bluuebunny/crossref_metadata_2025_split huggingface dataset:
5-Hydroxymethylcytosine Is Not Present in Appreciable Quantities in Arabidopsis DNA
Authors: Erdmann Robert M , Souza Amanda L , Clish Clary B , Gehring Mary 
Published: November 2014

Abstract
5-Hydroxymethylcytosine (5-hmC) is an intermediate in active demethylation in metazoans, as well as a potentially stable epigenetic mark. Previous reports investigating 5-hydroxymethylcytosine in plants have reached conflicting conclusions. We systematically investigated whether 5-hmC is present in plant DNA using a range of methods. Using the model organism Arabidopsis thaliana, in addition to other plant species, we assayed the amount or distribution of 5-hydroxymethylcytosine by thin-layer chromatography, immunoprecipitation-chip, ELISA, enzymatic radiolabeling, and mass spectrometry. The failure to observe 5-hydroxymethylcytosine by thin-layer chromatography established an upper bound for the possible fraction of the nucleotide in plant DNA. Antibody-based methods suggested that there were low levels of 5-hmC in plant DNA, but these experiments were potentially confounded by cross-reactivity with the abundant base 5-methylcytosine. Enzymatic radiolabeling and mass spectrometry, the most sensitive methods for detection that we used, failed to detect 5-hydroxymethylcytosine in A. thaliana genomic DNA isolated from a number of different tissue types and genetic backgrounds. Taken together, our results led us to conclude that 5-hmC is not present in biologically relevant quantities within plant genomic DNA.
How Big Is Your Y? A Genome Sequence-Based Estimate of the Size of the Male-Specific Region inMegaselia scalaris
Authors: Hoehn Kenneth B , Noor Mohamed A F 
Published: November 2014

AbstractThe scuttle fly, Megaselia scalaris, is often cited as a model in which to study early sex chromosome evolution because of its homomorphic sex chromosomes, low but measurable molecular differentiation between sex chromosomes, and occasional transposition of the male-determining element to different chromosomes in laboratory cultures. Counterintuitively, natural isolates consistently show sex linkage to the second chromosome. Frequent natural transposition of the male-determining element should lead to the loss of male specificity of any nontransposed material on the previous sex-linked chromosome pair. Using next-generation sequencing data from a newly obtained natural isolate of M. scalaris, we show that even highly conservative estimates for the size of the male-specific genome are likely too large to be contained within a transposable element. This result strongly suggests that transposition of the male-determining region either is extremely rare or has not persisted recently in natural populations, allowing for differentiation of the sex chromosomes of this species.
Relationships of RNA Polymerase II Genetic Interactors to Transcription Start Site Usage Defects and Growth inSaccharomyces cerevisiae
Authors: Jin Huiyan , Kaplan Craig D 
Published: November 2014

AbstractTranscription initiation by RNA Polymerase II (Pol II) is an essential step in gene expression and regulation in all organisms. Initiation requires a great number of factors, and defects in this process can be apparent in the form of altered transcription start site (TSS) selection in Saccharomyces cerevisiae (Baker’s yeast). It has been shown previously that TSS selection in S. cerevisiae is altered in Pol II catalytic mutants defective in a conserved active site feature known as the trigger loop. Pol II trigger loop mutants show growth phenotypes in vivo that correlate with biochemical defects in vitro and exhibit wide-ranging genetic interactions. We assessed how Pol II mutant growth phenotypes and TSS selection in vivo are modified by Pol II genetic interactors to estimate the relationship between altered TSS selection in vivo and organismal fitness of Pol II mutants. We examined whether the magnitude of TSS selection defects could be correlated with Pol II mutant-transcription factor double mutant phenotypes. We observed broad genetic interactions among Pol II trigger loop mutants and General Transcription Factor (GTF) alleles, with reduced-activity Pol II mutants especially sensitive to defects in TFIIB. However, Pol II mutant growth defects could be uncoupled from TSS selection defects in some Pol II allele-GTF allele double mutants, whereas a number of other Pol II genetic interactors did not influence ADH1 start site selection alone or in combination with Pol II mutants. Initiation defects are likely only partially responsible for Pol II allele growth phenotypes, with some Pol II genetic interactors able to exacerbate Pol II mutant growth defects while leaving initiation at a model TSS selection promoter unaffected.
Mechanisms and Regulation of Mitotic Recombination in Saccharomyces cerevisiae
Authors: Symington Lorraine S , Rothstein Rodney , Lisby Michael 
Published: November 2014

