bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optical spectra of the silicon-terminated carbon chain radicals SiCnH (n = 3,4,5)
Authors: Kokkin D. L. , Reilly N. J. , Fortenberry R. C. , Crawford T. D. , McCarthy M. C. 
Published: July 2014

The gas-phase optical spectra of three silicon-terminated carbon chain radicals, SiCnH (n = 3 − 5), formed in a jet-cooled discharge of silane and acetylene, have been investigated by resonant two-color two-photon ionization and laser-induced fluorescence/dispersed fluorescence. Analysis of the spectra was facilitated by calculations performed using equation-of-motion coupled cluster methods. For SiC3H and SiC5H, the observed transitions are well-described as excitations from a 2Π ground state to a 2Σ state, in which vibronic coupling, likely involving a higher-lying Π state with a very large predicted f-value (close to unity), is persistent. The lowest 2Σ states of both species are characterized by a rare silicon triple bond, which was identified previously [T. C. Smith, H. Y. Li, D. J. Clouthier, C. T. Kingston, and A. J. Merer, J. Chem. Phys. 112, 3662 (2000)] in the lowest 2Σ state of SiCH. Although a strong Π − Π transition is predicted for SiC4H, the observed spectrum near 505 nm more likely corresponds to excitation to a relatively dark Σ state which is vibronically coupled to a nearby Π state. In contrast to the chains with an odd number of carbon atoms, which exhibit relatively sharp spectral features and lifetimes in the 10–100 ns range, SiC4H shows intrinsically broadened spectral features consistent with a ∼100 fs lifetime, and a subsequent long-lived decay (&gt;50 μs) which we ascribe to mixing with a nearby quartet state arising from the same electronic configuration. The spin-orbit coupling constants for both SiC3H and SiC5H radicals were determined to be approximately 64 cm−1, similar to that of SiCH (69.8 cm−1), suggesting that the unpaired electron in these species is localized on the silicon atom. Motivated by the new optical work, the rotational spectrum of linear SiC3H was detected by cavity Fourier-transform microwave spectroscopy in the 13–34 GHz range. Each rotational transition from the \documentclass[12pt]{minimal}\begin{document}$^2\Pi _{\nicefrac{3}{2}}$\end{document}Π3/22 ground state exhibits well-resolved Λ-doubling and hyperfine structure; the derived rotational constant of B = 2.605 GHz is in excellent agreement with our calculations.
Strand-specific (asymmetric) contribution of phosphodiester linkages on RNA polymerase II transcriptional efficiency and fidelity
Authors: Xu Liang , Zhang Lu , Chong Jenny , Xu Jun , Huang Xuhui , Wang Dong 
Published: July 2014

Significance
The nonenzymatic RNA polymerization introduces backbone heterogeneity with a mixture of 2′–5′ and 3′–5′ linkages. RNA polymerase II (pol II) is a key modern enzyme responsible for synthesizing 3′–5′–linked RNA with high fidelity. It is unclear how pol II selectively recognizes the 3′–5′ over 2′–5′ linkage. Here, we systematically investigated how phosphodiester linkages of nucleic acids govern pol II transcriptional efficiency and fidelity. We revealed pol II has an asymmetric (strand-specific) recognition of phosphodiester linkage, which may reflect a universal principle of template-dependent genetic information transfer. Our results elucidate essential contributions of the phosphodiester linkage to pol II transcription and provide important understanding on nucleic acid recognition and genetic information transfer during molecular evolution.
National Osteoporosis Society Vitamin D Guideline Summary
Authors: Aspray Terry J. , Bowring Claire , Fraser William , Gittoes Neil , Javaid M. Kassim , Macdonald Helen , Patel Sanjeev , Selby Peter , Tanna Nuttan , Francis Roger M. 
Published: July 2014

