Avoidance of Long Mononucleotide Repeats in Codon Pair Usage

Protein is an essential component for life, and its synthesis is mediated by codons in any organisms on earth. While some codons encode the same amino acid, their usage is often highly biased. There are many factors that can cause the bias, but a potential effect of mononucleotide repeats, which are known to be highly mutable, on codon usage and codon pair preference is largely unknown. In this study we performed a genomic survey on the relationship between mononucleotide repeats and codon pair bias in 53 bacteria, 68 archaea, and 13 eukaryotes. By distinguishing the codon pair bias from the codon usage bias, four general patterns were revealed: strong avoidance of five or six mononucleotide repeats in codon pairs; lower observed/expected (o/e) ratio for codon pairs with C or G repeats (C/G pairs) than that with A or T repeats (A/T pairs); a negative correlation between genomic GC contents and the o/e ratios, particularly for C/G pairs; and avoidance of C/G pairs in highly conserved genes. These results support natural selection against long mononucleotide repeats, which could induce frameshift mutations in coding sequences. The fact that these patterns are found in all kingdoms of life suggests that this is a general phenomenon in living organisms. Thus, long mononucleotide repeats may play an important role in base composition and genetic stability of a gene and gene functions.

Recognition of familiar and unfamiliar music in normal aging and Alzheimer's disease

We tested normal young and elderly adults and elderly Alzheimer’s disease (AD) patients on recognition memory for tunes. In Experiment 1, AD patients and age-matched controls received a study list and an old/new recognition test of highly familiar, traditional tunes, followed by a study list and test of novel tunes. The controls performed better than did the AD patients. The controls showed the “mirror effect” of increased hits and reduced false alarms for traditional versus novel tunes, whereas the patients false-alarmed as often to traditional tunes as to novel tunes. Experiment 2 compared young adults and healthy elderly persons using a similar design. Performance was lower in the elderly group, but both younger and older subjects showed the mirror effect. Experiment 3 produced confusion between preexperimental familiarity and intraexperimental familiarity by mixing traditional and novel tunes in the study lists and tests. Here, the subjects in both age groups resembled the patients of Experiment 1 in failing to show the mirror effect. Older subjects again performed more poorly, and they differed qualitatively from younger subjects in setting stricter criteria for more nameable tunes. Distinguishing different sources of global familiarity is a factor in tune recognition, and the data suggest that this type of source monitoring is impaired in AD and involves different strategies in younger and older adults.

Reconstruction and 3D visualisation based on objective real 3D based documentation

Reconstructions based directly upon forensic evidence alone are called primary information. Historically this consists of documentation of findings by verbal protocols, photographs and other visual means. Currently modern imaging techniques such as 3D surface scanning and radiological methods (Computer Tomography, Magnetic Resonance Imaging) are also applied. Secondary interpretation is based on facts and the examiner's experience. Usually such reconstructive expertises are given in written form, and are often enhanced by sketches. However, narrative interpretations can, especially in complex courses of action, be difficult to present and can be misunderstood. In this report we demonstrate the use of graphic reconstruction of secondary interpretation with supporting pictorial evidence, applying digital visualisation (using 'Poser') or scientific animation (using '3D Studio Max', 'Maya') and present methods of clearly distinguishing between factual documentation and examiners' interpretation based on three cases. The first case involved a pedestrian who was initially struck by a car on a motorway and was then run over by a second car. The second case involved a suicidal gunshot to the head with a rifle, in which the trigger was pushed with a rod. The third case dealt with a collision between two motorcycles. Pictorial reconstruction of the secondary interpretation of these cases has several advantages. The images enable an immediate overview, give rise to enhanced clarity, and compel the examiner to look at all details if he or she is to create a complete image.

