bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Use of RelocaTE and Unassembled Short Reads to Produce High-Resolution Snapshots of Transposable Element Generated Diversity in Rice
Authors: Robb Sofia M C , Lu Lu , Valencia Elizabeth , Burnette James M , Okumoto Yutaka , Wessler Susan R , Stajich Jason E 
Published: April 2013

Abstract
Transposable elements (TEs) are dynamic components of genomes that often vary in copy number among members of the same species. With the advent of next-generation sequencing TE insertion-site polymorphism can be examined at an unprecedented level of detail when combined with easy-to-use bioinformatics software. Here we report a new tool, RelocaTE, that rapidly identifies specific TE insertions that are either polymorphic or shared between a reference and unassembled next-generation sequencing reads. Furthermore, a novel companion tool, CharacTErizer, exploits the depth of coverage to classify genotypes of nonreference insertions as homozygous, heterozygous or, when analyzing an active TE family, as rare somatic insertion or excision events. It does this by comparing the numbers of RelocaTE aligned reads to reads that map to the same genomic position without the TE. Although RelocaTE and CharacTErizer can be used for any TE, they were developed to analyze the very active mPing element which is undergoing massive amplification in specific strains of Oryza sativa (rice). Three individuals of one of these strains, A123, were resequenced and analyzed for mPing insertion site polymorphisms. The majority of mPing insertions found (~97%) are not present in the reference, and two siblings from a self-crossed of this strain were found to share only ~90% of their insertions. Private insertions are primarily heterozygous but include both homozygous and predicted somatic insertions. The reliability of the predicted genotypes was validated by polymerase chain reaction.
Genetic Polymorphisms in Host Innate Immune Sensor Genes and the Risk of Nasopharyngeal Carcinoma in North Africa
Authors: Moumad Khalid , Lascorz Jesus , Bevier Melanie , Khyatti Meriem , Ennaji Moulay Mustapha , Benider Abdellatif , Huhn Stefanie , Lu Shun , Chouchane Lotfi , Corbex Marilys , Hemminki Kari , Försti Asta 
Published: April 2013

Abstract
Nasopharyngeal carcinoma (NPC) is a rare malignancy in most parts of the world. It is an Epstein-Barr virus−associated malignancy with an unusual racial and geographical distribution. The host innate immune sensor genes play an important role in infection recognition and immune response against viruses. Therefore, we examined the association between polymorphisms in genes within a group of pattern recognition receptors (including families of Toll-like receptors, C-type lectin receptors, and retinoic acid−inducible gene I−like receptors) and NPC susceptibility. Twenty-six single-nucleotide polymorphisms (SNPs) in five pattern-recognition genes were genotyped in 492 North African NPC cases and 373 frequency-matched controls. TLR3_rs3775291 was the most significantly associated SNP (odds ratio [OR] 1.49; 95% confidence interval [95% CI] 1.11−2.00; P = 0.008; dominant model). The analysis showed also that CD209_rs7248637 (OR 0.69; 95% CI 0.52−0.93; P = 0.02; dominant model) and DDX58_rs56309110 (OR 0.70; 95% CI 0.51−0.98; P = 0.04) were associated with the risk of NPC. An 18% increased risk per allele was observed for the five most significantly associated SNPs, TLR3_rs3775291, CD209_rs7248637, DDX58_rs56309110, CD209_rs4804800, and MBL2_rs10824792, (ptrend = 8.2 × 10−4). Our results suggest that genetic variation in pattern-recognition genes is associated with the risk of NPC. These preliminary findings require replication in larger studies.
A Nucleosomal Region Important for Ensuring Proper Interactions Between the Transcription Elongation Factor Spt16 and Transcribed Genes inSaccharomyces cerevisiae
Authors: Nguyen Hoai-Trang T , Wharton William , Harper Jennifer A , Dornhoffer James R , Duina Andrea A 
Published: April 2013