AbstractThe National Osteoporosis Society (NOS) published its document, Vitamin D and Bone Health: A Practical Clinical Guideline for Patient Management, in 2013 as a practical clinical guideline on the management of vitamin D deficiency in adult patients with, or at risk of developing, bone disease. There has been no clear consensus in the UK on vitamin D deficiency its assessment and treatment, and clinical practice is inconsistent. This guideline is aimed at clinicians, including doctors, nurses and dieticians. It recommends the measurement of serum 25 (OH) vitamin D (25OHD) to estimate vitamin D status in the following clinical scenarios: bone diseases that may be improved with vitamin D treatment; bone diseases, prior to specific treatment where correcting vitamin D deficiency is appropriate; musculoskeletal symptoms that could be attributed to vitamin D deficiency. The guideline also states that routine vitamin D testing is unnecessary where vitamin D supplementation with an oral antiresorptive treatment is already planned and sets the following serum 25OHD thresholds: &lt;30 nmol/l is deficient; 30–50 nmol/l may be inadequate in some people; &gt;50 nmol/l is sufficient for almost the whole population.For treatment, oral vitamin D3 is recommended with fixed loading doses of oral vitamin D3 followed by regular maintenance therapy when rapid correction of vitamin D deficiency is required, although loading doses are not necessary where correction of deficiency is less urgent or when co-prescribing with an oral antiresorptive agent. For monitoring, serum calcium (adjusted for albumin) should be checked 1 month after completing a loading regimen, or after starting vitamin D supplementation, in case primary hyperparathyroidism has been unmasked. However, routine monitoring of serum 25OHD is generally unnecessary but may be appropriate in patients with symptomatic vitamin D deficiency or malabsorption and where poor compliance with medication is suspected.The guideline focuses on bone health as, although there are numerous putative effects of vitamin D on immunity modulation, cancer prevention and the risks of cardiovascular disease and multiple sclerosis, there remains considerable debate about the evaluation of extraskeletal factors and optimal vitamin D status in these circumstances.
FARVAT: a family-based rare variant association test
Authors: Choi Sungkyoung , Lee Sungyoung , Cichon Sven , Nöthen Markus M. , Lange Christoph , Park Taesung , Won Sungho 
Published: July 2014

AbstractMotivation : Individuals in each family are genetically more homogeneous than unrelated individuals, and family-based designs are often recommended for the analysis of rare variants. However, despite the importance of family-based samples analysis, few statistical methods for rare variant association analysis are available.Results: In this report, we propose a FA mily-based R are V ariant A ssociation T est ( FARVAT ). FARVAT is based on the quasi-likelihood of whole families, and is statistically and computationally efficient for the extended families. FARVAT assumed that families were ascertained with the disease status of family members, and incorporation of the estimated genetic relationship matrix to the proposed method provided robustness under the presence of the population substructure. Depending on the choice of working matrix, our method could be a burden test or a variance component test, and could be extended to the SKAT-O-type statistic. FARVAT was implemented in C++, and application of the proposed method to schizophrenia data and simulated data for GAW17 illustrated its practical importance.Availability: The software calculates various statistics for the analysis of related samples, and it is freely downloadable from http://healthstats.snu.ac.kr/software/farvat .Contact: won1@snu.ac.kr or tspark@stats.snu.ac.krSupplementary information: supplementary data are available at Bioinformatics online.
NetPathMiner: R/Bioconductor package for network path mining through gene expression
Authors: Mohamed Ahmed , Hancock Timothy , Nguyen Canh Hao , Mamitsuka Hiroshi 
Published: July 2014

Abstract
Summary: NetPathMiner is a general framework for mining, from genome-scale networks, paths that are related to specific experimental conditions. NetPathMiner interfaces with various input formats including KGML, SBML and BioPAX files and allows for manipulation of networks in three different forms: metabolic, reaction and gene representations. NetPathMiner ranks the obtained paths and applies Markov model-based clustering and classification methods to the ranked paths for easy interpretation. NetPathMiner also provides static and interactive visualizations of networks and paths to aid manual investigation.
Availability: The package is available through Bioconductor and from Github at http://github.com/ahmohamed/NetPathMiner
Contact: mohamed@kuicr.kyoto-u.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Greater power and computational efficiency for kernel-based association testing of sets of genetic variants
Authors: Lippert Christoph , Xiang Jing , Horta Danilo , Widmer Christian , Kadie Carl , Heckerman David , Listgarten Jennifer 
Published: July 2014

