluster, based on the Sloan Digital Sky Survey (SDSS) Data Release 7. The Extended Virgo Cluster Catalog (EVCC) covers an area of 725 deg2 or 60.1 Mpc2. It is 5.2 times larger than the footprint of the classical Virgo Cluster Catalog (VCC) and reaches out to 3.5 times the virial radius of the Virgo cluster. We selected 1324 spectroscopically targeted galaxies with radial velocities less than 3000 km s-1. In addition, 265 galaxies that have been overlooked in the SDSS spectroscopic survey but have available redshifts in the NASA Extragalactic Database are also included. Our selection process secured a total of 1589 galaxies, 676 of which are not included in the VCC. The certain and possible cluster members are defined by means of redshift comparison with a cluster infall model. We employed two independent and complementary galaxy classification schemes: the traditional morphological classification based on the visual inspection of optical images and a characterization of galaxies from their spectroscopic features. SDSS u, g, r, i, and z passband photometry of all EVCC galaxies was performed using Source Extractor. We compare the EVCC galaxies with the VCC in terms of morphology, spatial distribution, and luminosity function. The EVCC defines a comprehensive galaxy sample covering a wider range in galaxy density that is significantly different from the inner region of the Virgo cluster. It will be the foundation for forthcoming galaxy evolution studies in the extended Virgo cluster region, complementing ongoing and planned Virgo cluster surveys at various wavelengths.

  8. The Extended Virgo Cluster Catalog

    NASA Astrophysics Data System (ADS)

    Rey, Soo-Chang

    2015-08-01

    We present a new catalog of galaxies in the wider region of the Virgo cluster, based on the Sloan Digital Sky Survey (SDSS) Data Release 7. The Extended Virgo Cluster Catalog (EVCC) covers an area of 725 deg2 or 60.1 Mpc2. It is 5.2 times larger than the footprint of the classical Virgo Cluster Catalog (VCC) and reaches out to 3.5 times the virial radius of the Virgo cluster. We selected 1324 spectroscopically targeted galaxies with radial velocities less than 3000 km s-1. In addition, 265 galaxies that have been overlooked in the SDSS spectroscopic survey but have available redshifts in the NASA Extragalactic Database are also included. Our selection process secured a total of 1589 galaxies, 676 of which are not included in the VCC. The certain and possible cluster members are defined by means of redshift comparison with a cluster infall model. We employed two independent and complementary galaxy classification schemes: the traditional morphological classification based on the visual inspection of optical images and a characterization of galaxies from their spectroscopic features. SDSS u, g, r, i, and z passband photometry of all EVCC galaxies was performed using Source Extractor. We compare the EVCC galaxies with the VCC in terms of morphology, spatial distribution, and luminosity function. The EVCC defines a comprehensive galaxy sample covering a wider range in galaxy density that is significantly different from the inner region of the Virgo cluster. It will be the foundation for forthcoming galaxy evolution studies in the extended Virgo cluster region, complementing ongoing and planned Virgo cluster surveys at various wavelengths.

  9. THE EXTENDED VIRGO CLUSTER CATALOG

    SciTech Connect

    Kim, Suk; Rey, Soo-Chang; Lee, Youngdae; Chung, Jiwon; Pak, Mina; Yi, Wonhyeong; Lee, Woong; Jerjen, Helmut; Lisker, Thorsten; Sung, Eon-Chang

    2015-01-01

    We present a new catalog of galaxies in the wider region of the Virgo cluster, based on the Sloan Digital Sky Survey (SDSS) Data Release 7. The Extended Virgo Cluster Catalog (EVCC) covers an area of 725 deg{sup 2} or 60.1 Mpc{sup 2}. It is 5.2 times larger than the footprint of the classical Virgo Cluster Catalog (VCC) and reaches out to 3.5 times the virial radius of the Virgo cluster. We selected 1324 spectroscopically targeted galaxies with radial velocities less than 3000 km s{sup –1}. In addition, 265 galaxies that have been overlooked in the SDSS spectroscopic survey but have available redshifts in the NASA Extragalactic Database are also included. Our selection process secured a total of 1589 galaxies, 676 of which are not included in the VCC. The certain and possible cluster members are defined by means of redshift comparison with a cluster infall model. We employed two independent and complementary galaxy classification schemes: the traditional morphological classification based on the visual inspection of optical images and a characterization of galaxies from their spectroscopic features. SDSS u, g, r, i, and z passband photometry of all EVCC galaxies was performed using Source Extractor. We compare the EVCC galaxies with the VCC in terms of morphology, spatial distribution, and luminosity function. The EVCC defines a comprehensive galaxy sample covering a wider range in galaxy density that is significantly different from the inner region of the Virgo cluster. It will be the foundation for forthcoming galaxy evolution studies in the extended Virgo cluster region, complementing ongoing and planned Virgo cluster surveys at various wavelengths.

  10. The evolution of clusters of galaxies. I - Very rich clusters

    NASA Technical Reports Server (NTRS)

    Richstone, D. O.; Malumuth, E. M.

    1983-01-01

    A multiple one-body Monte Carlo code is used to investigate the evolution of galaxies in a steady cluster potential under the influence of dynamical friction, two-body relaxation, tidal stripping, and galaxy mergers. The basic assumptions, estimated time scales, method and computer program, and effects of uncertainties in galaxy encounter physics are addressed. Numerical experiments in which the mass initially carried by galaxies and the mass function are varied are reported. It is shown that the formation of a very massive cluster galaxy depends critically on the number of galaxies, the initial division of cluster material between galaxies and a smooth intracluster medium, the mass spectrum of the galaxies, and chance. By the end of all simulations, less than half of the mass in the central regions of the cluster is bound to galaxies. It appears possible to produce any of the Bautz-Morgan classes from very similar initial conditions.

  11. Clustering Acoustic Segments Using Multi-Stage Agglomerative Hierarchical Clustering

    PubMed Central

    2015-01-01

    Agglomerative hierarchical clustering becomes infeasible when applied to large datasets due to its O(N2) storage requirements. We present a multi-stage agglomerative hierarchical clustering (MAHC) approach aimed at large datasets of speech segments. The algorithm is based on an iterative divide-and-conquer strategy. The data is first split into independent subsets, each of which is clustered separately. Thus reduces the storage required for sequential implementations, and allows concurrent computation on parallel computing hardware. The resultant clusters are merged and subsequently re-divided into subsets, which are passed to the following iteration. We show that MAHC can match and even surpass the performance of the exact implementation when applied to datasets of speech segments. PMID:26517376

  12. Systolic architecture for heirarchical clustering

    SciTech Connect

    Ku, L.C.

    1984-01-01

    Several hierarchical clustering methods (including single-linkage complete-linkage, centroid, and absolute overlap methods) are reviewed. The absolute overlap clustering method is selected for the design of systolic architecture mainly due to its simplicity. Two versions of systolic architectures for the absolute overlap hierarchical clustering algorithm are proposed: one-dimensional version that leads to the development of a two dimensional version which fully takes advantage of the underlying data structure of the problems. The two dimensional systolic architecture can achieve a time complexity of O(m + n) in comparison with the conventional computer implementation of a time complexity of O(m/sup 2*/n).

  13. Spectral lineshapes of molecular clusters

    NASA Astrophysics Data System (ADS)

    Islampour, Reza; Mukamel, Shaul

    1984-06-01

    The electronic spectral lineshape of an impurity molecule in a cluster is calculated. Both a rigid (solid-like) and a non-rigid (droplet-like) model for the cluster are considered and compared. The spectrum is calculated using the spectral density J(ω) which is related to the correlation function of the time-dependent enegy gap between the two electronic states. Our calculations demonstrate how the information regarding individual eigenstates is lost under the broadened lineshape envelope in large clusters.

  14. Haplotyping Problem, A Clustering Approach

    SciTech Connect

    Eslahchi, Changiz; Sadeghi, Mehdi; Pezeshk, Hamid; Kargar, Mehdi; Poormohammadi, Hadi

    2007-09-06

    Construction of two haplotypes from a set of Single Nucleotide Polymorphism (SNP) fragments is called haplotype reconstruction problem. One of the most popular computational model for this problem is Minimum Error Correction (MEC). Since MEC is an NP-hard problem, here we propose a novel heuristic algorithm based on clustering analysis in data mining for haplotype reconstruction problem. Based on hamming distance and similarity between two fragments, our iterative algorithm produces two clusters of fragments; then, in each iteration, the algorithm assigns a fragment to one of the clusters. Our results suggest that the algorithm has less reconstruction error rate in comparison with other algorithms.

  15. Neurostimulation for chronic cluster headache

    PubMed Central

    Kaube, Holger

    2012-01-01

    Neurostimulation techniques for the treatment of primary headache syndromes, particularly of chronic cluster headache, have received much interest in recent years. Occipital nerve stimulation (ONS) has yielded favourable clinical results and, despite the limited numbers of published cases, is becoming a routine treatment for refractory chronic cluster headache in specialized centres. Meanwhile, other promising techniques such as spinal cord stimulation (SCS) or sphenopalate ganglion stimulation have emerged. In this article the current state of clinical research for neurostimulation techniques for chronic cluster headache is reviewed. PMID:22590481

  16. Properties of star clusters - II. Scaleheight evolution of clusters

    NASA Astrophysics Data System (ADS)

    Buckner, Anne S. M.; Froebrich, Dirk

    2014-10-01

    Until now, it has been impossible to observationally measure how star cluster scaleheight evolves beyond 1 Gyr as only small samples have been available. Here, we establish a novel method to determine the scaleheight of a cluster sample using modelled distributions and Kolmogorov-Smirnov tests. This allows us to determine the scaleheight with a 25 per cent accuracy for samples of 38 clusters or more. We apply our method to investigate the temporal evolution of cluster scaleheight, using homogeneously selected sub-samples of Kharchenko et al. (MWSC), Dias et al. (DAML02), WEBDA, and Froebrich et al. (FSR). We identify a linear relationship between scaleheight and log(age/yr) of clusters, considerably different from field stars. The scaleheight increases from about 40 pc at 1 Myr to 75 pc at 1 Gyr, most likely due to internal evolution and external scattering events. After 1 Gyr, there is a marked change of the behaviour, with the scaleheight linearly increasing with log(age/yr) to about 550 pc at 3.5 Gyr. The most likely interpretation is that the surviving clusters are only observable because they have been scattered away from the mid-plane in their past. A detailed understanding of this observational evidence can only be achieved with numerical simulations of the evolution of cluster samples in the Galactic disc. Furthermore, we find a weak trend of an age-independent increase in scaleheight with Galactocentric distance. There are no significant temporal or spatial variations of the cluster distribution zero-point. We determine the Sun's vertical displacement from the Galactic plane as Z⊙ = 18.5 ± 1.2 pc.

  17. AMOEBA clustering revisited. [cluster analysis, classification, and image display program

    NASA Technical Reports Server (NTRS)

    Bryant, Jack

    1990-01-01

    A description of the clustering, classification, and image display program AMOEBA is presented. Using a difficult high resolution aircraft-acquired MSS image, the steps the program takes in forming clusters are traced. A number of new features are described here for the first time. Usage of the program is discussed. The theoretical foundation (the underlying mathematical model) is briefly presented. The program can handle images of any size and dimensionality.

  18. Brightest cluster galaxies in the extended GMRT radio halo cluster sample. Radio properties and cluster dynamics

    NASA Astrophysics Data System (ADS)

    Kale, R.; Venturi, T.; Cassano, R.; Giacintucci, S.; Bardelli, S.; Dallacasa, D.; Zucca, E.

    2015-09-01

    Aims: First-ranked galaxies in clusters, usually referred to as brightest cluster galaxies (BCGs), show exceptional properties over the whole electromagnetic spectrum. They are the most massive elliptical galaxies and show the highest probability to be radio loud. Moreover, their special location at the centres of galaxy clusters raises the question of the role of the environment in shaping their radio properties. In the attempt to separate the effect of the galaxy mass and of the environment on their statistical radio properties, we investigate the possible dependence of the occurrence of radio loudness and of the fractional radio luminosity function on the dynamical state of the hosting cluster. Methods: We studied the radio properties of the BCGs in the Extended GMRT Radio Halo Survey (EGRHS), which consists of 65 clusters in the redshift range 0.2-0.4, with X-ray luminosity LX ≥ 5 × 1044 erg s-1, and quantitative information on their dynamical state from high-quality Chandra imaging. We obtained a statistical sample of 59 BCGs, which we divided into two classes, depending on whether the dynamical state of the host cluster was merging (M) or relaxed (R). Results: Of the 59 BCGs, 28 are radio loud and 31 are radio quiet. The radio-loud sources are favourably located in relaxed clusters (71%), while the reverse is true for the radio-quiet BCGs, which are mostly located in merging systems (81%). The fractional radio luminosity function for the BCGs in merging and relaxed clusters is different, and it is considerably higher for BCGs in relaxed clusters, where the total fraction of radio loudness reaches almost 90%, to be compared to the ~30% in merging clusters. For relaxed clusters, we found a positive correlation between the radio power of the BCGs and the strength of the cool core, consistent with previous studies on local samples. Conclusions: Our study suggests that the radio loudness of the BCGs strongly depends on the cluster dynamics; their fraction is

  19. Biological markers in reproductive epidemiology: prospects and precautions

    SciTech Connect

    Stein, Z.; Hatch, M.

