bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated serial extraction of DNA and RNA from biobanked tissue specimens
Authors: Mathot Lucy , Wallin Monica , Sjöblom Tobias 
Published: August 2013

Abstract

Background
With increasing biobanking of biological samples, methods for large scale extraction of nucleic acids are in demand. The lack of such techniques designed for extraction from tissues results in a bottleneck in downstream genetic analyses, particularly in the field of cancer research. We have developed an automated procedure for tissue homogenization and extraction of DNA and RNA into separate fractions from the same frozen tissue specimen. A purpose developed magnetic bead based technology to serially extract both DNA and RNA from tissues was automated on a Tecan Freedom Evo robotic workstation.

Results
864 fresh-frozen human normal and tumor tissue samples from breast and colon were serially extracted in batches of 96 samples. Yields and quality of DNA and RNA were determined. The DNA was evaluated in several downstream analyses, and the stability of RNA was determined after 9 months of storage. The extracted DNA performed consistently well in processes including PCR-based STR analysis, HaloPlex selection and deep sequencing on an Illumina platform, and gene copy number analysis using microarrays. The RNA has performed well in RT-PCR analyses and maintains integrity upon storage.

Conclusions
The technology described here enables the processing of many tissue samples simultaneously with a high quality product and a time and cost reduction for the user. This reduces the sample preparation bottleneck in cancer research. The open automation format also enables integration with upstream and downstream devices for automated sample quantitation or storage.
Gene-environment and protein-degradation signatures characterize genomic and phenotypic diversity in wild Caenorhabditis eleganspopulations
Authors: Volkers Rita JM , Snoek L Basten , Hubar Caspara J van Hellenberg , Coopman Renata , Chen Wei , Yang Wentao , Sterken Mark G , Schulenburg Hinrich , Braeckman Bart P , Kammenga Jan E 
Published: August 2013

Abstract

Background
Analyzing and understanding the relationship between genotypes and phenotypes is at the heart of genetics. Research on the nematode Caenorhabditis elegans has been instrumental for unraveling genotype-phenotype relations, and has important implications for understanding the biology of mammals, but almost all studies, including forward and reverse genetic screens, are limited by investigations in only one canonical genotype. This hampers the detection and functional analysis of allelic variants, which play a key role in controlling many complex traits. It is therefore essential to explore the full potential of the natural genetic variation and evolutionary context of the genotype-phenotype map in wild C. elegans populations.

Results
We used multiple wild C. elegans populations freshly isolated from local sites to investigate gene sequence polymorphisms and a multitude of phenotypes including the transcriptome, fitness, and behavioral traits. The genotype, transcriptome, and a number of fitness traits showed a direct link with the original site of the strains. The separation between the isolation sites was prevalent on all chromosomes, but chromosome V was the largest contributor to this variation. These results were supported by a differential food preference of the wild isolates for naturally co-existing bacterial species. Comparing polymorphic genes between the populations with a set of genes extracted from 19 different studies on gene expression in C. elegans exposed to biotic and abiotic factors, such as bacteria, osmotic pressure, and temperature, revealed a significant enrichment for genes involved in gene-environment interactions and protein degradation.

Conclusions
We found that wild C. elegans populations are characterized by gene-environment signatures, and we have unlocked a wealth of genotype-phenotype relations for the first time. Studying natural isolates provides a treasure trove of evidence compared with that unearthed by the current research in C. elegans, which covers only a diminutive part of the myriad of genotype-phenotype relations that are present in the wild.
Influenza B virus has global ordered RNA structure in (+) and (−) strands but relatively less stable predicted RNA folding free energy than allowed by the encoded protein sequence
Authors: Priore Salvatore F , Moss Walter N , Turner Douglas H 
Published: August 2013

Abstract

Background
Influenza A virus contributes to seasonal epidemics and pandemics and contains Global Ordered RNA structure (GORS) in the nucleoprotein (NP), non-structural (NS), PB2, and M segments. A related virus, influenza B, is also a major annual public health threat, but unlike influenza A is very selective to human hosts. This study extends the search for GORS to influenza B.