Abstract
Homology-dependent exchange of genetic information between DNA molecules has a profound impact on the maintenance of genome integrity by facilitating error-free DNA repair, replication, and chromosome segregation during cell division as well as programmed cell developmental events. This chapter will focus on homologous mitotic recombination in budding yeast Saccharomyces cerevisiae. However, there is an important link between mitotic and meiotic recombination (covered in the forthcoming chapter by Hunter et al. 2015) and many of the functions are evolutionarily conserved. Here we will discuss several models that have been proposed to explain the mechanism of mitotic recombination, the genes and proteins involved in various pathways, the genetic and physical assays used to discover and study these genes, and the roles of many of these proteins inside the cell.
Demographic Correlates of Anxiety and Depression Symptoms in Chronic Sinonasal Diseases
Authors: Katotomichelakis Michael , Simopoulos Efthimios , Tzikos Anthimos , Balatsouras Dimitrios , Tripsianis Gregory , Danielides Gerasimos , Xenitidis Kiriakos , Livaditis Miltos , Danielides Vassilios 
Published: November 2014

Objectives: To explore mental health of patients with olfactory loss due to chronic sinonasal diseases and investigate the effects of age-, gender-, and socio-economic variables on anxiety and depression symptoms. Methodology: One hundred and eight patients (62 males; mean age: 39.78 ± 16.11 years), suffering from olfactory impairment due to chronic rhinosinusitis and allergic rhinitis and 30 healthy subjects (16 males; mean age, 37.03 ± 13.09 years) were studied. Olfactory function was evaluated using “Sniffin‘ Sticks” test. All patients completed four validated questionnaires specific for assessing anxiety and depression (Zung Anxiety Scale, State-Trait Anxiety Inventory-STAI, Zung Depression Scale, and Beck Depression Inventory-BDI). Results: We found significantly more severe anxiety and depression symptoms in anosmic (all p < 0.001) and hyposmic patients compared to healthy controls. No significant differences were observed between normosmic patients and controls. Scores in all psychological measures were significantly higher in elderly and female patients as well as in low, compared to high, socio-economic status patients. No significant differences were found between low and medium socio-economic level. Conclusions: Olfactory loss in chronic sinonasal diseases was found to be associated with anxiety and depression symptoms. Moreover, anxiety was correlated with depression. With regard to patients' demographics, female gender and low socioeconomic status proved to be independently correlated with anxiety and depression levels.
Iterative learning control with sampled-data feedback for robot manipulators
Authors: Delchev Kamen , Boiadjiev George , Kawasaki Haruhisa , Mouri Tetsuya 
Published: November 2014

Abstract
This paper deals with the improvement of the stability of sampled-data (SD) feedback control for nonlinear multiple-input multiple-output time varying systems, such as robotic manipulators, by incorporating an off-line model based nonlinear iterative learning controller. The proposed scheme of nonlinear iterative learning control (NILC) with SD feedback is applicable to a large class of robots because the sampled-data feedback is required for model based feedback controllers, especially for robotic manipulators with complicated dynamics (6 or 7 DOF, or more), while the feedforward control from the off-line iterative learning controller should be assumed as a continuous one. The robustness and convergence of the proposed NILC law with SD feedback is proven, and the derived sufficient condition for convergence is the same as the condition for a NILC with a continuous feedback control input. With respect to the presented NILC algorithm applied to a virtual PUMA 560 robot, simulation results are presented in order to verify convergence and applicability of the proposed learning controller with SD feedback controller attached
Comparison of Methane Drainage Methods Used in Polish Coal Mines
Authors: Szlązak Nikodem , Borowski Marek , Obracaj Dariusz , Swolkień Justyna , Korzec Marek 
Published: November 2014