    1987-10-01

    We begin by defining ''biological markers'' for the purposes of the present review, distinguishing markers from other types of information, such as subject reports or conventional clinical data. We find the distinctions to be hazy. Next, from the standpoint of epidemiologists, we set out circumstances in which exposure markers might be needed, suggesting requirements for useful markers. We give two instances (lead, PCB), drawn from studies of female reproduction, where the use of exposure markers is compared to environmental or anamnestic data. Effect markers are considered in turn. It is argued that their usefulness (if they are to be more informative than exposure markers) depends on their sensitivity and specificity in relation to the disease outcome. Also, their timeliness, and the use that can be made of the gain in time, for individuals and populations is discussed. In this context, we consider markers of events before and around fertilization; more specifically, we consider those events that precede the clinical marker of the first missed period. In returning to the potential uses of biological markers in discovering or interpreting female reproductive disorders that might be owed to environmental causes, we compare markers of the pre- and peri-implantation phases with markers of the postimplantation phase, drawing on experience with studies of chromosome anomaly in spontaneous abortion. Finally, we suggest other sensitive reproductive processes for which biological markers might usefully be developed. 30 references.

  20. Utilization of RAPD markers to assess genetic diversity of wild populations of North American ginseng (Panax quinquefolium).

    PubMed

    Lim, Wansang; Mudge, Kenneth W; Weston, Leslie A

    2007-01-01

    The Catskill Mountains of New York State are an important source of wild-collected American ginseng (Panax quinquefolium) and, increasingly, of woods-cultivated ginseng. The objective of this study was to assess genetic diversity among 9 different wild ginseng populations in and adjacent to the Catskill Mountain region of New York State and to compare these to wild populations from other states including Kentucky, Tennessee, North Carolina, Pennsylvania, and Virginia, and one cultivated population from Wisconsin. Randomly amplified polymorphic DNA (RAPD) markers were used to estimate the genetic distance among samples from the 15 populations. Pooled DNA from 10 plants of each of 8 New York populations was initially screened with 64 random primers; subsequently, the 15 primers that exhibited the greatest number of reproducible polymorphic markers were selected for further experimentation. Gel electrophoresis with the selected 15 primers produced 124 highly reproducible polymorphic bands. The ratio of discordant bands to total bands scored was used to estimate the genetic distance within and among populations. Multidimensional scaling (MDS) of the relation matrix showed distinctly separate clusters between New York and non-New York populations, indicating separation between these two groupings. The MDS analysis was confirmed using pooled chi-square tests for fragment homogeneity. This study shows that RAPD markers can be used as population-specific markers for Panax quinquefolium, and may eventually be utilized as markers for ginsenoside assessment. PMID:17315311

  1. Identification of neutrophil surface marker changes in health and inflammation using high-throughput screening flow cytometry.

    PubMed

    Lakschevitz, Flavia S; Hassanpour, Siavash; Rubin, Ayala; Fine, Noah; Sun, Chunxiang; Glogauer, Michael

    2016-03-15

    Neutrophils are the most abundant white blood cell and are an essential component of the innate immune system. A complete cataloguing of cell surface markers has not been undertaken for neutrophils isolated from circulation as well as healthy and inflamed tissues. To identify cell-surface markers specific to human neutrophils, we used high-throughput flow cytometry to screen neutrophil populations isolated from blood and oral rinses from healthy and chronic periodontitis patients against a panel of 374 known cluster of differentiation (CD) antibodies. This screen identified CD11b, CD16, and CD66b as markers that are consistently expressed on neutrophils independent of the cell location, level of activation and disease state. Cell sorting against CD11b, CD16 and CD66b allowed for the enrichment of mature neutrophils, yielding neutrophil populations with up to 99% purity. These findings suggest an ideal surface marker set for isolating mature neutrophils from humans. The screen also demonstrated that tissue neutrophils from chronically inflamed tissue display a unique surface marker set compared to tissue neutrophils present in healthy, non-inflamed tissues. PMID:26970376

  2. Exploring genetic variability within lentil (Lens culinaris Medik.) and across related legumes using a newly developed set of microsatellite markers.

    PubMed

    Verma, Priyanka; Sharma, Tilak R; Srivastava, Prem S; Abdin, M Z; Bhatia, Sabhyata

    2014-09-01

    Lentil (Lens culinaris Medik.) is an economically important grain legume, yet the genetic and genomic resources remain largely uncharacterized and unexploited in this crop. Microsatellites have become markers of choice for crop improvement applications. Hence, simple sequence repeat (SSR) markers were developed for lentil through the construction of genomic library enriched for GA/CT motifs. As a result 122 functional SSR primer pairs were developed from 151 microsatellite loci and validated in L. culinaris cv. Precoz. Thirty three SSR markers were utilized for the analysis of genetic relationships between cultivated and wild species of Lens and related legumes. A total of 123 alleles were amplified at 33 loci ranging from 2-5 alleles with an average of 3.73 alleles per locus. Polymorphic information content (PIC) for all the loci ranged from 0.13 to 0.99 with an average of 0.66 per locus. Varied levels of cross genera transferability were obtained ranging from 69.70 % across Pisum sativum to 12.12 % across Vigna radiata. The UPGMA based dendrogram was able to establish the uniqueness of each genotype and grouped them into two major clusters clearly resolving the genetic relationships within lentil and related species. The new set of SSR markers reported here were efficient and highly polymorphic and would add to the existing repertoire of lentil SSR markers to be utilized in molecular breeding. Moreover, the improved knowledge about intra- and inter-specific genetic relationships would facilitate germplasm utilization for lentil improvement. PMID:24893599

  3. Development of simple sequence repeat markers in persimmon (Diospyros L.) and their potential use in related species.

    PubMed

    Yang, Y; Jing, Z B; Ruan, X F; Cheng, J M

    2015-01-01

    Persimmon (Diospyros L.) is an economically important fruit in the world, and it has been recognized as a healthy nutrient supply for human consumption. In this study, 14 microsatellite markers were developed from an AG/TC and AC/TG-enriched genomic library of Chinese persimmon Mopanshi. Twelve polymorphic markers were selected in 4 related species; these markers showed transferability to the 4 related persimmon species. In addition, 10 simple sequence repeat (SSR) markers were used to detect the genetic diversity among 51 persimmon accessions from China, Japan, and Korea. A total of 57 polymorphic bands with an average of 5.7 bands per primer pair were observed. According to cluster analysis and principal coordinate analysis, all persimmon accessions could be divided into 4 groups. A close relationship existed between D. kaki and D. oleifera, and D. glaucifolia and D. lotus. Jinzaoshi could be considered a separate species of persimmon. These new SSR markers provide tools for evaluating genetic relatedness among different persimmon species. PMID:25729996

  4. Review of methods for handling confounding by cluster and informative cluster size in clustered data

    PubMed Central

    Seaman, Shaun; Pavlou, Menelaos; Copas, Andrew

    2014-01-01

    Clustered data are common in medical research. Typically, one is interested in a regression model for the association between an outcome and covariates. Two complications that can arise when analysing clustered data are informative cluster size (ICS) and confounding by cluster (CBC). ICS and CBC mean that the outcome of a member given its covariates is associated with, respectively, the number of members in the cluster and the covariate values of other members in the cluster. Standard generalised linear mixed models for cluster-specific inference and standard generalised estimating equations for population-average inference assume, in general, the absence of ICS and CBC. Modifications of these approaches have been proposed to account for CBC or ICS. This article is a review of these methods. We express their assumptions in a common format, thus providing greater clarity about the assumptions that methods proposed for handling CBC make about ICS and vice versa, and about when different methods can be used in practice. We report relative efficiencies of methods where available, describe how methods are related, identify a previously unreported equivalence between two key methods, and propose some simple additional methods. Unnecessarily using a method that allows for ICS/CBC has an efficiency cost when ICS and CBC are absent. We review tools for identifying ICS/CBC. A strategy for analysis when CBC and ICS are suspected is demonstrated by examining the association between socio-economic deprivation and preterm neonatal death in Scotland. PMID:25087978

  5. Genetic Diversity and Relationships of Korean Chicken Breeds Based on 30 Microsatellite Markers

    PubMed Central

    Suh, Sangwon; Sharma, Aditi; Lee, Seunghwan; Cho, Chang-Yeon; Kim, Jae-Hwan; Choi, Seong-Bok; Kim, Hyun; Seong, Hwan-Hoo; Yeon, Seong-Hum; Kim, Dong-Hun; Ko, Yeoung-Gyu

    2014-01-01

    The effective management of endangered animal genetic resources is one of the most important concerns of modern breeding. Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. This study aimed to analyze the genetic diversity and population structure of six Korean native chicken breeds (n = 300), which were compared with three imported breeds in Korea (n = 150). For the analysis of genetic diversity, 30 microsatellite markers from FAO/ISAG recommended diversity panel or previously reported microsatellite markers were used. The number of alleles ranged from 2 to 15 per locus, with a mean of 8.13. The average observed heterozygosity within native breeds varied between 0.46 and 0.59. The overall heterozygote deficiency (FIT) in native chicken was 0.234±0.025. Over 30.7% of FIT was contributed by within-population deficiency (FIS). Bayesian clustering analysis, using the STRUCTURE software suggested 9 clusters. This study may provide the background for future studies to identify the genetic uniqueness of the Korean native chicken breeds PMID:25178290

  6. Assessment of Genetic Diversity of Bermudagrass (Cynodon dactylon) Using ISSR Markers

    PubMed Central

    Farsani, Tayebeh Mohammadi; Etemadi, Nematollah; Sayed-Tabatabaei, Badraldin Ebrahim; Talebi, Majid

    2012-01-01

    Bermudagrass (Cynodon spp.) is a major turfgrass for home lawns, public parks, golf courses and sport fields and is known to have originated in the Middle East. Morphological and physiological characteristics are not sufficient to differentiate some bermudagrass genotypes because the differences between them are often subtle and subjected to environmental influences. In this study, twenty seven bermudagrass accessions and introductions, mostly from different parts of Iran, were assayed by inter-simple sequence repeat (ISSR) markers to differentiate and explore their genetic relationships. Fourteen ISSR primers amplified 389 fragments of which 313 (80.5%) were polymorphic. The average polymorphism information content (PIC) was 0.328, which shows that the majority of primers are informative. Cluster analysis using the un-weighted paired group method with arithmetic average (UPGMA) method and Jaccard’s similarity coefficient (r = 0.828) grouped the accessions into six main clusters according to some degree to geographical origin, their chromosome number and some morphological characteristics. It can be concluded that there exists a wide genetic base of bermudograss in Iran and that ISSR markers are effective in determining genetic diversity and relationships among them. PMID:22312259

  7. Genetic diversity revealed by morphological traits and ISSR markers in 48 Okras (Abelmoschus escullentus L.).

    PubMed

    Yuan, Cong-Ying; Wang, Ping; Chen, Pang-Pang; Xiao, Wen-Jun; Zhang, Cheng; Hu, Shuai; Zhou, Ping; Chang, Hong-Ping; He, Zhuang; Hu, Rong; Lu, Xiu-Tao; Ye, Jia-Zhuo; Guo, Xin-Hong

    2015-07-01

    Okra is a widely distributed crop in the tropics, subtropics, and warmer areas of the temperate zones. Its major potential uses as a vegetable, oil and protein source, and source of paper pulp and fuel, or biomass are compatible. It is expected to have high value of exploitation and application. Due to the limited number of molecular studies focused on okras, the methods of morphological and ISSR markers were used to analysis the genetic diversity of 48 okras in the present study. The 22 primers were picked for ISSR-PCR, and a total of 154 fragments were amplified with an overall average polymorphism of 54.55 %. We used the 154 markers to construct the dendrogram based on the unweighted pair group method with arithmetic means (UPGMA). A high level of genetic diversity was found among 48 individuals. The 48 Okras was divided into four clusters at Dice's coefficient of 0.19 with clustering analysis. Based on these data of the genetic diversity, it will be possible to exploit the available resources of okra in more valuable ways. PMID:26261400

  8. Population genetic study of 34 X-Chromosome markers in 5 main ethnic groups of China

    PubMed Central

    Zhang, Suhua; Bian, Yingnan; Li, Li; Sun, Kuan; wang, Zheng; Zhao, Qi; Zha, Lagabaiyila; Cai, Jifeng; Gao, Yuzhen; Ji, Chaoneng; Li, Chengtao