Findings
A survey of all available influenza B sequences reveals GORS in the (+) and (−)RNAs of the NP, NS, PB2, and PB1 gene segments. The results are similar to influenza A, except GORS is observed for the M1 segment of influenza A but not for PB1. In general, the folding free energies of human-specific influenza B RNA segments are less stable than allowable by the encoded amino acid sequence. This is consistent with findings in influenza A, where human-specific influenza RNA folds are less stable than avian and swine strains.

Conclusions
These results reveal fundamental molecular similarities and differences between Influenza A and B and suggest a rational basis for choosing segments to target with therapeutics and for viral attenuation for live vaccines by altering RNA folding stability.
Comparing the genomes of Helicobacter pylori clinical strain UM032 and Mice-adapted derivatives
Authors: Khosravi Yalda , Rehvathy Vellaya , Wee Wei Yee , Wang Susana , Baybayan Primo , Singh Siddarth , Ashby Meredith , Ong Junxian , Amoyo Arlaine Anne , Seow Shih Wee , Choo Siew Woh , Perkins Tim , Chua Eng Guan , Tay Alfred , Marshall Barry James , Loke Mun Fai , Goh Khean Lee , Pettersson Sven , Vadivelu Jamuna 
Published: August 2013

Abstract

Background

Helicobacter pylori is a Gram-negative bacterium that persistently infects the human stomach inducing chronic inflammation. The exact mechanisms of pathogenesis are still not completely understood. Although not a natural host for H. pylori, mouse infection models play an important role in establishing the immunology and pathogenicity of H. pylori. In this study, for the first time, the genome sequences of clinical H. pylori strain UM032 and mice-adapted derivatives, 298 and 299, were sequenced using the PacBio Single Molecule, Real-Time (SMRT) technology.

Result
Here, we described the single contig which was achieved for UM032 (1,599,441 bp), 298 (1,604,216 bp) and 299 (1,601,149 bp). Preliminary analysis suggested that methylation of H. pylori genome through its restriction modification system may be determinative of its host specificity and adaptation.

Conclusion
Availability of these genomic sequences will aid in enhancing our current level of understanding the host specificity of H. pylori.
A special successive approximations method for solving boundary value problems including ordinary differential equations
Authors: Jahanshahi Mohammad , Nazari Davoud , Aliev Nihan 
Published: August 2013

Abstract
This paper deals with the solutions of boundary value problems based on the converting differential equation with boundary conditions to a mixed Voletrra and Fredholm integral equation; then, we will use the special case of successive approximations method for solving obtained equation. Convergence analysis and error estimate is discussed; also, a numerical example is presented to demonstrate the accuracy of the proposed technique.
PMMA-based Stimuli-responsive Flexible Thin-films
Authors: Mathew Roshan Jesus , Raj Sarika , Dhesingh Ravi Shankaran 
Published: August 2013

Abstract
Low-cost flexible thin-films exhibiting stimuli-responsive properties were fabricated on poly(methyl methacrylate) (PMMA) as the base supporting material. Labeling of this transparent thermoplastic with Congo red diazo dye revealed its simultaneous pH-responsive and temperature-responsive abilities. UV, FT-IR, and film stability studies identified the role of the dye and the polymer in the flexible thin-film stimuli-responsive behavior. This film is promising for future applications.
Why do we need to age?
Authors: Baniahmad Aria 
Published: August 2013

Abstract
A key question remains: why do multicellular organisms have a limited lifespan? The aging process is considered to be a decline of keeping the molecular, cellular and organ structure and interactions upright. It is hypothesized here that an evolutionary force has actively selected for limited lifespan and prior to that there is the process of aging. Many theories exist, including the endocrine theory of aging and reproduction-based aging. Here, a hypothesis is deduced for the driving force of the evolution of aging and lifespan limitation.
Estrogen receptor beta and its selective ligands: an option for treatment of menopausal vasomotor symptoms?
Authors: Jarry Hubertus 
Published: August 2013