Yolk Androstenedione in Domestic Chicks (Gallus Gallus Domesticus): Uptake and Sex-Dependent Alteration of Growth and Behavior

In birds, causes and consequences of variation in maternally-derived steroids in egg yolk have been the subject of intense experimentation. Many studies have quantified or manipulated testosterone ("T") and one of its immediate precursors, androstenedione ("A4") - often lumping the two steroids as "androgens" and treating them as functionally equivalent. However, yolk A4 is deposited in substantially higher concentrations than T, binds only weakly to the androgen receptor, and is readily converted into either T or estrone by steroidogenic enzymes present during embryonic development. Thus it may not be appropriate to assume that A4 has the same effect as T. In addition, A4's metabolic fate is likely to differ between females and males. The goals of this study were to examine the sex-specific uptake and metabolism of yolk A4 and consequences of elevated levels of yolk A4 on development and behavior of domestic chicks. Eggs were injected with 2mu Ci of tritiated androstenedione; radioactivity was detected in all tissues of day 7 and day 16 embryos and found in both aqueous and organics phases of day 7 yolk, with no difference between sexes. A second set of eggs was injected with 125ng of A4. A4 increased growth of morphological traits (tarsus, beak) in females, but not males. A4 males had smaller combs than controls; there was no treatment effect in females. A4 reduced tonic immobility behavior in both sexes. The results of this study illustrate the importance of distinguishing both between androgens and between sexes when investigating avian endocrine maternal effects. Copyright 2013 Elsevier Inc. All rights reserved.

Exploring High-resolution Magic Angle Spinning (HR-MAS) NMR Spectroscopy for Metabonomic Analysis of Apples

Classical liquid-state high-resolution (HR) NMR spectroscopy has proved a powerful tool in the metabonomic analysis of liquid food samples like fruit juices. In this paper the application of (1)H high-resolution magic angle spinning (HR-MAS) NMR spectroscopy to apple tissue is presented probing its potential for metabonomic studies. The (1)H HR-MAS NMR spectra are discussed in terms of the chemical composition of apple tissue and compared to liquid-state NMR spectra of apple juice. Differences indicate that specific metabolic changes are induced by juice preparation. The feasibility of HR-MAS NMR-based multivariate analysis is demonstrated by a study distinguishing three different apple cultivars by principal component analysis (PCA). Preliminary results are shown from subsequent studies comparing three different cultivation methods by means of PCA and partial least squares discriminant analysis (PLS-DA) of the HR-MAS NMR data. The compounds responsible for discriminating organically grown apples are discussed. Finally, an outlook of our ongoing work is given including a longitudinal study on apples.

MicroRNA Expression Array Identifies Novel Diagnostic Markers for Conventional and Oncocytic Follicular Thyroid Carcinomas

Objective:The most difficult thyroid tumors to be diagnosed by cytology and histology are conventional follicular carcinomas (cFTCs) and oncocytic follicular carcinomas (oFTCs). Several microRNAs (miRNAs) have been previously found to be consistently deregulated in papillary thyroid carcinomas; however, very limited information is available for cFTC and oFTC. The aim of this study was to explore miRNA deregulation and find candidate miRNA markers for follicular carcinomas that can be used diagnostically.Design:Thirty-eight follicular thyroid carcinomas (21 cFTCs, 17 oFTCs) and 10 normal thyroid tissue samples were studied for expression of 381 miRNAs using human microarray assays. Expression of deregulated miRNAs was confirmed by individual RT-PCR assays in all samples. In addition, 11 follicular adenomas, two hyperplastic nodules (HNs), and 19 fine-needle aspiration samples were studied for expression of novel miRNA markers detected in this study.Results:The unsupervised hierarchical clustering analysis demonstrated individual clusters for cFTC and oFTC, indicating the difference in miRNA expression between these tumor types. Both cFTCs and oFTCs showed an up-regulation of miR-182/-183/-221/-222/-125a-3p and a down-regulation of miR-542-5p/-574-3p/-455/-199a. Novel miRNA (miR-885-5p) was found to be strongly up-regulated (>40-fold) in oFTCs but not in cFTCs, follicular adenomas, and HNs. The classification and regression tree algorithm applied to fine-needle aspiration samples demonstrated that three dysregulated miRNAs (miR-885-5p/-221/-574-3p) allowed distinguishing follicular thyroid carcinomas from benign HNs with high accuracy.Conclusions:In this study we demonstrate that different histopathological types of follicular thyroid carcinomas have distinct miRNA expression profiles. MiR-885-5p is highly up-regulated in oncocytic follicular carcinomas and may serve as a diagnostic marker for these tumors. A small set of deregulated miRNAs allows for an accurate discrimination between follicular carcinomas and hyperplastic nodules and can be used diagnostically in fine-needle aspiration biopsies.