    2015-01-01

    As a multi-ethnic country, China has some indigenous population groups which vary in culture and social customs, perhaps as a result of geographic isolation and different traditions. However, upon close interactions and intermarriage, admixture of different gene pools among these ethnic groups may occur. In order to gain more insight on the genetic background of X-Chromosome from these ethnic groups, a set of X-markers (18 X-STRs and 16 X-Indels) was genotyped in 5 main ethnic groups of China (HAN, HUI, Uygur, Mongolian, Tibetan). Twenty-three private alleles were detected in HAN, Uygur, Tibetan and Mongolian. Significant differences (p < 0.0001) were all observed for the 3 parameters of heterozygosity (Ho, He and UHe) among the 5 ethnic groups. Highest values of Nei genetic distance were always observed at HUI-Uygur pairwise when analyzed with X-STRs or X-Indels separately and combined. Phylogenetic tree and PCA analyses revealed a clear pattern of population differentiation of HUI and Uygur. However, the HAN, Tibetan and Mongolian ethnic groups were closely clustered. Eighteen X-Indels exhibited in general congruent phylogenetic signal and similar cluster among the 5 ethnic groups compared with 16 X-STRs. Aforementioned results proved the genetic polymorphism and potential of the 34 X-markers in the 5 ethnic groups. PMID:26634331

  9. A Clustering Graph Generator

    SciTech Connect

    Winlaw, Manda; De Sterck, Hans; Sanders, Geoffrey

    2015-10-26

    In very simple terms a network can be de ned as a collection of points joined together by lines. Thus, networks can be used to represent connections between entities in a wide variety of elds including engi- neering, science, medicine, and sociology. Many large real-world networks share a surprising number of properties, leading to a strong interest in model development research and techniques for building synthetic networks have been developed, that capture these similarities and replicate real-world graphs. Modeling these real-world networks serves two purposes. First, building models that mimic the patterns and prop- erties of real networks helps to understand the implications of these patterns and helps determine which patterns are important. If we develop a generative process to synthesize real networks we can also examine which growth processes are plausible and which are not. Secondly, high-quality, large-scale network data is often not available, because of economic, legal, technological, or other obstacles [7]. Thus, there are many instances where the systems of interest cannot be represented by a single exemplar network. As one example, consider the eld of cybersecurity, where systems require testing across diverse threat scenarios and validation across diverse network structures. In these cases, where there is no single exemplar network, the systems must instead be modeled as a collection of networks in which the variation among them may be just as important as their common features. By developing processes to build synthetic models, so-called graph generators, we can build synthetic networks that capture both the essential features of a system and realistic variability. Then we can use such synthetic graphs to perform tasks such as simulations, analysis, and decision making. We can also use synthetic graphs to performance test graph analysis algorithms, including clustering algorithms and anomaly detection algorithms.

  10. Cluster Randomized Controlled Trial

    PubMed Central

    Young, John; Chapman, Katie; Nixon, Jane; Patel, Anita; Holloway, Ivana; Mellish, Kirste; Anwar, Shamaila; Breen, Rachel; Knapp, Martin; Murray, Jenni; Farrin, Amanda

    2015-01-01

    Background and Purpose— We developed a new postdischarge system of care comprising a structured assessment covering longer-term problems experienced by patients with stroke and their carers, linked to evidence-based treatment algorithms and reference guides (the longer-term stroke care system of care) to address the poor longer-term recovery experienced by many patients with stroke. Methods— A pragmatic, multicentre, cluster randomized controlled trial of this system of care. Eligible patients referred to community-based Stroke Care Coordinators were randomized to receive the new system of care or usual practice. The primary outcome was improved patient psychological well-being (General Health Questionnaire-12) at 6 months; secondary outcomes included functional outcomes for patients, carer outcomes, and cost-effectiveness. Follow-up was through self-completed postal questionnaires at 6 and 12 months. Results— Thirty-two stroke services were randomized (29 participated); 800 patients (399 control; 401 intervention) and 208 carers (100 control; 108 intervention) were recruited. In intention to treat analysis, the adjusted difference in patient General Health Questionnaire-12 mean scores at 6 months was −0.6 points (95% confidence interval, −1.8 to 0.7; P=0.394) indicating no evidence of statistically significant difference between the groups. Costs of Stroke Care Coordinator inputs, total health and social care costs, and quality-adjusted life year gains at 6 months, 12 months, and over the year were similar between the groups. Conclusions— This robust trial demonstrated no benefit in clinical or cost-effectiveness outcomes associated with the new system of care compared with usual Stroke Care Coordinator practice. Clinical Trial Registration— URL: http://www.controlled-trials.com. Unique identifier: ISRCTN 67932305. PMID:26152298

  11. Predictive Markers of Honey Bee Colony Collapse

    PubMed Central

    Dainat, Benjamin; Evans, Jay D.; Chen, Yan Ping; Gauthier, Laurent; Neumann, Peter

    2012-01-01

    Across the Northern hemisphere, managed honey bee colonies, Apis mellifera, are currently affected by abrupt depopulation during winter and many factors are suspected to be involved, either alone or in combination. Parasites and pathogens are considered as principal actors, in particular the ectoparasitic mite Varroa destructor, associated viruses and the microsporidian Nosema ceranae. Here we used long term monitoring of colonies and screening for eleven disease agents and genes involved in bee immunity and physiology to identify predictive markers of honeybee colony losses during winter. The data show that DWV, Nosema ceranae, Varroa destructor and Vitellogenin can be predictive markers for winter colony losses, but their predictive power strongly depends on the season. In particular, the data support that V. destructor is a key player for losses, arguably in line with its specific impact on the health of individual bees and colonies. PMID:22384162

  12. [Biochemical and immunological markers of autoimmune thyroiditis].

    PubMed

    Biktagirova, E M; Sattarova, L I; Vagapova, G R; Skibo, Y V; Chuhlovina, E N; Kravtsova, O A; Abramova, Z I

    2016-05-01

    Correlations between biochemical and immunological markers of programmed cell death (apoptosis), and the functional state of the thyroid gland (hyperthyroidism, euthyroidism, hypothyroidism) have been investigated in autoimmune thyroiditis (AT) (also known as chronic autoimmune thyroiditis). Annexin V, TRAIL and TNF-a, as well as DNA-hydrolyzing antibodies were used as the main markers. Increased levels of TRAIL were found in the serum of AT patients (hyperthyroidism>hypothyroidism>euthyroidism) compared with healthy individuals. The highest frequency of antibodies to denatured DNA (Abs-dDNA) had the highest frequency in AT patients (97%) compared with healthy controls. Among these patients, 75% had hyperthyroidism, 85% had hypothyroidism, and 84.7% had euthyroidism. Abs hydrolyzing activity demonstrated correlation dependence with symptoms of the thyroid dysfunction. PMID:27563001

  13. Architecture of Eph receptor clusters

    SciTech Connect

    Himanen, Juha P.; Yermekbayeva, Laila; Janes, Peter W.; Walker, John R.; Xu, Kai; Atapattu, Lakmali; Rajashankar, Kanagalaghatta R.; Mensinga, Anneloes; Lackmann, Martin; Nikolov, Dimitar B.; Dhe-Paganon, Sirano

    2010-10-04

    Eph receptor tyrosine kinases and their ephrin ligands regulate cell navigation during normal and oncogenic development. Signaling of Ephs is initiated in a multistep process leading to the assembly of higher-order signaling clusters that set off bidirectional signaling in interacting cells. However, the structural and mechanistic details of this assembly remained undefined. Here we present high-resolution structures of the complete EphA2 ectodomain and complexes with ephrin-A1 and A5 as the base unit of an Eph cluster. The structures reveal an elongated architecture with novel Eph/Eph interactions, both within and outside of the Eph ligand-binding domain, that suggest the molecular mechanism underlying Eph/ephrin clustering. Structure-function analysis, by using site-directed mutagenesis and cell-based signaling assays, confirms the importance of the identified oligomerization interfaces for Eph clustering.

  14. Distant Massive Clusters and Cosmology

    NASA Technical Reports Server (NTRS)

    Donahue, Megan

    1999-01-01

    We present a status report of our X-ray study and analysis of a complete sample of distant (z=0.5-0.8), X-ray luminous clusters of galaxies. We have obtained ASCA and ROSAT observations of the five brightest Extended Medium Sensitivity (EMSS) clusters with z > 0.5. We have constructed an observed temperature function for these clusters, and measured iron abundances for all of these clusters. We have developed an analytic expression for the behavior of the mass-temperature relation in a low-density universe. We use this mass-temperature relation together with a Press-Schechter-based model to derive the expected temperature function for different values of Omega-M. We combine this analysis with the observed temperature functions at redshifts from 0 - 0.8 to derive maximum likelihood estimates for the value of Omega-M. We report preliminary results of this analysis.

  15. Chemical evolution of star clusters.

    PubMed

    van Loon, Jacco Th

    2010-02-28

    I discuss the chemical evolution of star clusters, with emphasis on old Galactic globular clusters (GCs), in relation to their formation histories. GCs are clearly formed in a complex fashion, under markedly different conditions from any younger clusters presently known. Those special conditions must be linked to the early formation epoch of the Galaxy and must not have occurred since. While a link to the formation of GCs in dwarf galaxies has been suggested, present-day dwarf galaxies are not representative of the gravitational potential wells within which the GCs formed. Instead, a formation deep within the proto-Galaxy or within dark-matter mini-haloes might be favoured. Not all GCs may have formed and evolved similarly. In particular, we may need to distinguish Galactic Halo from Galactic Bulge clusters. PMID:20083507

  16. Virtual Cluster Management with Xen

    SciTech Connect

    Bhatia, Nikhil; Vetter, Jeffrey S

    2008-01-01

    Recently, virtualization of hardware resources to run multiple instances of independent virtual machines over physical hosts has gained popularity due to an industry-wide focus on the need to reduce the cost of operation of an enterprise computing infrastructure. Xen is an open source hypervisor that provides a virtual machine abstraction layer which is very similar to the underlying physical machine. Using multiple physical hosts, each hosting multiple virtual machines over a VMM like Xen, system administrators can setup a high-availability virtual cluster to meet the ever-increasing demands of their data centers. In such an environment, the Xen hypervisor enables live migration of individual virtual machine instances from one physical node to another without significantly affecting the performance of the applications running on a target virtual machine. This paper describes a scalable Virtual Cluster Manager that provides such application agnostic cluster management capabilities to the system administrators maintaining virtual clusters over Xen powered virtual nodes.

  17. Galaxy and cluster redshift surveys

    NASA Technical Reports Server (NTRS)

    Geller, Margaret J.; Huchra, John P.

    1988-01-01

    The present evaluation of galaxy and cluster redshift surveys gives attention to the CfA redshift survey and a deep Abell cluster redshift survey. These data support a structure in which galaxies lie on thin sheets which nearly surround vast, low-density voids. Voids such as that in Bootes are a common feature of galaxy distribution, posing a serious challenge for models. The Huchra et al. (1988) deep-cluster survey exhibits a correlation function amplitude that is a factor of about 2 smaller than that of the earlier Bahcall and Soneira (1983) sample; the difference may not be significant, however, because the cluster samples are sufficiently small to be dominated by single systems.

  18. Infrared spectroscopy of ionic clusters

    SciTech Connect

    Price, J.M. . Dept. of Chemistry Lawrence Berkeley Lab., CA )

    1990-11-01

    This thesis describes new experiments wherein the infrared vibrational predissociation spectra of a number of mass-selected ionic cluster systems have been obtained and analyzed in the 2600 to 4000 cm{sup {minus}1} region. The species studied include: the hydrated hydronium ions, H{sub 3}O{sup +} (H{sub 2}O){sub 3 {minus}10}, ammoniated ammonium ions, NH{sub 4}{sup +}(NH{sub 3}){sub 1 {minus}10} and cluster ions involving both water and ammonia around an ammonium ion core, (mixed clusters) NH{sub 4}{sup +}(NH{sub 3}){sub n}(H{sub 2}O){sub m} (n+m=4). In each case, the spectra reveal well resolved structures that can be assigned to transitions arising from the vibrational motions of both the ion core of the clusters and the surrounding neutral solvent molecules. 154 refs., 19 figs., 8 tabs.