Abstract
Methane drainage is used in Polish coal mines in order to reduce mine methane emissions as well as to keep methane concentration in mine workings at safe levels.
This article describes methods of methane drainage during mining used in Polish coal mines. The first method involves drilling boreholes from tailgate roadway to an unstressed zone in roof or floor layers of a mined seam. It is the main method used in Polish mining, where both the location of drilled boreholes as well as their parameters are dependent on mining and ventilation systems of longwalls. The second method is based on drilling overlying drainage galleries in seams situated under or over the mined seam.
This article compares these methods with regard to their effectiveness under mining conditions in Polish mines. High effectiveness of methane drainage of longwalls with different ventilation and methane drainage systems has been proven. The highest effectiveness of methane drainage has been observed for the system with overlying drainage gallery and with the parallel tailgate roadways. In case of classic U ventilation system of longwall panel, boreholes drilled from the tailgate roadway behind the longwall front are lost.
Predictive Regression Models of Monthly Seismic Energy Emissions Induced by Longwall Mining
Authors: Jakubowski Jacek , Tajduś Antoni 
Published: November 2014

Abstract
This article presents the development and validation of predictive regression models of longwall mining-induced seismicity, based on observations in 63 longwalls, in 12 seams, in the Bielszowice colliery in the Upper Silesian Coal Basin, which took place between 1992 and 2012. A predicted variable is the logarithm of the monthly sum of seismic energy induced in a longwall area. The set of predictors include seven quantitative and qualitative variables describing some mining and geological conditions and earlier seismicity in longwalls. Two machine learning methods have been used to develop the models: boosted regression trees and neural networks. Two types of model validation have been applied: on a random validation sample and on a time-based validation sample.
The set of a few selected variables enabled nonlinear regression models to be built which gave relatively small prediction errors, taking the complex and strongly stochastic nature of the phenomenon into account. The article presents both the models of periodic forecasting for the following month as well as long-term forecasting.
The Use of Fuzzy Systems in the Designing of Mining Process in Hard Coal Mines
Authors: Brzychczy Edyta , Kęsek Marek , Napieraj Aneta , Sukiennik Marta 
Published: November 2014

Abstract
This article presents examples of solutions supporting the design of certain elements of the mining process in coal mines. The focus is on two fuzzy systems: the first supports the selection of equipment for longwall faces (FSES); and the second supports the estimation of production results (FSOE). System FSES generates proposals for equipment in designed longwall faces. The module of fuzzing in this system enables a fuzzing operation for the following quantitative variables: longwall length; longwall height; longitudinal and crosswise incline of the longwall, workability of the coal and thickness of rock vein in a given section of the longwall. The knowledge base includes over 100 fuzzy rules indicating possible options for equipment under specified site conditions.
After a proposal of equipment is generated, it is then possible to insert the values obtained into the second system FSOE, which estimates output for a given shift time using the chosen parameters. The module of fuzzing in system FSOE includes 9 variables, which are crucial in determining shift output for the given longwall face. The knowledge base in this system contains over 2000 rules.
As a result of the operation of both systems, the designer receives both a proposal of equipment for the designed longwall face and the size of shift output under the given conditions.
Operation of the two systems has been presented using a case study.
Identification of the Oscillation Period of Chemical Reactors by Chaotic Sampling of the Conversion Degree
Authors: Lawnik Marcin , Berezowski Marek 
Published: November 2014

Abstract
To stabilise the periodic operation of a chemical reactor the oscillation period should be determined precisely in real time. The method discussed in the paper is based on adaptive sampling of the state variable with the use of chaotic mapping to itself. It enables precise determination of the oscillation period in real time and could be used for a proper control system, that can successfully control the process of chemical reaction and maintain the oscillation period at a set level. The method was applied to a tank reactor and tubular reactor with recycle.
Broadband Input Block of Radio Receiver for Software-Defined Radio Devices
Authors: Magnuski Mirosław , Surma Maciej , Wójcik Dariusz 
Published: November 2014