Ranking of parameters of pain hypersensitivity according to their discriminative ability in chronic low back pain

Low back pain is associated with plasticity changes and central hypersensitivity in a subset of patients. We performed a case-control study to explore the discriminative ability of different quantitative sensory tests in distinguishing between 40 cases with chronic low back pain and 300 pain-free controls, and to rank these tests according to the extent of their association with chronic pain. Gender, age, height, weight, body mass index, and psychological measures were recorded as potential confounders. We used 26 quantitative sensory tests, including different modalities of pressure, heat, cold, and electrical stimulation. As measures of discrimination, we estimated receiver operating characteristics (ROC) and likelihood ratios. Six tests seemed useful (in order of their discriminative ability): (1) pressure pain detection threshold at the site of most severe pain (fitted area under the ROC, 0.87), (2) single electrical stimulation pain detection threshold (0.87), (3) single electrical stimulation reflex threshold (0.83), (4) pressure pain tolerance threshold at the site of most severe pain (0.81), (5) pressure pain detection threshold at suprascapular region (0.80), and (6) temporal summation pain threshold (0.80). Pressure and electrical pain modalities seemed most promising and may be used for diagnosis of pain hypersensitivity and potentially for identifying individuals at risk of developing chronic low back pain over time.

Pediatric and adult eosinophilic esophagitis: similarities and differences

Early in the 1990s, several case series described adults suffering from dysphagia and children with refractory reflux symptoms, both accompanied by an eosinophil-predominant infiltration, thereby conclusively distinguishing it from gastroesophageal reflux disease. Eosinophilic esophagitis (EoE) was recognized as its own entity in the adult and in the pediatric literature. In the last decade, evidence has accumulated that EoE represents a T-helper (Th)2-type inflammatory disease. Remodeling of the esophagus is a hallmark of EoE, leading to esophageal dysfunction and bolus impaction. Familial occurrence and disease association with single-nucleotide polymorphisms underscore the influence of genetics in this disease. Eosinophilic esophagitis may affect individuals at any age, although the clinical presentation is highly age dependent. There is a significant allergic bias in the EoE population, with the majority of patients having concurrent allergic rhinitis, asthma, eczema, and/or a history of atopy. One noteworthy difference is that in children, EoE seems to be primarily a food antigen-driven disease, whereas in adults, mainly aeroallergen sensitization has been observed. Treatment modalities for EoE include the 3Ds: drugs, diet, and dilation. The crucial question of whether adult and pediatric EoE are different phenotypes of one single entity or whether we are confronted with two different diseases is still open. Here, we review similarities and differences between EoE in adults and children.