  19. Optical Follow-Up Observations for the High-z COBRA (Clusters Occupied by Bent Radio AGN) Survey

    NASA Astrophysics Data System (ADS)

    Golden-Marx, Emmet; Blanton, Elizabeth L.; Paterno-Mahler, Rachel; Wing, Joshua; Ashby, Matthew; Brodwin, Mark

    2015-01-01

    Galaxy clusters are unique laboratories for exploring galaxy formation and evolution. Relatively few galaxy clusters have been spectroscopically confirmed beyond a redshift of 1. Different methods of searching for galaxy clusters are adding to these numbers, including detecting regions with a high-density of galaxies in the optical and IR regimes, detecting the hot intracluster medium in the X-ray, and measuring the Sunyaev-Zel'dovich effect. Another promising method for discovering high-redshift galaxy clusters uses radio observations of AGN. In particular, we use bent-double lobed radio sources, known often to reside in nearby clusters, as markers for distant galaxy clusters. We present initial results from the high-redshift COBRA (Clusters Occupied by Bent Radio AGN) survey. We have Spitzer IRAC observations of 653 bent-double radio sources with hosts too faint to be detected in the SDSS. Since the host galaxies for these radio sources are usually giant ellipticals, lack of detection in the SDSS means they are likely at z > 0.7. We have begun deep follow-up optical observations using the 4.3 m Discovery Channel Telescope and have determined from these initial optical observations that ~50% of the observed fields are overdense and thus good cluster candidates. Additionally, we have created optical-IR color magnitude diagrams to estimate the redshifts of our cluster candidates by identifying the red sequence. The distribution of galaxies on the red sequence can be used to limit galaxy formation models.

  20. vanI: a novel D-Ala-D-Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense.

    PubMed

    Kruse, Thomas; Levisson, Mark; de Vos, Willem M; Smidt, Hauke

    2014-09-01

    The glycopeptide vancomycin was until recently considered a drug of last resort against Gram-positive bacteria. Increasing numbers of bacteria, however, are found to carry genes that confer resistance to this antibiotic. So far, 10 different vancomycin resistance clusters have been described. A chromosomal vancomycin resistance gene cluster was previously described for the anaerobic Desulfitobacterium hafniense Y51. We demonstrate that this gene cluster, characterized by its d-Ala-d-Lac ligase-encoding vanI gene, is present in all strains of D. hafniense, D. chlororespirans and some strains of Desulfosporosinus spp. This gene cluster was not found in vancomycin-sensitive Desulfitobacterium or Desulfosporosinus spp., and we show that this antibiotic resistance can be exploited as an intrinsic selection marker for Desulfitobacterium hafniense and D. chlororespirans. The gene cluster containing vanI is phylogenetically only distantly related with those described from soil and gut bacteria, but clusters instead with vancomycin resistance genes found within the phylum Actinobacteria that include several vancomycin-producing bacteria. It lacks a vanH homologue, encoding a D-lactate dehydrogenase, previously thought to always be present within vancomycin resistance gene clusters. The location of vanH outside the resistance gene cluster likely hinders horizontal gene transfer. Hence, the vancomycin resistance cluster in D. hafniense should be regarded a novel one that we here designated vanI after its unique d-Ala-d-Lac ligase. PMID:25042042

  1. Pyostomatitis vegetans. Clinical marker of ulcerative colitis.

    PubMed

    Lopez-Jornet, P; Gomez-Garcia, F; Camacho-Alonso, F

    2012-03-01

    Pyodermatitis-pyostomatitis vegetans (PV), a rare disorder of the skin and oral mucosa, is considered a highly specific marker for inflammatory bowel disease, especially ulcerative colitis. We have presented the case of a patient with PV. This report emphasizes the relationship of PV to inflammatory bowel disease and the importance of the oral lesions as initial presenting signs of systemic disease or activity. PMID:22685913

  2. Lung cancer: chemoprevention and intermediate effect markers.

    PubMed

    Tockman, M S

    2001-01-01

    Even after smoking cessation, genetic damage in the airways epithelium may lead to focal progression of lung carcinogenesis. Some centres now report as many new lung cancer cases among former smokers as among current smokers. Chemoprevention is a potential approach to diminish the progression of pre-clinical genetic damage. The most intensively studied lung cancer chemoprevention agents are the retinoids, including vitamin A and its synthetic analogues and precursors. While effective in suppressing lung carcinogenesis in animal models, retinoids have failed to inhibit carcinogenesis in human chemoprevention trials with premalignant end-points (sputum atypia, bronchial metaplasia). In trials with lung cancer end-points, administration of retinoids either was ineffective or, in the case of beta-carotene, led to greater lung cancer incidence and mortality. In view of these findings, markers of specific retinoid effect (i.e., levels of RAR-beta) become less relevant. Other markers of genetic instability and proliferation may be useful for both early detection and potentially as intermediate-effect markers for new chemoprevention trials. Cytological atypia, bronchial metaplasia, protein (hnRNP A2/B1) overexpression, ras oncogene activation and tumour-suppressor gene deletion, genomic instability (loss of heterozygosity, microsatellite alterations), abnormal methylation, helical CT detection of atypical adenomatous hyperplasia and fluorescent bronchoscopic detection of angiogenic squamous dysplasia offer great promise for molecular diagnosis of lung cancer far in advance of clinical presentation. These end-points can now be evaluated as monitors of response to chemoprevention as potential intermediate-effect markers. PMID:11220665

  3. Automated genotyping of dinucleotide repeat markers

    SciTech Connect

    Perlin, M.W.; Hoffman, E.P. |

    1994-09-01

    The dinucleotide repeats (i.e., microsatellites) such as CA-repeats are a highly polymorphic, highly abundant class of PCR-amplifiable markers that have greatly streamlined genetic mapping experimentation. It is expected that over 30,000 such markers (including tri- and tetranucleotide repeats) will be characterized for routine use in the next few years. Since only size determination, and not sequencing, is required to determine alleles, in principle, dinucleotide repeat genotyping is easily performed on electrophoretic gels, and can be automated using DNA sequencers. Unfortunately, PCR stuttering with these markers generates not one band for each allele, but a pattern of bands. Since closely spaced alleles must be disambiguated by human scoring, this poses a key obstacle to full automation. We have developed methods that overcome this obstacle. Our model is that the observed data is generated by arithmetic superposition (i.e., convolution) of multiple allele patterns. By quantitatively measuring the size of each component band, and exploiting the unique stutter pattern associated with each marker, closely spaced alleles can be deconvolved; this unambiguously reconstructs the {open_quotes}true{close_quotes} allele bands, with stutter artifact removed. We used this approach in a system for automated diagnosis of (X-linked) Duchenne muscular dystrophy; four multiplexed CA-repeats within the dystrophin gene were assayed on a DNA sequencer. Our method accurately detected small variations in gel migration that shifted the allele size estimate. In 167 nonmutated alleles, 89% (149/167) showed no size variation, 9% (15/167) showed 1 bp variation, and 2% (3/167) showed 2 bp variation. We are currently developing a library of dinucleotide repeat patterns; together with our deconvolution methods, this library will enable fully automated genotyping of dinucleotide repeats from sizing data.

  4. Deep RGS Observations of Clusters

    NASA Technical Reports Server (NTRS)

    Smith, R.; Mushotzky, R.; Loewenstein, M.

    2007-01-01

    This viewgraph presentation reviews the Reflection Grating Spectrometers (RGS) observations of clusters. It includes charts detailing the resolution difference between the European Photon Imaging Camera (EPIC) and the RGS and a partial review of existing observations, in graphic format, and as a table. Other sources show up in the ROSAT observations. The presentation reviews possible results that could be achieved in the event that 300 ks of time were allocated for the observations of clusters.

  5. PC Clusters for Lattice QCD

    NASA Astrophysics Data System (ADS)

    Holmgren, D. J.

    2005-03-01

    In the last several years, tightly coupled PC clusters have become widely applied, cost effective resources for lattice gauge computations. This paper discusses the practice of building such clusters, in particular balanced design requirements. I review and quantify the improvements over time of key performance parameters and overall price to performance ratio. Applying these trends and technology forecasts given by computer equipment manufacturers, I predict the range of price to performance for lattice codes expected in the next several years.

  6. Reactions and properties of clusters

    NASA Astrophysics Data System (ADS)

    Castleman, A. W., Jr.

    1992-09-01

    The elucidation from a molecular point of view of the differences and similarities in the properties and reactivity of matter in the gaseous compared to the condensed state is a subject of considerable current interest. One of the promising approaches to this problem is to utilize mass spectrometry in conjunction with laser spectroscopy and fast-flow reaction devices to investigate the changing properties, structure and reactivity of clusters as a function of the degree of solvation under well-controlled conditions. In this regard, an investigation of molecular cluster ions has provided considerable new insight into the basic mechanisms of ion reactions within a cluster, and this paper reviews some of the recent advances in cluster production, the origin of magic numbers and relationship to cluster ion stabilities, and solvation effects on reactions. There have been some notable advances in the production of large cluster ions under thermal reaction conditions, enabling a systematic study of the influence of solvation on reactions to be carried out. These and other new studies of magic numbers have traced their origin to the thermochemical stability of cluster ions. There are several classes of reaction where solvation has a notable influence on reactivity. A particularly interesting example comes from recent studies of the reactions of the hydroxyl anion with CO2 and SO2, studied as a function of the degree of hydration of OH-. Both reactions are highly exothermic, yet the differences in reactivity are dramatic. In the case of SO2, the reaction occurs at near the collision rate. By contrast, CO2 reactivity plummets dramatically for clusters having more than four water molecules. The slow rate is in accord with observations in the liquid phase.

  7. Re-shaping colloidal clusters

    NASA Astrophysics Data System (ADS)

    Kraft, Daniela

    2015-03-01

    Controlling the geometry and yield of anisotropic colloidal particles remains a challenge for hierarchical self-assembly. I will discuss a synthetic strategy for fabricating colloidal clusters by creating order in randomly aggregated polymer spheres using surface tension and geometrical constraints. The technique can be extended to a variety of charge-stabilized polymer spheres and offers control over the cluster size distribution. VENI grant from The Netherlands Organization for Scientific Research (NWO).

  8. Malignancy markers in the cerebrospinal fluid.

    PubMed

    Koskiniemi, M

    1988-10-01

    The specificity and sensitivity of malignancy marker determinations in cerebrospinal fluid (CSF) are often insufficient. Even at the subclinical stage of the disease the marker should be present. The effect of therapy should be monitored and relapses noted. Thus high standards of methodology are required. There are many substances that may indicate a malignant process in the central nervous system. However, there are many pitfalls in their determination. Malignant cells may occur in CSF via processes involving leptomeningeal structures such as metastases and leukaemia, but primary brain tumours seldom show cells in CSF. Human chorionic gonadotrophin and alpha-fetoprotein determinations assist in the early detection of cerebral germ cell tumours and of relapses, even in the subclinical stage. Desmosterol may aid in the diagnosis of medulloblastomas and malignant gliomas and in monitoring therapy. Putrescine levels are elevated in CSF of patients with medulloblastoma and correlate with the clinical state, and serial analyses may reveal relapses. Fibronectin, when determined in CSF at the time of diagnosis, appears to be of great significance for the prognosis of acute lymphoblastic leukaemia. Ferritin and beta-2-microglobulin may help in some well-defined conditions. Brain-specific proteins and antibodies to them are non-specific markers whereas tumour-specific antigens and growth factors may be more significant. PMID:3058481

  9. Selected oxidative stress markers in gynecological laparoscopy

    PubMed Central

    Koźlik, Jacek; Przybyłowska, Joanna; Mikrut, Kinga; Zwoliński, Jacek; Piątek, Jacek; Sobczak, Paweł

    2014-01-01

    Introduction The surgical stress response after laparoscopy is smaller when compared with open surgery, and it is expected that after minimally invasive surgery the possible development of oxidative stress will be less severe. Aim To evaluate markers of pro-oxidant activity – levels of lipid peroxides and malondialdehyde – and activity of the antioxidant enzymes superoxide dismutase and glutathione peroxidase in the perioperative period in patients undergoing gynecological laparoscopy and to determine whether the duration of laparoscopy can affect these changes. Material and methods The study included 64 patients, divided into two groups: group 1 with duration of laparoscopy up to 20 min, and group 2 with duration of the operation over 40 min. Blood samples were collected before anesthesia, 5 min after release of pneumoperitoneum, and 10 h after surgery. Results A statistically significant increase in the levels of lipid peroxides and malondialdehyde in samples collected after surgery was found in comparison with values obtained before surgery. Also statistically significant differences existed between groups of patients with different duration of surgery. Superoxide dismutase and glutathione peroxidase activity values were significantly decreased. They were also significantly different between the two groups with different duration of surgery. Conclusions In our study, levels of the markers of pro-oxidant activity increased and levels of the markers of antioxidant enzymes decreased, suggesting development of oxidative stress. The duration of laparoscopic procedures affects the severity of the presented changes. PMID:25960799

  10. Prognostic DNA Methylation Markers for Prostate Cancer

    PubMed Central

    Strand, Siri H.; Orntoft, Torben F.; Sorensen, Karina D.