Abstract
In the paper a cost-effective input block of the SDR receiver for 0.9 — 2.4 GHz frequency band built of capacitive-tuned selective amplifier and broadband Vivaldi antenna is presented. The applied selective amplifier consists of three identical sections of tunable filters and two stages of monolithic broadband amplifiers. The single filter section proposed by the authors, due to its ability to absorb parasitic inductances of varicap diodes, simplifies usage of encapsulated varicap diodes in design of tunable in broad band selective filters dedicated to input stages of the receivers. Moreover, proposed filter section has small variation of in-band insertion loss in comparison to varicap-tuned filters built of coupled transmission lines which are commonly applied in input blocks of the microwave receivers. The described selective amplifier could be easily integrated on a single substrate with the Vivaldi antenna which is a cost effective way of fabrication of the tunable in broad band input block of a receiver that has desired gain, selectivity and directivity of the antenna.
Influence of Pumping Beam Width on Vecsel Output Power
Authors: Sokoł Adam K. , Sarzała Robert P. 
Published: November 2014

Abstract
The paper is devoted to a numerical analysis of an influence of a pumping beam diameter on output power of optically pumped vertical-external-cavity surface-emitting lasers. Simulations have been carried out for a structure with a GaInNAs/GaAs active region operating at 1.32 urn. Various assembly configurations have been considered. Results obtained show that laser power scaling is strongly affected by thermal properties of the device.
Modelling and Simulation of Normally-Off AlGaN/GaN MOS-HEMTs
Authors: Taube Andrzej , Sochacki Mariusz , Szmidt Jan , Kaminska Eliana , Piotrowska Anna 
Published: November 2014

Abstract
The article presents the results of modelling and simulation of normally-off AlGaN/GaN MOS-HEMT transistors. The effect of the resistivity of the GaN:C layer, the channel mobility and the use of high-k dielectrics on the electrical characteristics of the transistor has been examined. It has been shown that a low leakage current of less than 10−6 A/mm can be achieved for the acceptor dopant concentration at the level of 5 X 1015 cm−3. The limitation of the maximum on-state current due to the low carrier channel mobility has been shown. It has also been demonstrated that the use of HfO2, instead of SiO2, as a gate dielectric increases on-state current above 0.7A/mm and reduces the negative influence of the charge accumulated in the dielectric layer.
An Overview of Free Space Optics with Quantum Cascade Lasers
Authors: Mikołajczyk Janusz 
Published: November 2014

Abstract
The article presents an overview of the work on quantum cascade lasers application in free space optical systems (Free Space Optics - FSO). There are discussed the main issues of the open-space laser communications and their practical construction. Comparative analyses of each FSO technology were performed. Brief description of quantum cascade (QC) lasers and some developments related to the use of these lasers in optical data link are also presented. In summary, the constructed models of FSO links with QC lasers are characterized.
Singular M-matrices which may not have a nonnegative generalized inverse
Authors: Sushama Agrawal N. , Premakumari K. , Sivakumar K.C. 
Published: November 2014

Abstract
A matrix A ∈ ℝn×n is a GM-matrix if A = sI − B, where 0 < ρ(B) ≤ s and B ∈WPFn i.e., both B and Bthave ρ(B) as their eigenvalues and their corresponding eigenvector is entry wise nonnegative. In this article,we consider a generalization of a subclass of GM-matrices having a nonnegative core nilpotent decompositionand prove a characterization result for such matrices. Also, we study various notions of splitting of matricesfrom this new class and obtain sufficient conditions for their convergence.
Segregation of phosphorus to ferrite grain boundaries during transformation in an Fe–P alloy
Authors: Kim Jeong In , Pak Jun Hak , Park Kyong-Su , Jang Jae Hoon , Suh Dong-Woo , Bhadeshia Harshad Kumar Dharamshi Hansraj 
Published: November 2014

Abstract
A binary alloy of iron containing 0.17 wt.% of phosphorus has been heat treated under a variety of conditions in order to see whether the segregation of phosphorus to grain boundaries can be controlled. The alloy transforms fully into ferrite. It is found that the majority of solute found at the ferrite grain boundaries has its origins in the temperature range where phase transformation occurs, in other words, phosphorus that is accumulated and dragged with the growing ferrite–austenite transformation front. As a consequence, it cannot be suppressed using cooling rates as high as 400 K s−1.
Cerebral paragonimiasis: a retrospective analysis of 27 cases
Authors: Xia Yong , Ju Yan , Chen Jing , You Chao 
Published: November 2014

OBJECT
The authors retrospectively analyzed the clinical characteristics, existing problems, and treatment experiences in recently diagnosed cerebral paragonimiasis (CP) cases and sought to raise awareness of CP and to supply reference data for early diagnosis and treatment.