Compensation, Incentives and Risk: Economic Theory and Russian Practise

Mr. Pechersky set out to examine a specific feature of the employer-employee relationship in Russian business organisations. He wanted to study to what extent the so-called "moral hazard" is being solved (if it is being solved at all), whether there is a relationship between pay and performance, and whether there is a correlation between economic theory and Russian reality. Finally, he set out to construct a model of the Russian economy that better reflects the way it actually functions than do certain other well-known models (for example models of incentive compensation, the Shapiro-Stiglitz model etc.). His report was presented to the RSS in the form of a series of manuscripts in English and Russian, and on disc, with many tables and graphs. He begins by pointing out the different examples of randomness that exist in the relationship between employee and employer. Firstly, results are frequently affected by circumstances outside the employee's control that have nothing to do with how intelligently, honestly, and diligently the employee has worked. When rewards are based on results, uncontrollable randomness in the employee's output induces randomness in their incomes. A second source of randomness involves the outside events that are beyond the control of the employee that may affect his or her ability to perform as contracted. A third source of randomness arises when the performance itself (rather than the result) is measured, and the performance evaluation procedures include random or subjective elements. Mr. Pechersky's study shows that in Russia the third source of randomness plays an important role. Moreover, he points out that employer-employee relationships in Russia are sometimes opposite to those in the West. Drawing on game theory, he characterises the Western system as follows. The two players are the principal and the agent, who are usually representative individuals. The principal hires an agent to perform a task, and the agent acquires an information advantage concerning his actions or the outside world at some point in the game, i.e. it is assumed that the employee is better informed. In Russia, on the other hand, incentive contracts are typically negotiated in situations in which the employer has the information advantage concerning outcome. Mr. Pechersky schematises it thus. Compensation (the wage) is W and consists of a base amount, plus a portion that varies with the outcome, x. So W = a + bx, where b is used to measure the intensity of the incentives provided to the employee. This means that one contract will be said to provide stronger incentives than another if it specifies a higher value for b. This is the incentive contract as it operates in the West. The key feature distinguishing the Russian example is that x is observed by the employer but is not observed by the employee. So the employer promises to pay in accordance with an incentive scheme, but since the outcome is not observable by the employee the contract cannot be enforced, and the question arises: is there any incentive for the employer to fulfil his or her promises? Mr. Pechersky considers two simple models of employer-employee relationships displaying the above type of information symmetry. In a static framework the obtained result is somewhat surprising: at the Nash equilibrium the employer pays nothing, even though his objective function contains a quadratic term reflecting negative consequences for the employer if the actual level of compensation deviates from the expectations of the employee. This can lead, for example, to labour turnover, or the expenses resulting from a bad reputation. In a dynamic framework, the conclusion can be formulated as follows: the higher the discount factor, the higher the incentive for the employer to be honest in his/her relationships with the employee. If the discount factor is taken to be a parameter reflecting the degree of (un)certainty (the higher the degree of uncertainty is, the lower is the discount factor), we can conclude that the answer to the formulated question depends on the stability of the political, social and economic situation in a country. Mr. Pechersky believes that the strength of a market system with private property lies not just in its providing the information needed to compute an efficient allocation of resources in an efficient manner. At least equally important is the manner in which it accepts individually self-interested behaviour, but then channels this behaviour in desired directions. People do not have to be cajoled, artificially induced, or forced to do their parts in a well-functioning market system. Instead, they are simply left to pursue their own objectives as they see fit. Under the right circumstances, people are led by Adam Smith's "invisible hand" of impersonal market forces to take the actions needed to achieve an efficient, co-ordinated pattern of choices. The problem is that, as Mr. Pechersky sees it, there is no reason to believe that the circumstances in Russia are right, and the invisible hand is doing its work properly. Political instability, social tension and other circumstances prevent it from doing so. Mr. Pechersky believes that the discount factor plays a crucial role in employer-employee relationships. Such relationships can be considered satisfactory from a normative point of view, only in those cases where the discount factor is sufficiently large. Unfortunately, in modern Russia the evidence points to the typical discount factor being relatively small. This fact can be explained as a manifestation of aversion to risk of economic agents. Mr. Pechersky hopes that when political stabilisation occurs, the discount factors of economic agents will increase, and the agent's behaviour will be explicable in terms of more traditional models.