    2014-01-01

    Prostate cancer (PC) is the most commonly diagnosed neoplasm and the third most common cause of cancer-related death amongst men in the Western world. PC is a clinically highly heterogeneous disease, and distinction between aggressive and indolent disease is a major challenge for the management of PC. Currently, no biomarkers or prognostic tools are able to accurately predict tumor progression at the time of diagnosis. Thus, improved biomarkers for PC prognosis are urgently needed. This review focuses on the prognostic potential of DNA methylation biomarkers for PC. Epigenetic changes are hallmarks of PC and associated with malignant initiation as well as tumor progression. Moreover, DNA methylation is the most frequently studied epigenetic alteration in PC, and the prognostic potential of DNA methylation markers for PC has been demonstrated in multiple studies. The most promising methylation marker candidates identified so far include PITX2, C1orf114 (CCDC181) and the GABRE~miR-452~miR-224 locus, in addition to the three-gene signature AOX1/C1orf114/HAPLN3. Several other biomarker candidates have also been investigated, but with less stringent clinical validation and/or conflicting evidence regarding their possible prognostic value available at this time. Here, we review the current evidence for the prognostic potential of DNA methylation markers in PC. PMID:25238417

  11. Prognostic DNA methylation markers for prostate cancer.

    PubMed

    Strand, Siri H; Orntoft, Torben F; Sorensen, Karina D

    2014-01-01

    Prostate cancer (PC) is the most commonly diagnosed neoplasm and the third most common cause of cancer-related death amongst men in the Western world. PC is a clinically highly heterogeneous disease, and distinction between aggressive and indolent disease is a major challenge for the management of PC. Currently, no biomarkers or prognostic tools are able to accurately predict tumor progression at the time of diagnosis. Thus, improved biomarkers for PC prognosis are urgently needed. This review focuses on the prognostic potential of DNA methylation biomarkers for PC. Epigenetic changes are hallmarks of PC and associated with malignant initiation as well as tumor progression. Moreover, DNA methylation is the most frequently studied epigenetic alteration in PC, and the prognostic potential of DNA methylation markers for PC has been demonstrated in multiple studies. The most promising methylation marker candidates identified so far include PITX2, C1orf114 (CCDC181) and the GABRE~miR-452~miR-224 locus, in addition to the three-gene signature AOX1/C1orf114/HAPLN3. Several other biomarker candidates have also been investigated, but with less stringent clinical validation and/or conflicting evidence regarding their possible prognostic value available at this time. Here, we review the current evidence for the prognostic potential of DNA methylation markers in PC. PMID:25238417

  12. Genetic markers: Potential candidates for cardiovascular disease.

    PubMed

    Rather, Riyaz Ahmad; Dhawan, Veena

    2016-10-01

    The effective prevention of cardiovascular disease depends upon the ability to recognize the high-risk individuals at an early stage of the disease or long before the development of adverse events. Evolving technologies in the fields of proteomics, metabolomics, and genomics have played a significant role in the discovery of cardiovascular biomarkers, but so far these methods have achieved the modest success. Hence, there is a crucial need for more reliable, suitable, and lasting diagnostic and therapeutic markers to screen the disease well in time to start the clinical aid to the patients. Gene polymorphisms associated with the cardiovascular disease play a decisive role in the disease onset. Therefore, the genetic marker evaluation to classify high-risk patients from low-risk patients trends an effective approach to patient management and care. Currently, there are no genetic markers available for extensive adoption as risk factors for coronary vascular disease, yet, there are numerous promising, biologically acceptable candidates. Many of these gene biomarkers, alone or in combination, can play an essential role in the prediction of cardiovascular risk. The present review highlights some putative emerging genetic biomarkers that could facilitate more authentic and fast diagnosis of CVD. This review also briefly describes few technological approaches employed in the biomarker search. PMID:27416153

  13. MACD: an imaging marker for cardiovascular disease

    NASA Astrophysics Data System (ADS)

    Ganz, Melanie; de Bruijne, Marleen; Nielsen, Mads

    2010-03-01

    Despite general acceptance that a healthy lifestyle and the treatment of risk factors can prevent the development of cardiovascular diseases (CVD), CVD are the most common cause of death in Europe and the United States. It has been shown that abdominal aortic calcifications (AAC) correlate strongly with coronary artery calcifications. Hence an early detection of aortic calcified plaques helps to predict the risk of related coronary diseases. Also since two thirds of the adverse events have no prior symptoms, possibilities to screen for risk in low cost imaging are important. To this end the Morphological Atherosclerotic Calcification Distribution (MACD) index was developed. In the following several potential severity scores relating to the geometrical outline of the calcified deposits in the lumbar aortic region are introduced. Their individual as well as their combined predictive power is examined and a combined marker, MACD, is constructed. This is done using a Cox regression analysis, also known as survival analysis. Furthermore we show how a Cox regression yields MACD to be the most efficient marker. We also demonstrate that MACD has a larger individual predictive power than any of the other individual imaging markers described. Finally we present that the MACD index predicts cardiovascular death with a hazard ratio of approximately four.

  14. Functional molecular markers for crop improvement.

    PubMed

    Kage, Udaykumar; Kumar, Arun; Dhokane, Dhananjay; Karre, Shailesh; Kushalappa, Ajjamada C

    2016-10-01

    A tremendous decline in cultivable land and resources and a huge increase in food demand calls for immediate attention to crop improvement. Though molecular plant breeding serves as a viable solution and is considered as "foundation for twenty-first century crop improvement", a major stumbling block for crop improvement is the availability of a limited functional gene pool for cereal crops. Advancement in the next generation sequencing (NGS) technologies integrated with tools like metabolomics, proteomics and association mapping studies have facilitated the identification of candidate genes, their allelic variants and opened new avenues to accelerate crop improvement through development and use of functional molecular markers (FMMs). The FMMs are developed from the sequence polymorphisms present within functional gene(s) which are associated with phenotypic trait variations. Since FMMs obviate the problems associated with random DNA markers, these are considered as "the holy grail" of plant breeders who employ targeted marker assisted selections (MAS) for crop improvement. This review article attempts to consider the current resources and novel methods such as metabolomics, proteomics and association studies for the identification of candidate genes and their validation through virus-induced gene silencing (VIGS) for the development of FMMs. A number of examples where the FMMs have been developed and used for the improvement of cereal crops for agronomic, food quality, disease resistance and abiotic stress tolerance traits have been considered. PMID:26171816

  15. [THE EVOLUTION OF MARKERS OF PROSTATE CANCER].

    PubMed

    Peshkov, M N; Generozov, E V; Kostryukova, E S

    2016-03-01

    The implementation of biochemical laboratory tests in oncology practice increased exponentially during last decades and continues to be in progress nowadays. The application of modern molecular genetic technologies permits using diagnostic systems with greater diagnostic sensitivity and specificity. The new tests are actively implemented permitting to diagnose physical presence of tumor systemic manifestations of malignant neoplasm (cachexia, pyrexia), paraneoplastic syndromes and also to detect tumor markers. The oncomarker permits to differentiate malignant from benign tumor on the basis of quantitative differences in content of corresponding antigene-tumor marker in blood serum independently of localization of tumor nidus. The prostate cancer is a medical social problem of male population. On initial stages, this disease can take its course asymptomatically or with symptomatic conditioned by such concomitant and more prevalent pathologies as chronic prostatitis and prostate benign hyperplasia. The early diagnostic ofprostate cancer permits implementing timely radical treatment frequently contributing to total recovery of patients. The article presents detailed description of evolutionary conception of markers using in diagnostic, staging and prognostication of course of prostate cancer. The acid phosphatase was applied for the first time in early diagnostic of staging of prostate cancer in 1974. Nowadays, in century of "OMX"-technologies, in common clinical practice detection of RNA in urine of patient is used for staging diagnostic and prognostication of progression of process of tissue neotransformation. PMID:27506103

  16. Uniparental ancestry markers in Chilean populations.

    PubMed

    Vieira-Machado, Camilla Dutra; Tostes, Maluah; Alves, Gabrielle; Nazer, Julio; Martinez, Liliana; Wettig, Elisabeth; Pizarro Rivadeneira, Oscar; Diaz Caamaño, Marcela; Larenas Ascui, Jessica; Pavez, Pedro; Dutra, Maria da Graça; Castilla, Eduardo Enrique; Orioli, Ieda Maria

    2016-08-01

    The presence of Native Americans, Europeans, and Africans has led to the development of a multi-ethnic, admixed population in Chile. This study aimed to contribute to the characterization of the uniparental genetic structure of three Chilean regions. Newborns from seven hospitals in Independencia, Providencia, Santiago, Curicó, Cauquenes, Valdívia, and Puerto Montt communes, belonging to the Chilean regions of Santiago, Maule, and Los Lagos, were studied. The presence of Native American mitochondrial DNA (mtDNA) haplogroups and two markers present in the non-recombinant region of the Y chromosome, DYS199 and DYS287, indicative of Native American and African ancestry, respectively, was determined. A high Native American matrilineal contribution and a low Native American and African patrilineal contributions were found in all three studied regions. As previously found in Chilean admixed populations, the Native American matrilineal contribution was lower in Santiago than in the other studied regions. However, there was an unexpectedly higher contribution of Native American ancestry in one of the studied communes in Santiago, probably due to the high rate of immigration from other regions of the country. The population genetic sub-structure we detected in Santiago using few uniparental markers requires further confirmation, owing to possible stratification for autosomal and X-chromosome markers. PMID:27494198

  17. [Interpretation of hemostatic and fibrinolytic markers].

    PubMed

    Asakura, Hidesaku

    2011-10-01

    Blood dose not normally coagulate in the blood vessels covered with endothelial cells, because these cells contain some substances responsible for antithrombotic action such as thrombomodulin, heparin-like substance, prostacyclin, nitric oxide and tissue plasminogen activator. Most important role of blood coagulation is hemostasis. Blood can coagulate in two ways: intrinsic coagulation pathway and extrinsic coagulation pathway that is activated by negatively charged substances and FVIIa-tissue-factor (TF) complex, respectively. Prothrombin time(PT) can represent extrinsic pathway, while activated partial thromboplastin time (APTT) can represent intrinsic pathway. PT is prolonged in such diseases as vitamin K deficiency, hepatic failure and warfarin intake, while APTT is prolonged such diseases as hemophilia A & B, von Willebrand disease and lupus anticoagulant. Cross mixing test is very useful to assess prolonged clotting time. FDP means fibrin/fibrinogen degradation products and D-dimer is the smallest products of fibrin degradation. These markers are often used to diagnose disseminated intravascular coagulation (DIC) and deep vein thrombosis (DVT). Thrombin-antithrombin complex (TAT) and plasmin-alpha2 plasmin inhibitor (PIC) can be used to evaluate the extent of coagulation and fibrinolysis activation, respectively. These two markers is essential for classify the pathophysiology of DIC: DIC with suppressed fibrinolysis, enhanced fibrinolysis or balanced fibrinolysis. In conclusion, exact interpretation of hemostatic and fibrinolytic markers is one of the most important abilities in clinical situation. PMID:22184880

  18. Autophagy selectivity through receptor clustering

    NASA Astrophysics Data System (ADS)

    Rutenberg, Andrew; Brown, Aidan

    Substrate selectivity in autophagy requires an all-or-none cellular response. We focus on peroxisomes, for which autophagy receptor proteins NBR1 and p62 are well characterized. Using computational models, we explore the hypothesis that physical clustering of autophagy receptor proteins on the peroxisome surface provides an appropriate all-or-none response. We find that larger peroxisomes nucleate NBR1 clusters first, and lose them due to competitive coarsening last, resulting in significant size-selectivity. We then consider a secondary hypothesis that p62 inhibits NBR1 cluster formation. We find that p62 inhibition enhances size-selectivity enough that, even if there is no change of the pexophagy rate, the volume of remaining peroxisomes can significantly decrease. We find that enhanced ubiquitin levels suppress size-selectivity, and that this effect is more pronounced for individual peroxisomes. Sufficient ubiquitin allows receptor clusters to form on even the smallest peroxisomes. We conclude that NBR1 cluster formation provides a viable physical mechanism for all-or-none substrate selectivity in pexophagy. We predict that cluster formation is associated with significant size-selectivity. Now at Simon Fraser University.

  19. Collective thermoregulation in bee clusters.

    PubMed

    Ocko, Samuel A; Mahadevan, L

    2014-02-01

    Swarming is an essential part of honeybee behaviour, wherein thousands of bees cling onto each other to form a dense cluster that may be exposed to the environment for several days. This cluster has the ability to maintain its core temperature actively without a central controller. We suggest that the swarm cluster is akin to an active porous structure whose functional requirement is to adjust to outside conditions by varying its porosity to control its core temperature. Using a continuum model that takes the form of a set of advection-diffusion equations for heat transfer in a mobile porous medium, we show that the equalization of an effective 'behavioural pressure', which propagates information about the ambient temperature through variations in density, leads to effective thermoregulation. Our model extends and generalizes previous models by focusing the question of mechanism on the form and role of the behavioural pressure, and allows us to explain the vertical asymmetry of the cluster (as a consequence of buoyancy-driven flows), the ability of the cluster to overpack at low ambient temperatures without breaking up at high ambient temperatures, and the relative insensitivity to large variations in the ambient temperature. Our theory also makes testable hypotheses for the response of the cluster to external temperature inhomogeneities and suggests strategies for biomimetic thermoregulation. PMID:24335563

  20. Understanding Galaxy Cluster MKW10

    NASA Astrophysics Data System (ADS)

    Sanders, Tim; Henry, Swain; Coble, Kimberly A.; Rosenberg, Jessica L.; Koopmann, Rebecca A.