Abstract
In the human female, menopause is the permanent end of fertility, defined as occurring 12 months after the last menstrual period. During peri- and postmenopausal stages, the vast majority of women experience moderate-to-severe vasomotor symptoms, such as hot flashes and night sweats, which interfere with sleep and may be severe enough to affect quality of life. The only treatment approved by national health authorities is hormone therapy with estrogen alone or in combination with a progestagen. However, this therapeutic regimen is associated with severe side effects, such as stimulation of growth of breast cancer or cardiovascular events. Thus, there is a demand for efficient and safe alternative treatments for menopausal complaints.
After the discovery of estrogen receptor beta in many organs, and confirmation of its presence in the brain, many researchers raised the question of whether ERβ-specific ligands may be novel therapeutic agents for treatment of menopausal complaints with the desirable effects of estrogen but without increased risk of tumor incidence. This minireview will briefly summarize the relevance of estrogen receptor beta and its specific ligands for the treatment of menopausal symptoms with a focus on vasomotor menopausal symptoms. At present, estrogen receptor beta-selective ligands do not seem to be active in models of prevention or reversal of osteoporosis. However, data from animal experiments suggest that estrogen receptor beta-selective ligands might be safe therapeutics for the treatment of vasomotor menopausal symptoms.
Molecular triggers of neuroinflammation in mouse models of demyelinating diseases
Authors: Barrette Benoit , Nave Klaus-Armin , Edgar Julia M. 
Published: August 2013

Abstract
Myelinating cells wrap axons with multi-layered myelin sheaths for rapid impulse propagation. Dysfunctions of oligodendrocytes or Schwann cells are often associated with neuroinflammation, as observed in animal models of leukodystrophies and peripheral neuropathies, respectively. The neuroinflammatory response modulates the pathological changes, including demyelination and axonal injury, but also remyelination and repair. Here we discuss different immune mechanisms as well as factors released or exposed by myelinating glia in disease conditions. The spectrum of inflammatory mediators varies with different myelin disorders and has a major impact on the beneficial or detrimental role of immune cells in keeping nervous system integrity.
On the General Gauss-Markov Model for Experiments in Block Designs
Authors: Caliński Tadeusz 
Published: August 2013

Summary The main estimation and hypothesis testing results related to the Gauss- Markov model, in its general form, are recalled and the application of these results to the analysis of experiments in block designs is considered. Special attention is given to the randomization-derived model for a general block design, and for a proper block design in particular. The question whether the randomization-derived model can be considered as a particular general Gauss-Markov model is discussed. It is indicated that the former, as a mixed model, is in fact an extension of the general Gauss-Markov model. Thus, the analysis based on the randomization-derived model requires a more extended methodical approach. The present paper has been inspired by one of the last papers of Professor Wiktor Oktaba.
Comparison of clinical data based on limits of agreement
Authors: Grilo Luís M. , Grilo Helena L. 
Published: August 2013

Summary Two different medical measurement methods, which usually do not produce exactly the same results, are used to analyse the serum levels of folic acid in a blood sample. We assess the (dis)agreement of the available data in order to replace the old method (the reference method, which involves a lot of human intervention) with the new one (which uses mostly machines), without causing problems in clinical interpretation. The 95% limits of agreement are estimated, before and after a logarithmic transformation, and an appropriate use of regression and a nonparametric approach are also considered. The application of these different statistical techniques is very useful and easily interpreted by medical researchers, but the results obtained do not provide confidence that the new method can be used in place of the old one for clinical purposes.
On the relevance of the 3D retinal vascular network from OCT data
Authors: Serranho P. , Guimarães P. , Rodrigues P. , Bernardes R. 
Published: August 2013