AbstractThe highly conserved FACT (FAcilitates Chromatin Transactions) histone chaperone assists in the transcription elongation process first by facilitating the removal of histones in front of transcribing RNA polymerase II (Pol II) and then by contributing to nucleosome reassembly in the wake of Pol II passage. Whereas it is well established that FACT localizes across actively transcribed genes, the mechanisms that regulate FACT recruitment to and disengagement from chromatin during transcription still remain to be elucidated. Using the Saccharomyces cerevisiae model system, we previously showed that a histone H3 mutant—H3-L61W—greatly perturbs interactions between the yeast FACT (yFACT) complex and chromatin during transcription, resulting in a pronounced shift in yFACT occupancy toward the 3′ ends of transcribed genes. In the present study we report that two histone H4 mutants—H4-R36A and H4-K31E—alter the association pattern of the yFACT subunit Spt16 across transcribed genes in a fashion similar to that seen for H3-L61W. Interestingly, H4-R36, H4-K31, and H3-L61 are in close proximity to each other on the side of the nucleosome. We also provide evidence that the H4-R36A and H3-L61W mutants impair proper Spt16−chromatin interactions by perturbing a common process. Collectively, our results suggest that a nucleosomal region encompassing the H4-R36, H4-K31, and H3-L61 residues plays an important role in ensuring proper association of yFACT across transcribed genes.
The Decision‐Making Process for Ridge Preservation Procedures After Tooth Extraction
Authors: Frost Natalie A. , Banjar Arwa A. , Galloway Patrick B. , Huynh‐Ba Guy , Mealey Brian L. 
Published: April 2013

Focused Clinical Question:How should the extraction socket be managed after tooth removal?Summary:Resorptive changes that take place after tooth extraction can result in a significant reduction in alveolar ridge width and height. This may create a problem for proper implant placement and fabrication of esthetic restorations. Ridge preservation has been shown to be effective in decreasing alveolar bone resorption after tooth removal. During ridge preservation, the extraction socket is filled with graft material, and a barrier is generally used to contain the graft. Flap reflection is usually not recommended if the socket walls are intact and the ridge width is sufficient after tooth removal. However, if significant breakdown of the buccal bony plate is present, mucoperiosteal flap elevation may be required to allow proper placement of the bone graft and membrane. Different types of bone grafts (autograft, allograft, and xenograft) and barrier membranes (resorbable and non‐resorbable) have been evaluated in clinical studies. They all are shown to be effective regardless of the material or technique used.Conclusions:Ridge preservation is an effective procedure for minimizing horizontal and vertical alveolar ridge resorption after tooth extraction. Current evidence does not support one technique as being superior to another. The selection of the technique to be used should be based on the clinical situation.
Ramm Wholesale: Reviewing Audit Work (Retracted)
Authors: Kalesnikoff Douglas , Phillips Fred 
Published: April 2013

ABSTRACT:
Designed to be used in an undergraduate or Master's auditing course, this Case asks students to evaluate work performed on the financial statement audit of a private wholesale merchandiser. Through this evaluation, students can uncover issues relating to gaining knowledge of a client and its environment, risk assessment, materiality, audit strategy, and specific audit procedures for the revenue/receivables/receipts accounting cycle. The Teaching Notes provide support both for instructors who ask students to prepare the Case in advance of class and for instructors who instead assign the Case for analysis in real-time during class, whereby the Case is read aloud paragraph-by-paragraph and issues are discussed as they are detected.
Role of polyaniline morphology in Pd particles dispersion. Hydrogenation of alkynes in the presence of Pd-polyaniline catalysts
Authors: Kosydar Robert , Goral Monika , Drelinkiewicz Alicja , Stejskal Jaroslav 
Published: April 2013