Social Policy Facing the Problems of Youth Employment

Rumiana Stoilova (Bulgaria). Social Policy Facing the Problems of Youth Employment. Ms. Stoilova is a researcher in the Institute of Sociology in Sofia and worked on this project from October 1996 to September 1998. This project involved collecting both statistical and empirical data on the state of youth employment in Bulgaria, which was then compared with similar data from other European countries. One significant aspect was the parallel investigation of employment and unemployment, which took as a premise the continuity of professional experience where unemployment is just a temporary condition caused by external and internal factors. These need to be studied and changed on a systematic basis so as to create a more favourable market situation and to improve individuals' resources for improving their market opportunities. A second important aspect of the project was an analysis of the various entities active on the labour market, including government and private institutions, associations of unemployed persons, of employers or of trade unions, all with their specific legal powers and interests, and of the problems in communication between these. The major trends in youth unemployment during the period studied include a high proportion of the registered unemployed who are not eligible for social assistance, a lengthening of the average period of unemployment, an increase in the percentage of people who are unemployed for the first time and an increasing percentage of these who are not eligible for assistance, particularly among newly registered young people. At the same time the percentage of those for who work has been found is rising and during the last three years an increasing number of the unemployed have started some independent economic activity. Regional differences are also considerable and in the case of the Haskovo region represent a danger of losing the youngest generation, with resulting negative demographic effects. One major weakness of the existing institutional structure is the large scale of the black labour market, with clear negative implications for the young people drawn into it. The role of non-governmental organisations in providing support and information for the unemployed is growing and the government has recently introduced special preferences for organisations offering jobs to unemployed persons. Social policy in the labour market has however been largely restricted to passive measures, mostly because of the risk that poverty poses to people continuously excluded from the labour market. Among the active measures taken, well over half are concerned with providing jobs for the unemployed and there are very limited programmes for providing or improving qualifications. The nature of youth employment in Bulgaria can be seen in the influence of sustained structures (generation) and institutions (family and school). Ms. Stoilova studied the situation of the modern generation through a series of profiles, mostly those of continuously unemployed and self-employed persons, but also distinguishing between students and the unemployed, and between high school and university students. The different categories of young people were studied in separate mini-studies and the survey was carried out in five town in order to gather objective and subjective information on the state of the labour market in the different regions. She conducted interviews with several hundred young people covering questions of family background, career plans, attitudes to the labour situation and government measures to deal with it, and such questions as independence, mobility, attitude to work, etc. The interviews with young people unemployed for a long period of time show the risk involved in starting work and its link with dynamics of economic development. Their approval of structural reforms, of the financial restrictions connected with the introduction of a currency board and the inevitability of unemployment was largely declarative. The findings indicate that the continuously unemployed need practical knowledge and skills to "translate" the macroeconomic realities in concrete alternatives of individual work and initiative. The unemployed experience their exclusion from the labour market not only as a professional problem but also as an existential threat, of poverty, forced mobility and dependence on their parents' generation. The exclusion from the market of goods and services means more than just exercising restraint in their consumption, as it places restrictions on their personal development. Ms. Stoilova suggests that more efficient ways of providing financial aid and mobilisation are needed to counteract the social disintegration and marginalisation of the continuously unemployed. In measuring the speed of reform, university students took both employment opportunities and the implementation of the meritocratic principle in employment into account. When offered a hypothetical choice between a well-paid job and work in one's own profession, 62% would prefer opt for the well-paid job and for working for a company that offered career opportunities rather than employment in a family or own company. While most see the information gained during their studies as useful and interesting, relatively few see their education as competitive on a wider level and many were pessimistic about employment opportunities based on their qualifications. Very similar attitudes were found among high school students, with differences being due rather to family and personal situations. The unemployed, on the other hand, placed greater emphasis on possibilities of gaining or improving qualifications on a job and for the opportunities it would offer for personal contacts. High school students tend to attribute more significance to opportunities for personal accomplishment. A significant difference that five times fewer high school students were willing to work for state-owned companies, and many fewer expected to find permanent employment or to find a job in the area where they lived, Within the family situation, actual support for children seems to be higher than the feelings of confidence expressed in interviews. The attitudes of the families towards past experience seems to be linked with their ability to cope with the difficulties of the present, with those families which show an optimistic and active attitude towards the future having a greater respect for parents experience and tolerance in communication between parents and children.

Implications of Transdisciplinarity for Sustainability Research

In ecological economics the terms sustainable development and transdisciplinarity are closely related. It is shown that this close relation is due to the fact that research for sustainable development has to be issue oriented and reflect the diversity, complexity and dynamics of the processes involved as well as their variability between specific problem situations. Furthermore, the knowledge of people involved and their needs and interests at stake have to be taken into account. There are three basic and interrelated questions about issues to be addressed in sustainability research: (1) In which way do processes constitute a problem field and where are the needs for change? (2) What are more sustainable practices? (3) How can existing practices be transformed? To treat them properly, transdisciplinary research is needed. The emergence of transdisciplinary research in the North and the South is described. By distinguishing analytically among basic, applied and transdisciplinary research the challenges that have to be tackled in transdisciplinary projects are analyzed.

Regulation of ecto-5'-nucleotidase activity via Ca2+-dependent, annexin 2-mediated membrane rearrangement?