METHODS
Twenty-seven patients (22 male and 5 female; median age 20.3 years, range 4–47 years) with CP were diagnosed between September 2008 and September 2013. These diagnoses were confirmed by IgG enzyme-linked immunosorbent assays. Follow-up was performed in 24 cases for a period of 6–56 months.

RESULTS
Cerebral paragonimiasis accounted for 21.6% of paragonimiasis cases (27 of 125). The average duration from onset to praziquantel treatment was 69 days. All patients resided in rural areas. Twenty patients had positive lung results, which included visible lung lesions in 14 cases. The lesions were surgically removed in 8 of these cases. Twenty-four patients had high eosinophil counts (≥ 0.08 × 109/L), and eosinophilic meningitis was noted in 17 cases. The rate of misdiagnosis and missed diagnosis was 30.4%. Most symptoms were markedly improved after treatment, but mild movement disorders combined with impaired memory and personality changes remained in a small number of patients.

CONCLUSIONS
Clinicians should be alert to the possibility of CP in young patients (4–16 years) with the primary symptoms of epilepsy and hemorrhage. Early diagnosis and timely treatment can reduce the need for surgery and further impairments to brain function. Liquid-based cytological examination of CSF and peripheral blood eosinophil counts can aid in differentiating CP from similar lesions.
Spinal stimulator peri-electrode masses: case report
Authors: Scranton Robert A. , Skaribas Ioannis M. , Simpson Richard K. 
Published: November 2014

The authors describe a case of delayed spastic quadriparesis caused by a peri-electrode mass following the implantation of a minimally invasive percutaneous spinal cord stimulator (SCS). Prior reports with paddle-type electrodes are reviewed, and a detailed histological and pathophysiological comparison with the present case is made.
The patient developed tolerance to a cervical percutaneous SCS 4 months after implantation, followed by the onset of spastic quadriparesis 9 months after implantation. The stimulator was removed, and contrast-enhanced MRI revealed an enhancing epidural mass where the system had been placed, with severe spinal cord compression. Decompression was carried out, and the patient experienced neurological improvement. Pathological examination revealed fibrotic tissue with granulomatous and multinucleated giant cell reactions. No evidence of infection or hemorrhage was found. Professionals treating patients with SCSs or contemplating their insertion should be aware of this delayed complication and associated risk factors.
Evaluation of monoenergetic imaging to reduce metallic instrumentation artifacts in computed tomography of the cervical spine
Authors: Komlosi Peter , Grady Deborah , Smith Justin S. , Shaffrey Christopher I. , Goode Allen R. , Judy Patricia G. , Shaffrey Mark , Wintermark Max 
Published: November 2014

OBJECT
Monoenergetic imaging with dual-energy CT has been proposed to reduce metallic artifacts in comparison with conventional polychromatic CT. The purpose of this study is to systematically evaluate and define the optimal dual-energy CT imaging parameters for specific cervical spinal implant alloy compositions.

METHODS
Spinal fixation rods of cobalt-chromium or titanium alloy inserted into the cervical spine section of an Alderson Rando anthropomorphic phantom were imaged ex vivo with fast-kilovoltage switching CT at 80 and 140 peak kV. The collimation width and field of view were varied between 20 and 40 mm and medium to large, respectively. Extrapolated monoenergetic images were generated at 70, 90, 110, and 130 kiloelectron volts (keV). The standard deviation of voxel intensities along a circular line profile around the spine was used as an index of the magnitude of metallic artifact.

RESULTS
The metallic artifact was more conspicuous around the fixation rods made of cobalt-chromium than those of titanium alloy. The magnitude of metallic artifact seen with titanium fixation rods was minimized at monoenergies of 90 keV and higher, using a collimation width of 20 mm and large field of view. The magnitude of metallic artifact with cobalt-chromium fixation rods was minimized at monoenergies of 110 keV and higher; collimation width or field of view had no effect.

CONCLUSIONS
Optimization of acquisition settings used with monoenergetic CT studies might yield reduced metallic artifacts.