    2015-01-01

    As part of the Undergraduate ALFALFA Team (UAT), we are studying the galaxy cluster MKW 10 (RA = 175.454, Dec = 10.306, z ~ 0.02), a poor cluster with a compact core in which tidal interactions have occurred. This cluster has been observed in HI and Hα. We used SDSS and NED to search for optical counterparts. By comparing data at multiple wavelengths, we hope to understand the structure, environment, and star formation history of this cluster. Following the techniques of others involved in the groups project and using the program TOPCAT to manipulate the data, we explored both the spatial and velocity distributions to determine cluster membership. We have determined that this cluster consists of 11 galaxies, mostly spiral in shape. Chicago State University is new the UAT and we began our work after taking part in the winter workshop at Arecibo.This work was supported by: Undergraduate ALFALFA Team NSF Grant AST-1211005 and the Illinois Space Grant Consortium.

  1. AMIC@: All MIcroarray Clusterings @ once

    PubMed Central

    Geraci, Filippo; Pellegrini, Marco; Renda, M. Elena

    2008-01-01

    The AMIC@ Web Server offers a light-weight multi-method clustering engine for microarray gene-expression data. AMIC@ is a highly interactive tool that stresses user-friendliness and robustness by adopting AJAX technology, thus allowing an effective interleaved execution of different clustering algorithms and inspection of results. Among the salient features AMIC@ offers, there are: (i) automatic file format detection, (ii) suggestions on the number of clusters using a variant of the stability-based method of Tibshirani et al. (iii) intuitive visual inspection of the data via heatmaps and (iv) measurements of the clustering quality using cluster homogeneity. Large data sets can be processed efficiently by selecting algorithms (such as FPF-SB and k-Boost), specifically designed for this purpose. In case of very large data sets, the user can opt for a batch-mode use of the system by means of the Clustering wizard that runs all algorithms at once and delivers the results via email. AMIC@ is freely available and open to all users with no login requirement at the following URL http://bioalgo.iit.cnr.it/amica. PMID:18477631

  2. AMIC@: All MIcroarray Clusterings @ once.

    PubMed

    Geraci, Filippo; Pellegrini, Marco; Renda, M Elena

    2008-07-01

    The AMIC@ Web Server offers a light-weight multi-method clustering engine for microarray gene-expression data. AMIC@ is a highly interactive tool that stresses user-friendliness and robustness by adopting AJAX technology, thus allowing an effective interleaved execution of different clustering algorithms and inspection of results. Among the salient features AMIC@ offers, there are: (i) automatic file format detection, (ii) suggestions on the number of clusters using a variant of the stability-based method of Tibshirani et al. (iii) intuitive visual inspection of the data via heatmaps and (iv) measurements of the clustering quality using cluster homogeneity. Large data sets can be processed efficiently by selecting algorithms (such as FPF-SB and k-Boost), specifically designed for this purpose. In case of very large data sets, the user can opt for a batch-mode use of the system by means of the Clustering wizard that runs all algorithms at once and delivers the results via email. AMIC@ is freely available and open to all users with no login requirement at the following URL http://bioalgo.iit.cnr.it/amica. PMID:18477631

  3. Calibrating AGN Feedback in Clusters

    NASA Astrophysics Data System (ADS)

    Wise, M. W.

    2009-12-01

    Whether caused by AGN jets, shocks, or mergers, the most definitive evidence for heating in cluster cores comes from X-ray spectroscopy. Unfortunately such spectra are essentially limited to studying the emission spectrum from the cluster as a whole. However since the same underlying emission measure distribution produces both the observed CCD and RGS spectra, X-ray imaging can still provide spatial information on the heating process. Using Chandra archival data for a sample of 9 clusters, we demonstrate how imaging data can be used to constrain departures from a canonical, isobaric cooling flow model as a function of position in a given cluster. The results of this analysis are also shown for the deep archival exposure of the Perseus cluster. Such ``heating maps'' can provide constraints on both the location and magnitude of the heating in the cores of clusters. When combined with detections and spectral index maps from low-frequency radio observations, these maps can be used to distinguish between different models for heating in these objects.

  4. Collective thermoregulation in bee clusters

    PubMed Central

    Ocko, Samuel A.; Mahadevan, L.

    2014-01-01

    Swarming is an essential part of honeybee behaviour, wherein thousands of bees cling onto each other to form a dense cluster that may be exposed to the environment for several days. This cluster has the ability to maintain its core temperature actively without a central controller. We suggest that the swarm cluster is akin to an active porous structure whose functional requirement is to adjust to outside conditions by varying its porosity to control its core temperature. Using a continuum model that takes the form of a set of advection–diffusion equations for heat transfer in a mobile porous medium, we show that the equalization of an effective ‘behavioural pressure’, which propagates information about the ambient temperature through variations in density, leads to effective thermoregulation. Our model extends and generalizes previous models by focusing the question of mechanism on the form and role of the behavioural pressure, and allows us to explain the vertical asymmetry of the cluster (as a consequence of buoyancy-driven flows), the ability of the cluster to overpack at low ambient temperatures without breaking up at high ambient temperatures, and the relative insensitivity to large variations in the ambient temperature. Our theory also makes testable hypotheses for the response of the cluster to external temperature inhomogeneities and suggests strategies for biomimetic thermoregulation. PMID:24335563

  5. Electrodynamic properties of fractal clusters

    NASA Astrophysics Data System (ADS)

    Maksimenko, V. V.; Zagaynov, V. A.; Agranovski, I. E.

    2014-07-01

    An influence of interference on a character of light interaction both with individual fractal cluster (FC) consisting of nanoparticles and with agglomerates of such clusters is investigated. Using methods of the multiple scattering theory, effective dielectric permeability of a micron-size FC composed of non-absorbing nanoparticles is calculated. The cluster could be characterized by a set of effective dielectric permeabilities. Their number coincides with the number of particles, where space arrangement in the cluster is correlated. If the fractal dimension is less than some critical value and frequency corresponds to the frequency of the visible spectrum, then the absolute value of effective dielectric permeability becomes very large. This results in strong renormalization (decrease) of the incident radiation wavelength inside the cluster. The renormalized photons are cycled or trapped inside the system of multi-scaled cavities inside the cluster. A lifetime of a photon localized inside an agglomerate of FCs is a macroscopic value allowing to observe the stimulated emission of the localized light. The latter opens up a possibility for creation of lasers without inverse population of energy levels. Moreover, this allows to reconsider problems of optical cloaking of macroscopic objects. One more feature of fractal structures is a possibility of unimpeded propagation of light when any resistance associated with scattering disappears.

  6. Identification of Urban Leprosy Clusters

    PubMed Central

    Paschoal, José Antonio Armani; Paschoal, Vania Del'Arco; Nardi, Susilene Maria Tonelli; Rosa, Patrícia Sammarco; Ismael, Manuela Gallo y Sanches; Sichieri, Eduvaldo Paulo

    2013-01-01

    Overpopulation of urban areas results from constant migrations that cause disordered urban growth, constituting clusters defined as sets of people or activities concentrated in relatively small physical spaces that often involve precarious conditions. Aim. Using residential grouping, the aim was to identify possible clusters of individuals in São José do Rio Preto, Sao Paulo, Brazil, who have or have had leprosy. Methods. A population-based, descriptive, ecological study using the MapInfo and CrimeStat techniques, geoprocessing, and space-time analysis evaluated the location of 425 people treated for leprosy between 1998 and 2010. Clusters were defined as concentrations of at least 8 people with leprosy; a distance of up to 300 meters between residences was adopted. Additionally, the year of starting treatment and the clinical forms of the disease were analyzed. Results. Ninety-eight (23.1%) of 425 geocoded cases were located within one of ten clusters identified in this study, and 129 cases (30.3%) were in the region of a second-order cluster, an area considered of high risk for the disease. Conclusion. This study identified ten clusters of leprosy cases in the city and identified an area of high risk for the appearance of new cases of the disease. PMID:24288467

  7. Spectral clustering of protein sequences

    PubMed Central

    Paccanaro, Alberto; Casbon, James A.; Saqi, Mansoor A. S.

    2006-01-01

    An important problem in genomics is automatically clustering homologous proteins when only sequence information is available. Most methods for clustering proteins are local, and are based on simply thresholding a measure related to sequence distance. We first show how locality limits the performance of such methods by analysing the distribution of distances between protein sequences. We then present a global method based on spectral clustering and provide theoretical justification of why it will have a remarkable improvement over local methods. We extensively tested our method and compared its performance with other local methods on several subsets of the SCOP (Structural Classification of Proteins) database, a gold standard for protein structure classification. We consistently observed that, the number of clusters that we obtain for a given set of proteins is close to the number of superfamilies in that set; there are fewer singletons; and the method correctly groups most remote homologs. In our experiments, the quality of the clusters as quantified by a measure that combines sensitivity and specificity was consistently better [on average, improvements were 84% over hierarchical clustering, 34% over Connected Component Analysis (CCA) (similar to GeneRAGE) and 72% over another global method, TribeMCL]. PMID:16547200

  8. Multi-focus cluster labeling.

    PubMed

    Eikvil, Line; Jenssen, Tor-Kristian; Holden, Marit

    2015-06-01

    Document collections resulting from searches in the biomedical literature, for instance, in PubMed, are often so large that some organization of the returned information is necessary. Clustering is an efficient tool for organizing search results. To help the user to decide how to continue the search for relevant documents, the content of each cluster can be characterized by a set of representative keywords or cluster labels. As different users may have different interests, it can be desirable with solutions that make it possible to produce labels from a selection of different topical categories. We therefore introduce the concept of multi-focus cluster labeling to give users the possibility to get an overview of the contents through labels from multiple viewpoints. The concept for multi-focus cluster labeling has been established and has been demonstrated on three different document collections. We illustrate that multi-focus visualizations can give an overview of clusters along axes that general labels are not able to convey. The approach is generic and should be applicable to any biomedical (or other) domain with any selection of foci where appropriate focus vocabularies can be established. A user evaluation also indicates that such a multi-focus concept is useful. PMID:25869415

  9. GOLD CLUSTER LABELS AND RELATED TECHNOLOGIES IN MOLECULAR MORPHOLOGY.

    SciTech Connect

    HAINFELD,J.F.; POWELL,R.D.

    2004-02-04

    Although intensely colored, even the largest colloidal gold particles are not, on their own, sufficiently colored for routine use as a light microscopy stain: only with very abundant antigens or with specialized illumination methods can bound gold be seen. Colloidal gold probes were developed primarily as markers for electron microscopy, for which their very high electron density and selectivity for narrow size distributions when prepared in different ways rendered them highly suited. The widespread use of gold labeling for light microscopy was made possible by the introduction of autometallographic enhancement methods. In these processes, the bound gold particles are exposed to a solution containing metal ions and a reducing agent; they catalyze the reduction of the ions, resulting in the deposition of additional metal selectively onto the particles. On the molecular level, the gold particles are enlarged up to 30-100 nm in diameter; on the macroscale level, this results in the formation of a dark stain in regions containing bound gold particles, greatly increasing visibility and contrast. The applications of colloidal gold have been described elsewhere in this chapter, we will focus on the use of covalently linked cluster complexes of gold and other metals. A gold cluster complex is a discrete molecular coordination compound comprising a central core, or ''cluster'' of electron-dense metal atoms, ligated by a shell of small organic molecules (ligands), which are linked to the metal atoms on the surface of the core. This structure gives clusters several important advantages as labels. The capping of the metal surface by ligands prevents non-specific binding to cell and tissue components, which can occur with colloidal gold. Cluster compounds are more stable and may be used under a wider range of conditions. Unlike colloidal gold, clusters do not require additional macromolecules such as bovine serum albumin or polyethylene glycol for stabilization, and the total

  10. A marker chromosome in post-transplant bone marrow.

    PubMed

    Morsberger, Laura; Powell, Kerry; Ning, Yi

    2016-01-01

    Detection of small supernumerary marker chromosomes in karyotype analysis represents a diagnostic challenge. While such markers are usually detected during cytogenetic studies of constitutional chromosome abnormalities, they have also been found in specimens submitted from patients with acquired malignancies. We report here the detection of a marker chromosome in a bone marrow specimen from a patient who received a bone marrow transplantation. We discuss the importance of proper characterization and interpretation of marker chromosomes in clinical practice. PMID:27252781

  11. Development of DArT Marker Platforms and Genetic Diversity Assessment of the U.S. Collection of the New Oilseed Crop Lesquerella and Related Species

    PubMed Central

    Cruz, Von Mark V.; Kilian, Andrzej; Dierig, David A.