Summary Abnormal patterns of the retinal vascular system have been associated with several heart and cerebral diseases. However, these correlations were obtained using 2D imaging of the eye fundus, disregarding information on the third component (depth) of the vascular system. In this paper, we show that the depth component is relevant and should not be disregarded in this analysis. In this way, the relevance of analysis of the retinal vascular network as a biometrical marker for the general health status of an individual can be increased.
On the small sample properties of variants of Mardia’s and Srivastava’s kurtosis-based tests for multivariate normality
Authors: Hanusz Zofia , Tarasińska Joanna , Osypiuk Zbigniew 
Published: August 2013

Summary The kurtosis-based tests of Mardia and Srivastava for assessing multivariate normality (MVN) are considered. The asymptotic standard normal distribution of their test statistics, under normality, is often misused for too small samples. The purpose of this paper is to suggest mean-and-variance corrected versions of the Mardia and Srivastava test statistics. Simulation studies evaluating both the true sizes and the powers of original and corrected tests against selected alternatives are presented and compared to the size and the power of the Henze-Zirkler test. The proposed corrected statistics have empirical sizes closer to a nominal significance level than the original ones. It is also shown that the corrected versions of the tests can be more powerful than the original ones.
The scale and the dynamics of permanent migration in rural and peri-urban areas in Poland – some problems
Authors: Biegańska Jadwiga , Szymańska Daniela 
Published: August 2013

Abstract
This article refers to the analysis and the evaluation of permanent migration as observed in rural areas of Poland, especially in peri-urban areas of the Polish cities between the years 1995 and 2011. The article covered all 2,173 rural and rural-urban (excluding urban parts) gminas in the country. In the article there were shown what are the migration volumes and dynamics in rural areas and what is the situation of large cities’ peri-urban areas in terms of permanent migration.
A more efficient match between firms’ demand, VET supply and human capital capacities through bottom-up, participative governance
Authors: Noguera Joan 
Published: August 2013

Abstract
One of the main challenges facing EU territories is the development of strategies to better adapt to changing global socio-economic trends. Lifelong education and training is a main strategic tool and a key component in the achievement of EU goals. One component of the lifelong education concept is Vocational Education and Training (VET), aimed at closing the gap between workers’ skills and qualification and changing demand in labour markets. Although local partnerships seem to be an adequate tool to implement VET strategies, some authors identify obstacles that can be attributed to bad practices. Thus, more evidence is needed to support the idea that local development and public-private partnerships are optimal organisational environments for the design and implementation of VET strategies and actions at local and sub-regional levels. The purpose of this paper is to contribute to an analysis of the state of the art as regards local VET partnerships in Europe and to provide recommendations for the process of initiation and management of expert VET partnerships.
The Upper-Silesian conurbation on the path towards the “Silesia” metropolis
Authors: Szajnowska-Wysocka Alicja , Zuzańska-Żyśko Elżbieta 
Published: August 2013

Abstract
In its methodological context, the article, expands on the idea of the organization of the “Silesia” superstructure. The idea of establishing a common urban organism emerged with the local governments of the Upper Silesian conurbation cities and was dictated by the need to find a way to change the traditional image of the Silesian region and its post-industrial role in the economic space of the country, as well as Europe. Therefore, in 2009, the Metropolitan Association of Upper- Silesia, an association for the initial institutionalization of “Silesia”, was registered, because “Silesia” does not hold any administrative or legal force. Such an organizational “revolution” of the Upper Silesian conurbation initiated a wide social debate, in which the arguments of both supporters and opponents of such an enterprise in the Silesian region became apparent, together with misunderstandings related to the term “metropolis”, and the idea of establishing “Silesia”. Representatives of local governments chose the more prestigious term “metropolis” as if a complex metropolisation had taken place in the Upper Silesian conurbation. It would be adequate, however, to look only for the first features of metropolitan functions in this de-industrialized and restructured region, which are going to shape the longlasting metropolisation process under the influence of globalisation.
A Quantification of The Rhythmic Qualities of Salience and Kinesis
Authors: Lopes Eduardo , Gonçalves André 
Published: August 2013