AbstractTwo polyaniline (PANI) samples of various molecular masses were used for the preparation of palladium catalysts (with 2 mass % of Pd). The physicochemical features of starting polyanilines were found to substantially affect the size and extent of palladium nanoparticles aggregation. Strongly aggregated large palladium particles appeared in the PANI sample of more compact morphology (PANI-H), higher crystallinity and lower specific surface area. Pd nanoparticles of a definitively smaller size were formed in the more amorphous PANI sample of looser morphology (PANI-L) and the extent of particles aggregation was markedly lower. The catalytic properties of Pd/PANI samples were studied in a liquid phase hydrogenation of unsaturated triple bond (C≡C) in alkynes reactants, phenylacetylene, and cyclohexylacetylene. The 2 mass % Pd/PANI-L catalyst prepared using polymer of less compact texture exhibited much higher activity in both reactions. In the presence of the 2 mass % Pd/PANI-L catalyst, alkene products were formed with a high selectivity (approximately 90 %) attained at the almost complete conversion of alkynes. This highly selective hydrogenation of the C≡C to the C=C bond was related to the presence of an electroactive polymer, PANI, in close proximity with Pd active sites. Polyaniline could have a role in a steric effect as well as in a modification of adsorptive properties of Pd centres.
CFD-based atmospheric dispersion modeling in real urban environments
Authors: Labovský Juraj , Jelemenský Ľudovít 
Published: April 2013

AbstractThe process of CFD model application for atmospheric dispersion modeling is presented. Increasing the CPU power opens new possibilities of the CFD approach application for consequence analysis in real complex urban environments. As successful CFD simulation is directly dependent on the quality and complexity of the computational mesh, a new methodology of transferring the Geographic Information System (GIS) data to the computational mesh can be utilized. A user software for importing and manipulation with the GIS data and their subsequent transfer to an instructional file for the generation of the computational mesh was prepared and tested. The introduced methodology is relatively simple and it requires only a small amount of input data. The process of creating a computational mesh is very straightforward and fast, which enables the application of CFD modeling in urban environments in all fields of engineering applications in safety analysis. Several recommendations concerning proper definition of boundary conditions for atmospheric dispersion modeling were summarized. The presented approach was tested on a realistic case study of liquefied chlorine release in a real town. Results obtained by the CFD approach were compared with those obtained by a simpler but standard integral model.
Alexandroff Manifolds and Homogeneous Continua
Authors: Karassev A. , Todorov V. , Valov V. 
Published: April 2013

AbstractWe prove the following result announced by the second and third authors: Any homogeneous, metric ANR-continuum is a -continuum provided dimGX = n ≥ 1 and , where G is a principal ideal domain. This implies that any homogeneous n-dimensional metric ANR-continuum is a Vn-continuum in the sense of Alexandroff. We also prove that any finite-dimensional cyclic in dimension n homogeneous metric continuum X, satisfying for some group G and n ≥ 1, cannot be separated by a compactum K with and dimGK ≤ n – 1. This provides a partial answer to a question of Kallipoliti–Papasoglu as to whether a two-dimensional homogeneous Peano continuum can be separated by arcs.
Animals and Moral Motivation: A Response to Clement
Authors: Rowlands Mark 
Published: April 2013

Abstract
In her article "Animals and Moral Agency: The Recent Debate and Its Implications," Grace Clement (2013) provides a lucid overview of the debate concerning the possibility of moral action in animals and a suggestive proposal for how to advance this debate. This article takes up certain themes from Clement’s article, themes that, it is argued, are either problematic or insufficiently developed.
Size Matters: Animal Size, Contributory Causation, and Ethical Vegetarianism
Authors: MacClellan Joel 
Published: April 2013

Abstract
Animal size is a relevant and unappreciated consideration in moral evaluations of killing animals for food, especially for utilitarians, who must weigh the gustatory satisfaction of eating meat-the quantity of which varies greatly throughout the animal kingdom-against animal suffering in utilitarian calculations. I argue that animal size can drastically alter not only the extent but even the valence of such calculations. Then I show how the business ethics literature on vegetarianism is deficient for not taking animal size into account. Last, I argue that market conditions are also relevant in moral assessments of vegetarianism.
An Opportune Quest: The Development of Animal Law Courses in the United States
Authors: Townsend Akisha 
Published: April 2013