The spatial segregation of the plasma membrane plays a prominent role in distinguishing and sorting a large number of signals a cell receives simultaneously. The plasma membrane comprises regions known as lipid rafts, which serve as signal-transduction hubs and platforms for sorting membrane-associated proteins. Ca(2+)-binding proteins of the annexin family have been ascribed a role in the regulation of raft dynamics. Glycosylphosphatidylinositol-anchored 5'-nucleotidase is an extracellular, raft-associated enzyme responsible for conversion of extracellular ATP into adenosine. Our results point to a regulation of ecto-5'-nucleotidase activity by Ca(2+)-dependent, annexin-mediated stabilization of membrane rafts.

A Data-Analytic Strategy for Protein-Biomarker Discovery: Profiling of High-Dimensional Proteomic Data for Cancer Detection

With recent advances in mass spectrometry techniques, it is now possible to investigate proteins over a wide range of molecular weights in small biological specimens. This advance has generated data-analytic challenges in proteomics, similar to those created by microarray technologies in genetics, namely, discovery of "signature" protein profiles specific to each pathologic state (e.g., normal vs. cancer) or differential profiles between experimental conditions (e.g., treated by a drug of interest vs. untreated) from high-dimensional data. We propose a data analytic strategy for discovering protein biomarkers based on such high-dimensional mass-spectrometry data. A real biomarker-discovery project on prostate cancer is taken as a concrete example throughout the paper: the project aims to identify proteins in serum that distinguish cancer, benign hyperplasia, and normal states of prostate using the Surface Enhanced Laser Desorption/Ionization (SELDI) technology, a recently developed mass spectrometry technique. Our data analytic strategy takes properties of the SELDI mass-spectrometer into account: the SELDI output of a specimen contains about 48,000 (x, y) points where x is the protein mass divided by the number of charges introduced by ionization and y is the protein intensity of the corresponding mass per charge value, x, in that specimen. Given high coefficients of variation and other characteristics of protein intensity measures (y values), we reduce the measures of protein intensities to a set of binary variables that indicate peaks in the y-axis direction in the nearest neighborhoods of each mass per charge point in the x-axis direction. We then account for a shifting (measurement error) problem of the x-axis in SELDI output. After these pre-analysis processing of data, we combine the binary predictors to generate classification rules for cancer, benign hyperplasia, and normal states of prostate. Our approach is to apply the boosting algorithm to select binary predictors and construct a summary classifier. We empirically evaluate sensitivity and specificity of the resulting summary classifiers with a test dataset that is independent from the training dataset used to construct the summary classifiers. The proposed method performed nearly perfectly in distinguishing cancer and benign hyperplasia from normal. In the classification of cancer vs. benign hyperplasia, however, an appreciable proportion of the benign specimens were classified incorrectly as cancer. We discuss practical issues associated with our proposed approach to the analysis of SELDI output and its application in cancer biomarker discovery.

MRI for differentiating ganglion and synovitis in the chronic painful wrist

OBJECTIVE: The purpose of our study was to determine if preoperative MRI can differentiate between occult ganglion and synovitis in the chronic painful wrist. CONCLUSION: MRI is accurate in preoperatively distinguishing between ganglion and synovitis in the setting of chronic dorsal wrist pain. Four main criteria were useful: margin, shape, internal structure, and enhancement after administration of contrast material, with shape and internal structure being most helpful.

Diagnosis of erosive tooth wear

The clinical diagnosis 'erosion' is made from characteristic deviations from the original anatomical tooth morphology, thus, distinguishing acid induced tissue loss from other forms of wear. Primary pathognomonic features are shallow concavities on smooth surfaces occurring coronal from the enamel-cementum junction. Problems from diagnosing occlusal surfaces and exposed dentine are discussed. Indices for recording erosive wear include morphological as well as quantitative criteria. Currently, various indices are used making the comparison of prevalence studies difficult. The most important and frequently used indices are described. In addition to recording erosive lesions, the assessment of progression is important as the indication of treatment measures depends on erosion activity. A number of evaluated and sensitive methods for in vitro and in situ approaches are available, but the fundamental problem for their clinical use is the lack of re-identifiable reference areas. Tools for clinical monitoring are described.