    2013-01-01

    The advantages of using molecular markers in modern genebanks are well documented. They are commonly used to understand the distribution of genetic diversity in populations and among species which is crucial for efficient management and effective utilization of germplasm collections. We describe the development of two types of DArT molecular marker platforms for the new oilseed crop lesquerella (Physaria spp.), a member of the Brassicaceae family, to characterize a collection in the National Plant Germplasm System (NPGS) with relatively little known in regards to the genetic diversity and traits. The two types of platforms were developed using a subset of the germplasm conserved ex situ consisting of 87 Physaria and 2 Paysonia accessions. The microarray DArT revealed a total of 2,833 polymorphic markers with an average genotype call rate of 98.4% and a scoring reproducibility of 99.7%. On the other hand, the DArTseq platform developed for SNP and DArT markers from short sequence reads showed a total of 27,748 high quality markers. Cluster analysis and principal coordinate analysis indicated that the different accessions were successfully classified by both systems based on species, by geographical source, and breeding status. In the germplasm set analyzed, which represented more than 80% of the P. fendleri collection, we observed that a substantial amount of variation exists in the species collection. These markers will be valuable in germplasm management studies and lesquerella breeding, and augment the microsatellite markers previously developed on the taxa. PMID:23724020

  12. Integration of DNA marker information into breeding value predictions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Calves from seven breeds including 20 herds were genotyped with a reduced DNA marker panel for weaning weight. The marker panel used was derived using USMARC Cycle VII animals. The results from the current study suggest marker effects are not robust across breeds and that methodology exists to integ...

  13. 21 CFR 886.4570 - Ophthalmic surgical marker.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Ophthalmic surgical marker. 886.4570 Section 886...) MEDICAL DEVICES OPHTHALMIC DEVICES Surgical Devices § 886.4570 Ophthalmic surgical marker. (a) Identification. An ophthalmic surgical marker is a device intended to mark by use of ink, dye, or indentation...

  14. Genetic and biological markers in drug abuse and alcoholism

    SciTech Connect

    Braude, M.C.; Chao, H.M.

    1986-01-01

    This book contains 11 selections. Some of the titles are: Polymorphic Gene Marker Studies; Pharmacogenetic Approaches to the Prediction of Drug Response; Genetic Markers of Drug Abuse in Mouse Models; Genetics as a Tool for Identifying Biological Markers of Drug Abuse; and Studies of an Animal Model of Alcoholism.

  15. Developmnent of molecular markers for powdery mildew resistance in grapevines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular markers have been used as a tool for plant breeding for two decades. Markers linked to disease resistance can be used to pyramid resistance genes for improved durability and to improve the efficiency of evaluation. To develop molecular markers linked to resistance to grape powdery mildew ...

  16. Discourse Markers in EFL Setting: Perceptions of Turkish EFL Teachers

    ERIC Educational Resources Information Center

    Asik, Asuman

    2015-01-01

    Discourse markers are seen as one of the fundamental units in spoken discourse due to their frequent and multifunctional use by native speakers of English. Discourse markers also have significance in foreign language instruction. In this respect, this study explored the perceptions of Turkish EFL teachers towards the use of discourse markers in…

  17. L-split marker for augmented reality in aircraft assembly

    NASA Astrophysics Data System (ADS)

    Han, Pengfei; Zhao, Gang

    2016-04-01

    In order to improve the performance of conventional square markers widely used by marker-based augmented reality systems in aircraft assembly environments, an L-split marker is proposed. Every marker consists of four separate L-shaped parts and each of them contains partial information about the marker. Geometric features of the L-shape, which are more discriminate than the symmetrical square shape adopted by conventional markers, are used to detect proposed markers from the camera images effectively. The marker is split into four separate parts in order to improve the robustness to occlusion and curvature to some extent. The registration process can be successfully completed as long as three parts are detected (up to about 80% of the area could be occluded). Moreover, when we attach the marker on nonplanar surfaces, the curvature status of the marker can be roughly analyzed with every part's normal direction, which can be obtained since their six corners have been explicitly determined in the previous detection process. And based on the marker design, new detection and recognition algorithms are proposed and detailed. The experimental results show that the marker and the algorithms are effective.

  18. 21 CFR 880.6305 - Ingestible event marker.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Ingestible event marker. 880.6305 Section 880.6305... Devices § 880.6305 Ingestible event marker. (a) Identification. An ingestible event marker is a prescription device used to record time-stamped, patient-logged events. The ingestible component...

  19. 30 CFR 817.11 - Signs and markers.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 3 2013-07-01 2013-07-01 false Signs and markers. 817.11 Section 817.11... ACTIVITIES § 817.11 Signs and markers. (a) Specifications. Signs and markers required under this part shall... durable material; and (4) Conform to local laws and regulations. (b) Duration of maintenance. Signs...

  20. 30 CFR 817.11 - Signs and markers.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 3 2012-07-01 2012-07-01 false Signs and markers. 817.11 Section 817.11... ACTIVITIES § 817.11 Signs and markers. (a) Specifications. Signs and markers required under this part shall... durable material; and (4) Conform to local laws and regulations. (b) Duration of maintenance. Signs...

  1. 30 CFR 817.11 - Signs and markers.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 3 2014-07-01 2014-07-01 false Signs and markers. 817.11 Section 817.11... ACTIVITIES § 817.11 Signs and markers. (a) Specifications. Signs and markers required under this part shall... durable material; and (4) Conform to local laws and regulations. (b) Duration of maintenance. Signs...

  2. 30 CFR 817.11 - Signs and markers.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 3 2010-07-01 2010-07-01 false Signs and markers. 817.11 Section 817.11... ACTIVITIES § 817.11 Signs and markers. (a) Specifications. Signs and markers required under this part shall... durable material; and (4) Conform to local laws and regulations. (b) Duration of maintenance. Signs...

  3. 30 CFR 817.11 - Signs and markers.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 3 2011-07-01 2011-07-01 false Signs and markers. 817.11 Section 817.11... ACTIVITIES § 817.11 Signs and markers. (a) Specifications. Signs and markers required under this part shall... durable material; and (4) Conform to local laws and regulations. (b) Duration of maintenance. Signs...

  4. 14 CFR 171.269 - Marker beacon performance requirements.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 14 Aeronautics and Space 3 2011-01-01 2011-01-01 false Marker beacon performance requirements. 171.269 Section 171.269 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF... Landing System (ISMLS) § 171.269 Marker beacon performance requirements. ISMLS marker beacon...

  5. 14 CFR 171.269 - Marker beacon performance requirements.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 14 Aeronautics and Space 3 2010-01-01 2010-01-01 false Marker beacon performance requirements. 171.269 Section 171.269 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF... Landing System (ISMLS) § 171.269 Marker beacon performance requirements. ISMLS marker beacon...

  6. 14 CFR 171.269 - Marker beacon performance requirements.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 14 Aeronautics and Space 3 2014-01-01 2014-01-01 false Marker beacon performance requirements. 171.269 Section 171.269 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF... Landing System (ISMLS) § 171.269 Marker beacon performance requirements. ISMLS marker beacon...

  7. 14 CFR 171.269 - Marker beacon performance requirements.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 14 Aeronautics and Space 3 2012-01-01 2012-01-01 false Marker beacon performance requirements. 171.269 Section 171.269 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF... Landing System (ISMLS) § 171.269 Marker beacon performance requirements. ISMLS marker beacon...

  8. 14 CFR 171.269 - Marker beacon performance requirements.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 14 Aeronautics and Space 3 2013-01-01 2013-01-01 false Marker beacon performance requirements. 171.269 Section 171.269 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF... Landing System (ISMLS) § 171.269 Marker beacon performance requirements. ISMLS marker beacon...

  9. SSR LINKAGES TO EIGHT ADDITIONAL MORPHOLOGICAL MARKER TRAITS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    More than 1000 morphological markers have been identified in barley. Less than half of these markers have been incorporated into the barley consensus linkage maps. We characterized and mapped eight additional morphological marker traits in this report including one eceriferum (cer-zt.389, three dens...

  10. Detecting a hierarchical genetic population structure via Multi-InDel markers on the X chromosome

    PubMed Central

    Fan, Guang Yao; Ye, Yi; Hou, Yi Ping

    2016-01-01

    Detecting population structure and estimating individual biogeographical ancestry are very important in population genetics studies, biomedical research and forensics. Single-nucleotide polymorphism (SNP) has long been considered to be a primary ancestry-informative marker (AIM), but it is constrained by complex and time-consuming genotyping protocols. Following up on our previous study, we propose that a multi-insertion-deletion polymorphism (Multi-InDel) with multiple haplotypes can be useful in ancestry inference and hierarchical genetic population structures. A validation study for the X chromosome Multi-InDel marker (X-Multi-InDel) as a novel AIM was conducted. Genetic polymorphisms and genetic distances among three Chinese populations and 14 worldwide populations obtained from the 1000 Genomes database were analyzed. A Bayesian clustering method (STRUCTURE) was used to discern the continental origins of Europe, East Asia, and Africa. A minimal panel of ten X-Multi-InDels was verified to be sufficient to distinguish human ancestries from three major continental regions with nearly the same efficiency of the earlier panel with 21 insertion-deletion AIMs. Along with the development of more X-Multi-InDels, an approach using this novel marker has the potential for broad applicability as a cost-effective tool toward more accurate determinations of individual biogeographical ancestry and population stratification. PMID:27535707

  11. Use of Microsatellite and SNP Markers for Biotype Characterization in Hessian Fly

    PubMed Central

    Crane, Yan Ma; Cambron, Sue E.; Crane, Charles F.; Shukle, Richard H.

    2015-01-01

    Exploration of the biotype structure of Hessian fly, Mayetiola destructor (Say) (Diptera: Cecidomyiidae), would improve our knowledge regarding variation in virulence phenotypes and difference in genetic background. Microsatellites (simple sequence repeats) and single-nucleotide polymorphisms (SNPs) are highly variable genetic markers that are widely used in population genetic studies. This study developed and tested a panel of 18 microsatellite and 22 SNP markers to investigate the genetic structure of nine Hessian fly biotypes: B, C, D, E, GP, L, O, vH9, and vH13. The simple sequence repeats were more polymorphic than the SNP markers, and their neighbor-joining trees differed in consequence. Microsatellites suggested a simple geographic association of related biotypes that did not progressively gain virulence with increasing genetic distance from a founder type. Use of the k-means clustering algorithm in the STRUCTURE program shows that the nine biotypes comprise six to eight populations that are related to geography or history within laboratory cultures. PMID:26543089

  12. Population structure and genotypic variation of Crataegus pontica inferred by molecular markers.

    PubMed

    Rahmani, Mohammad-Shafie; Shabanian, Naghi; Khadivi-Khub, Abdollah; Woeste, Keith E; Badakhshan, Hedieh; Alikhani, Leila

    2015-11-01

    Information about the natural patterns of genetic variability and their evolutionary bases are of fundamental practical importance for sustainable forest management and conservation. In the present study, the genetic diversity of 164 individuals from fourteen natural populations of Crataegus pontica K.Koch was assessed for the first time using three genome-based molecular techniques; inter-retrotransposon amplified polymorphism (IRAP); inter-simple sequence repeats (ISSR) and start codon targeted (SCoT) polymorphism. IRAP, ISSR and SCoT analyses yielded 126, 254 and 199 scorable amplified bands, respectively, of which 90.48, 93.37 and 83.78% were polymorphic. ISSR revealed efficiency over IRAP and SCoT due to high effective multiplex ratio, marker index and resolving power. The dendrograms based on the markers used and combined data divided individuals into three major clusters. The correlation between the coefficient matrices for the IRAP, ISSR and SCoT data was significant. A higher level of genetic variation was observed within populations than among populations based on the markers used. The lower divergence levels depicted among the studied populations could be seen as evidence of gene flow. The promotion of gene exchange will be very beneficial to conserve and utilize the enormous genetic variability. PMID:26143753

  13. Detecting a hierarchical genetic population structure via Multi-InDel markers on the X chromosome.

    PubMed

    Fan, Guang Yao; Ye, Yi; Hou, Yi Ping

    2016-01-01

    Detecting population structure and estimating individual biogeographical ancestry are very important in population genetics studies, biomedical research and forensics. Single-nucleotide polymorphism (SNP) has long been considered to be a primary ancestry-informative marker (AIM), but it is constrained by complex and time-consuming genotyping protocols. Following up on our previous study, we propose that a multi-insertion-deletion polymorphism (Multi-InDel) with multiple haplotypes can be useful in ancestry inference and hierarchical genetic population structures. A validation study for the X chromosome Multi-InDel marker (X-Multi-InDel) as a novel AIM was conducted. Genetic polymorphisms and genetic distances among three Chinese populations and 14 worldwide populations obtained from the 1000 Genomes database were analyzed. A Bayesian clustering method (STRUCTURE) was used to discern the continental origins of Europe, East Asia, and Africa. A minimal panel of ten X-Multi-InDels was verified to be sufficient to distinguish human ancestries from three major continental regions with nearly the same efficiency of the earlier panel with 21 insertion-deletion AIMs. Along with the development of more X-Multi-InDels, an approach using this novel marker has the potential for broad applicability as a cost-effective tool toward more accurate determinations of individual biogeographical ancestry and population stratification. PMID:27535707