Abstract
In recent years, the study of animal law has grown exceptionally in the U.S., along with an increased recognition and interest in this burgeoning field. A growing eagerness among students to study animal law, as well as strong academic and financial support are all important contributors to successful animal law programs. This article explores the development of animal law scholarship in U.S. law schools and provides an overview of the types of courses offered as well as various academic, professional, and financial resources available to the next generation of animal law practitioners.
A longitudinal evaluation of the relationship between first morning urinary and salivary cortisol
Authors: Sarkar Phoebe L. , Zeng Leilei , Chen Yingying , Salvante Katrina G. , Nepomnaschy Pablo A. 
Published: April 2013

AbstractCortisol is one of the most frequently used stress biomarkers in humans. Urine and saliva are the matrices of choice to longitudinally monitor cortisol levels. Salivary and urinary cortisol are often discussed as though they provide similar information. However, the relationship between “free” cortisol levels in urine (nonconjugated) and saliva (non‐protein‐bound) has yet to be properly evaluated using naturalistic designs.ObjectivesTo investigate the longitudinal relationship between salivary cortisol (SC) and first morning urinary cortisol (FMUC), and to compare the advantages and disadvantages of these matrices in assessing longitudinal changes in cortisol secretion using naturalistic designs.MethodsCortisol levels from 31 healthy, Kakchiquel Mayan women in Guatemala were compared in one first morning urine (FMU) and four saliva specimens collected daily across three alternate days. Linear mixed‐effect regression models including fixed and random effects were used to analyze the repeated‐measures data.ResultsFMUC levels (16.04–242.18 ng/ml) were higher than SC levels (0.21–5.16 ng/ml). A small but statistically significant relationship was found between FMUC and SC (each 1 ng/ml increase in FMUC predicted a 0.1% increase in SC; P < 0.05).ConclusionsNonconjugated FMUC levels are related to non‐protein‐bound SC levels collected throughout the day. FMU presents several advantages over saliva for the longitudinal assessment of cortisol in naturalistic studies. Cortisol levels are about 53‐fold higher in FMU than in saliva, which makes between‐ and within‐individual variation easier to detect, and FMUC levels are less likely to be affected by confounders than diurnal SC levels. Am. J. Hum. Biol. 25:351–358, 2013. © 2013 Wiley Periodicals, Inc.
Father absence and age at first birth in a western sample
Authors: Boothroyd Lynda G. , Craig Peter S. , Crossman Richard J. , Perrett David I. 
Published: April 2013

ObjectivesAlthough a large literature has shown links between “father absence” during early childhood, and earlier puberty and sexual behavior in girls in Western populations, there are only a few studies which have looked at timing of reproduction, and only one of these fully incorporated childless respondents to investigate whether father absence is associated with increased hazard of becoming a parent at one time point (early) more than another. Here we sought to clarify exactly when, if at all, father absence increased the likelihood of first birth in a Western sample.MethodsAn online sample of 954 women reported on their childhood living circumstances, their age of menarche, first coitus, first pregnancy, and first birth.ResultsCox regression and Kaplan–Meier plots showed an increased risk of becoming a parent for father absent women in their 20s, but no overall greater likelihood of parenthood.ConclusionThese data support the suggestion that father absence is associated with an acceleration of reproductive behavior in Western samples, rather than a simple increase in likelihood of reproduction. Am. J. Hum. Biol. 25:366–369, 2013. © 2013 Wiley Periodicals, Inc.
Adiposity, muscle, and physical activity: Predictors of perturbations in heart rate variability
Authors: Andrew Michael E. , Shengqiao LI , Wactawski‐Wende Jean , Dorn Joan P. , Mnatsakanova Anna , Charles Luenda E. , Fekedulegn Desta , Miller Diane B. , Violanti John M. , Burchfiel Cecil M. , Sharp Dan S. 
Published: April 2013