Abstract
From a cognitive point of view, it is easily perceived that some music rhythmic structures are able to create saliences (i.e. pulses perceived as louder). Depending where in a metrical grid these salient pulses are located, a sense of stability or instability will arise. When instability is present in a rhythmic structure one will tend to psychological feel kinesis (i.e. a sense of motion). Salience and kinesis can then be identified as basic rhythmic qualities. Inspired by the theoretical construct Just in Time - an empirical based music theoretical construct for the analysis of rhythm - we decided to quantify some of its analytical output; more specifically the measure of salience and kinesis of a rhythmic sequence. We then developed a web-based tool that calculates the amount of salience and kinesis for a particular rhythmic sequence. We conclude this article pointing how this tool can be used in analysis and music education as well as other possible applications, and future research.
Somatotype Characteristics of Female Patients with Type 2 Diabetes Mellitus / Характеристика Соматотипа Жен Щин, Больных Сахарным Диабетом Типа 2
Authors: Baltadjiev Atanas G. 
Published: August 2013

Abstract
The AIM of the present study was to determine the somatotype of females patients with type 2 diabetes mellitus.
MATERIAL AND METHODS: Two-hundreds and twelve female patients with type 2 diabetes mellitus were measured. The patients were of Bulgarian ethnicity and were divided into two age groups: Group 1: 40-60 years of age and Group 2: 61-80 years of age. The control group comprised healthy females of Bulgarian ethnicity without any metabolic, neoplastic, or other disease divided into age matched groups. Measurements obtained directly were height, body weight, biepicondylar width of humerus, biepicondylar width of femur, arm circumference in relaxed state, arm circumference in contracted state, and calf circumference. Skin folds: subscapular, suprailiac, over triceps and calf. Parameters calculated: the components of the Heath-Carter anthrpometric somatotype.
RESULTS: The mean somatotype of 40-60-year-old female diabetics was mesomorph endomorph, (meso 6.09; endo 6.59; ecto 1.57). The mean somatotype of 40-60-year-old female controls was mesomorphic endomorph (meso 5.65; endo 6.82; ecto 2.75). The mean somatotype of 61-80-year-old diabetic females was endomorphic mesomorph (endo-mesomorph), (meso 9.41; endo 5.39; ecto 1.55). The mean somatotype of 61-80-year-old female controls was mesomorph-endomorph (meso 6.70; endo 6.66; ecto 2.95). Between-age comparison of female diabetics: the endomorph component dominated in the group of 40-60-year-old patients, and the mesomorph component dominated in the group of 61-80-year-old patients. In both groups ectomorphy markedly lagged behind.
CONCLUSION: The mean somatotype of diabetic females aged 40-60 years is mesomoph-endomorph; it differs from the mesomorphic mesomorph somatotype of the control subjects. Endomorphy and mesomorphy dominate clearly, and ectomorphy significantly lags behind. This was the reason we get a distorted somatoplot with a sharp shift to endomorphy and mesomorhpy. The mean somatotype of diabetic women aged 60-80 years was endomorphic mesomorphy with the mesomorphy component leading. It differed from the somatotype of the controls, where mesomorphy and endomorphy scored equally (mesomorph-endomorph). The somatotype of female diabetics suggests that they have a relatively massive skeleton with well-developed muscles and greater body weight relative to height. Unlike the results of studies in other countries presenting with markedly dominating endomorphy, in our study the Bulgarian diabetic females presented with dominating mesomorphy.
This can be regarded as a peculiarity of the Bulgarian diabetic patients. The somatotype of the Bulgarian diabetic females is more favorable on the risk, course and prognosis of the disease.