  14. SAT, a flexible and optimized Web application for SSR marker development

    PubMed Central

    Dereeper, Alexis; Argout, Xavier; Billot, Claire; Rami, Jean-François; Ruiz, Manuel

    2007-01-01

    Background Simple Sequence Repeats (SSRs), or microsatellites, are among the most powerful genetic markers known. A common method for the development of SSR markers is the construction of genomic DNA libraries enriched for SSR sequences, followed by DNA sequencing. However, designing optimal SSR markers from bulk sequence data is a laborious and time-consuming process. Results SAT (SSR Analysis Tool) is a user-friendly Web application developed to minimize tedious manual operations and reduce errors. This tool facilitates the integration, analysis and display of sequence data from SSR-enriched libraries. SAT is designed to successively perform base calling and quality evaluation of chromatograms, eliminate cloning vector, adaptors and low quality sequences, detect chimera or partially digested sequences, search for SSR motifs, cluster and assemble the redundant sequences, and design SSR primer pairs. An additional virtual PCR step establishes primer specificity. Users may modify the different parameters of each step of the SAT analysis. Although certain steps are compulsory, such as SSR motifs search and sequence assembly, users do not have to run the entire pipeline, and they can choose selectively which steps to perform. A database allows users to store and query results, and to redo individual steps of the workflow. Conclusion The SAT Web application is available at , and a standalone command-line version is also freely downloadable. Users must send an email to the SAT administrator tropgene@cirad.fr to request a login and password. PMID:18047663

  15. Diversity in 113 cowpea [Vigna unguiculata (L) Walp] accessions assessed with 458 SNP markers.

    PubMed

    Egbadzor, Kenneth F; Ofori, Kwadwo; Yeboah, Martin; Aboagye, Lawrence M; Opoku-Agyeman, Michael O; Danquah, Eric Y; Offei, Samuel K

    2014-01-01

    Single Nucleotide Polymorphism (SNP) markers were used in characterization of 113 cowpea accessions comprising of 108 from Ghana and 5 from abroad. Leaf tissues from plants cultivated at the University of Ghana were genotyped at KBioscience in the United Kingdom. Data was generated for 477 SNPs, out of which 458 revealed polymorphism. The results were used to analyze genetic dissimilarity among the accessions using Darwin 5 software. The markers discriminated among all of the cowpea accessions and the dissimilarity values which ranged from 0.006 to 0.63 were used for factorial plot. Unexpected high levels of heterozygosity were observed on some of the accessions. Accessions known to be closely related clustered together in a dendrogram drawn with WPGMA method. A maximum length sub-tree which comprised of 48 core accessions was constructed. The software package structure was used to separate accessions into three groups, and the programme correctly identified varieties that were known hybrids. The hybrids were those accessions with numerous heterozygous loci. The structure plot showed closely related accessions with similar genome patterns. The SNP markers were more efficient in discriminating among the cowpea germplasm than morphological, seed protein polymorphism and simple sequence repeat studies reported earlier on the same collection. PMID:25332852

  16. A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.)

    PubMed Central

    2009-01-01

    Background Chickpea (Cicer arietinum L.), an important grain legume crop of the world is seriously challenged by terminal drought and salinity stresses. However, very limited number of molecular markers and candidate genes are available for undertaking molecular breeding in chickpea to tackle these stresses. This study reports generation and analysis of comprehensive resource of drought- and salinity-responsive expressed sequence tags (ESTs) and gene-based markers. Results A total of 20,162 (18,435 high quality) drought- and salinity- responsive ESTs were generated from ten different root tissue cDNA libraries of chickpea. Sequence editing, clustering and assembly analysis resulted in 6,404 unigenes (1,590 contigs and 4,814 singletons). Functional annotation of unigenes based on BLASTX analysis showed that 46.3% (2,965) had significant similarity (≤1E-05) to sequences in the non-redundant UniProt database. BLASTN analysis of unique sequences with ESTs of four legume species (Medicago, Lotus, soybean and groundnut) and three model plant species (rice, Arabidopsis and poplar) provided insights on conserved genes across legumes as well as novel transcripts for chickpea. Of 2,965 (46.3%) significant unigenes, only 2,071 (32.3%) unigenes could be functionally categorised according to Gene Ontology (GO) descriptions. A total of 2,029 sequences containing 3,728 simple sequence repeats (SSRs) were identified and 177 new EST-SSR markers were developed. Experimental validation of a set of 77 SSR markers on 24 genotypes revealed 230 alleles with an average of 4.6 alleles per marker and average polymorphism information content (PIC) value of 0.43. Besides SSR markers, 21,405 high confidence single nucleotide polymorphisms (SNPs) in 742 contigs (with ≥ 5 ESTs) were also identified. Recognition sites for restriction enzymes were identified for 7,884 SNPs in 240 contigs. Hierarchical clustering of 105 selected contigs provided clues about stress- responsive candidate genes

  17. Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea)

    PubMed Central

    Cuc, Luu M; Mace, Emma S; Crouch, Jonathan H; Quang, Vu D; Long, Tran D; Varshney, Rajeev K

    2008-01-01

    Background Cultivated peanut or groundnut (Arachis hypogaea L.) is the fourth most important oilseed crop in the world, grown mainly in tropical, subtropical and warm temperate climates. Due to its origin through a single and recent polyploidization event, followed by successive selection during breeding efforts, cultivated groundnut has a limited genetic background. In such species, microsatellite or simple sequence repeat (SSR) markers are very informative and useful for breeding applications. The low level of polymorphism in cultivated germplasm, however, warrants a need of larger number of polymorphic microsatellite markers for cultivated groundnut. Results A microsatellite-enriched library was constructed from the genotype TMV2. Sequencing of 720 putative SSR-positive clones from a total of 3,072 provided 490 SSRs. 71.2% of these SSRs were perfect type, 13.1% were imperfect and 15.7% were compound. Among these SSRs, the GT/CA repeat motifs were the most common (37.6%) followed by GA/CT repeat motifs (25.9%). The primer pairs could be designed for a total of 170 SSRs and were optimized initially on two genotypes. 104 (61.2%) primer pairs yielded scorable amplicon and 46 (44.2%) primers showed polymorphism among 32 cultivated groundnut genotypes. The polymorphic SSR markers detected 2 to 5 alleles with an average of 2.44 per locus. The polymorphic information content (PIC) value for these markers varied from 0.12 to 0.75 with an average of 0.46. Based on 112 alleles obtained by 46 markers, a phenogram was constructed to understand the relationships among the 32 genotypes. Majority of the genotypes representing subspecies hypogaea were grouped together in one cluster, while the genotypes belonging to subspecies fastigiata were grouped mainly under two clusters. Conclusion Newly developed set of 104 markers extends the repertoire of SSR markers for cultivated groundnut. These markers showed a good level of PIC value in cultivated germplasm and therefore would be

  18. Assessment of genetic diversity among faba bean genotypes using agro-morphological and molecular markers.

    PubMed

    Ammar, Megahed H; Alghamdi, Salem S; Migdadi, Hussein M; Khan, Muhammad A; El-Harty, Ehab H; Al-Faifi, Sulieman A

    2015-05-01

    Forty faba bean (Vicia faba L.) genotypes were evaluated for their agro-morphological performance and molecular diversity under Central Region of Saudi Arabia conditions during 2010-11 and 2011-12 seasons. Field performance results showed that faba genotypes exhibited a significant amount of variation for their agro-morphological studied parameters. Giza40 recorded the tallest genotype (139.5 cm), highest number of seeds per plants (100.8), and the highest seed yield per plant (70.8 g). The best performing genotypes were Giza40, FLIP03-014FB, Gazira1 and Goff1. Genetic variability among genotypes was determined using Sequence Related Amplified Polymorphism (SRAP) and Amplified Fragment Length Polymorphism (AFLP) markers. A total of 183 amplified fragments (alleles) and 1758 polymorphic fragments (bands) in SRAP and 202 alleles and 716 bands in AFLP were obtained using six SRAP and four AFLP primer combinations respectively. Polymorphism information content (PIC) values for AFLP and SRAP markers were higher than 0.8, indicating the existence of a considerable amount of genetic diversity among faba tested genotypes. The UPGMA based clustering of faba genotypes was largely based on origin and/or genetic background. Result of cluster analysis based on SRAP showed weak and not significant correlation while, it was highly significant based on AFLP analysis with agro-morphological characters (r = 0.01, p > 0.54 and r = 0.26, p < 0.004 respectively). Combined SRAP and AFLP markers proved to be significantly useful for genetic diversity assessment at molecular level. They exhibited high discrimination power, and were able to distinguish the faba bean genotypes with high efficiency and accuracy levels. PMID:25972757

  19. Assessment of genetic diversity among faba bean genotypes using agro-morphological and molecular markers

    PubMed Central

    Ammar, Megahed H.; Alghamdi, Salem S.; Migdadi, Hussein M.; Khan, Muhammad A.; El-Harty, Ehab H.; Al-Faifi, Sulieman A.

    2015-01-01

    Forty faba bean (Vicia faba L.) genotypes were evaluated for their agro-morphological performance and molecular diversity under Central Region of Saudi Arabia conditions during 2010–11 and 2011–12 seasons. Field performance results showed that faba genotypes exhibited a significant amount of variation for their agro-morphological studied parameters. Giza40 recorded the tallest genotype (139.5 cm), highest number of seeds per plants (100.8), and the highest seed yield per plant (70.8 g). The best performing genotypes were Giza40, FLIP03-014FB, Gazira1 and Goff1. Genetic variability among genotypes was determined using Sequence Related Amplified Polymorphism (SRAP) and Amplified Fragment Length Polymorphism (AFLP) markers. A total of 183 amplified fragments (alleles) and 1758 polymorphic fragments (bands) in SRAP and 202 alleles and 716 bands in AFLP were obtained using six SRAP and four AFLP primer combinations respectively. Polymorphism information content (PIC) values for AFLP and SRAP markers were higher than 0.8, indicating the existence of a considerable amount of genetic diversity among faba tested genotypes. The UPGMA based clustering of faba genotypes was largely based on origin and/or genetic background. Result of cluster analysis based on SRAP showed weak and not significant correlation while, it was highly significant based on AFLP analysis with agro-morphological characters (r = 0.01, p > 0.54 and r = 0.26, p < 0.004 respectively). Combined SRAP and AFLP markers proved to be significantly useful for genetic diversity assessment at molecular level. They exhibited high discrimination power, and were able to distinguish the faba bean genotypes with high efficiency and accuracy levels. PMID:25972757

  20. Genetic bottlenecks in Turkish okra germplasm and utility of iPBS retrotransposon markers for genetic diversity assessment.

    PubMed

    Yıldız, M; Koçak, M; Baloch, F S

    2015-01-01

    Lack of requisite genetic variation in Turkish okra has necessitated the use of different types of markers for estimating the genetic diversity and identifying the source of variation. Transposable elements, present abundantly in plant genomes, generate genomic diversity through their replication and are thus an excellent source of molecular markers. We hypothesized that inter-primer binding site (iPBS)-retrotransposons could be the source of variation because of their genome plasticity nature. In the present study, genetic diversity of 66 okra landraces was analyzed using iPBS-retrotransposon markers. iPBS-retrotransposons detected 88 bands with 40.2% polymorphism and an average of 6.8 bands per primer. Gene diversity and Shannon's information index ranged from 0.01 to 0.13 and 0.02 to 0.21 for iPBS-retrotransposons and from 0.06 to 0.46 and 0.14 to 0.65 for simple sequence repeat (SSR) markers, respectively. Polymorphism information content value for retrotransposons varied between 0.12 and 0.99, while that for SSR was from 0.52 to 0.81. Neighbor joining analysis based on retrotransposons and SSRs divided all the accessions into four clusters; however, SSR markers were more efficient in clustering the landraces based on their origin. Using the STRUCTURE software for determining population structure, and two populations (at the number of hypothetical subpopulations, K = 2) were identified among the landraces. Low genetic diversity in Turkish okra highlights the need for the introduction of plants from countries with greater genetic diversity for these crops. This study also demonstrates the utility and role of iPBS-retrotransposons, a dominant and ubiquitous part of eukaryotic genomes, for diversity studies in okra. PMID:26400290