ABSTRACTObjectivesThis study examines cross‐sectional associations of indices of adiposity, lean body mass, and physical activity, with heart rate variability (HRV), a marker for parasympathetic cardiac vagal control.MethodsThe study population consists of 360 officers from the Buffalo New York Police Department. Indices of adiposity include body mass index, waist circumference, and a fat‐mass index taken from dual‐energy X‐ray absorptiometry (DEXA) measurements. Lean body mass indices were derived from DEXA measurements of trunk mass and extremity lean mass. Physical activity was measured using a 7‐day self‐report questionnaire. HRV was obtained from 5‐min electrocardiogram measurements by means of parametric spectral analysis resulting in estimates for high‐frequency (HF) and low‐frequency (LF) HRV.ResultsBoth HF and LF HRV were significantly associated with markers for adiposity, two components of lean mass and physical activity with all associations being in the expected direction except that for trunk lean mass. This unexpected result is explained by the possibility that trunk mass is a marker for visceral adiposity rather than lean mass. Body mass index did not explain any additional variance in HRV above and beyond waist circumference and the DEXA indices.ConclusionsHigher levels of physical activity, lower levels of markers for central adiposity and higher lean mass in the extremities predict higher levels of HRV in this population of police officers. This association between modifiable risk factors and markers for autonomic function suggest possible interventions that may improve health and performance. Am. J. Hum. Biol. 25:370–377, 2013. © 2013 Wiley Periodicals, Inc.
Orphan PTMs: Rare, yet functionally important modifications of cysteine
Authors: Shannon D. Alexander , Weerapana Eranthie 
Published: April 2013

ABSTRACTThe enhanced nucleophilicity and redox sensitivity of the thiol group renders cysteine residues susceptible to numerous electrophilic and oxidative post‐translational modifications to form disulfides, sulfenic acids, nitrosothiols, and lipid‐modified species. Outside of these well‐characterized modifications of cysteine, there are reports of cysteine modification through phosphorylation, methylation, and ubiquitination. Although these post‐translational modifications are highly abundant on other amino acids, they play a less pervasive role in cysteine biology. Despite the rarity of these modifications of cysteine, they have been shown to play critical roles in catalysis and regulation. Here we describe these rare post‐translational modifications of cysteine in detail, by describing their discovery and functional characterization on diverse proteins. Furthermore, we highlight potential proteomic tools that may aid in globally identifying these modifications to fully elucidate their abundance in biological systems. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 156–164, 2014.
The Isotropic Semicircle Law and Deformation of Wigner Matrices
Authors: Knowles Antti , Yin Jun 
Published: April 2013

We analyze the spectrum of additive finite‐rank deformations of N × N Wigner matrices H. The spectrum of the deformed matrix undergoes a transition, associated with the creation or annihilation of an outlier, when an eigenvalue di of the deformation crosses a critical value ± 1. This transition happens on the scale . We allow the eigenvalues di of the deformation to depend on N under the condition . We make no assumptions on the eigenvectors of the deformation. In the limit N → ∞, we identify the law of the outliers and prove that the nonoutliers close to the spectral edge have a universal distribution coinciding with that of the extremal eigenvalues of a Gaussian matrix ensemble.A key ingredient in our proof is the isotropic local semicircle law, which establishes optimal high‐probability bounds on where m(z) is the Stieltjes transform of Wigner's semicircle law and v, w are arbitrary deterministic vectors.© 2013 Wiley Periodicals, Inc.
A flexible and robust approach for segmenting cell nuclei from 2D microscopy images using supervised learning and template matching
Authors: Chen Cheng , Wang Wei , Ozolek John A. , Rohde Gustavo K. 
Published: April 2013

AbstractWe describe a new supervised learning‐based template matching approach for segmenting cell nuclei from microscopy images. The method uses examples selected by a user for building a statistical model that captures the texture and shape variations of the nuclear structures from a given dataset to be segmented. Segmentation of subsequent, unlabeled, images is then performed by finding the model instance that best matches (in the normalized cross correlation sense) local neighborhood in the input image. We demonstrate the application of our method to segmenting nuclei from a variety of imaging modalities, and quantitatively compare our results to several other methods. Quantitative results using both simulated and real image data show that, while certain methods may work well for certain imaging modalities, our software is able to obtain high accuracy across several imaging modalities studied. Results also demonstrate that, relative to several existing methods, the template‐based method we propose presents increased robustness in the sense of better handling variations in illumination, variations in texture from different imaging modalities, providing more smooth and accurate segmentation borders, as well as handling better cluttered nuclei. © 2013 International Society for Advancement of Cytometry