AbstractMotivation: Set-based variance component tests have been identified as a way to increase power in association studies by aggregating weak individual effects. However, the choice of test statistic has been largely ignored even though it may play an important role in obtaining optimal power. We compared a standard statistical test—a score test—with a recently developed likelihood ratio (LR) test. Further, when correction for hidden structure is needed, or gene–gene interactions are sought, state-of-the art algorithms for both the score and LR tests can be computationally impractical. Thus we develop new computationally efficient methods.Results: After reviewing theoretical differences in performance between the score and LR tests, we find empirically on real data that the LR test generally has more power. In particular, on 15 of 17 real datasets, the LR test yielded at least as many associations as the score test—up to 23 more associations—whereas the score test yielded at most one more association than the LR test in the two remaining datasets. On synthetic data, we find that the LR test yielded up to 12% more associations, consistent with our results on real data, but also observe a regime of extremely small signal where the score test yielded up to 25% more associations than the LR test, consistent with theory. Finally, our computational speedups now enable (i) efficient LR testing when the background kernel is full rank, and (ii) efficient score testing when the background kernel changes with each test, as for gene–gene interaction tests. The latter yielded a factor of 2000 speedup on a cohort of size 13 500.Availability: Software available at http://research.microsoft.com/en-us/um/redmond/projects/MSCompBio/Fastlmm/ .Contact: heckerma@microsoft.comSupplementary information: Supplementary data are available at Bioinformatics online.
Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG
Authors: Crabtree Jonathan , Agrawal Sonia , Mahurkar Anup , Myers Garry S. , Rasko David A. , White Owen 
Published: July 2014

Abstract
Summary: Circleator is a Perl application that generates circular figures of genome-associated data. It leverages BioPerl to support standard annotation and sequence file formats and produces publication-quality SVG output. It is designed to be both flexible and easy to use. It includes a library of circular track types and predefined configuration files for common use-cases, including. (i) visualizing gene annotation and DNA sequence data from a GenBank flat file, (ii) displaying patterns of gene conservation in related microbial strains, (iii) showing Single Nucleotide Polymorphisms (SNPs) and indels relative to a reference genome and gene set and (iv) viewing RNA-Seq plots.
Availability and implementation: Circleator is freely available under the Artistic License 2.0 from http://jonathancrabtree.github.io/Circleator/ and is integrated with the CloVR cloud-based sequence analysis Virtual Machine (VM), which can be downloaded from http://clovr.org or run on Amazon EC2.
Contact: jcrabtree@som.umaryland.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Metabomxtr: an R package for mixture-model analysis of non-targeted metabolomics data
Authors: Nodzenski Michael , Muehlbauer Michael J. , Bain James R. , Reisetter Anna C. , Lowe William L. , Scholtens Denise M. 
Published: July 2014

Abstract
Summary: Non-targeted metabolomics technologies often yield data in which abundance for any given metabolite is observed and quantified for some samples and reported as missing for other samples. Apparent missingness can be due to true absence of the metabolite in the sample or presence at a level below detectability. Mixture-model analysis can formally account for metabolite ‘missingness’ due to absence or undetectability, but software for this type of analysis in the high-throughput setting is limited. The R package metabomxtr has been developed to facilitate mixture-model analysis of non-targeted metabolomics data in which only a portion of samples have quantifiable abundance for certain metabolites.
Availability and implementation: metabomxtr is available through Bioconductor. It is released under the GPL-2 license.
Contact: dscholtens@northwestern.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Retro: concept-based clustering of biomedical topical sets
Authors: Yeganova Lana , Kim Won , Kim Sun , Wilbur W. John 
Published: July 2014

AbstractMotivation: Clustering methods can be useful for automatically grouping documents into meaningful clusters, improving human comprehension of a document collection. Although there are clustering algorithms that can achieve the goal for relatively large document collections, they do not always work well for small and homogenous datasets.Methods: In this article, we present Retro—a novel clustering algorithm that extracts meaningful clusters along with concise and descriptive titles from small and homogenous document collections. Unlike common clustering approaches, our algorithm predicts cluster titles before clustering. It relies on the hypergeometric distribution model to discover key phrases, and generates candidate clusters by assigning documents to these phrases. Further, the statistical significance of candidate clusters is tested using supervised learning methods, and a multiple testing correction technique is used to control the overall quality of clustering.Results: We test our system on five disease datasets from OMIM ® and evaluate the results based on MeSH ® term assignments. We further compare our method with several baseline and state-of-the-art methods, including K-means, expectation maximization, latent Dirichlet allocation-based clustering, Lingo, OPTIMSRC and adapted GK-means. The experimental results on the 20-Newsgroup and ODP-239 collections demonstrate that our method is successful at extracting significant clusters and is superior to existing methods in terms of quality of clusters. Finally, we apply our system to a collection of 6248 topical sets from the HomoloGene ® database, a resource in PubMed ® . Empirical evaluation confirms the method is useful for small homogenous datasets in producing meaningful clusters with descriptive titles.Availability and implementation: A web-based demonstration of the algorithm applied to a collection of sets from the HomoloGene database is available at http://www.ncbi.nlm.nih.gov/CBBresearch/Wilbur/IRET/CLUSTERING_HOMOLOGENE/index.html .Contact: lana.yeganova@nih.govSupplementary Information: Supplementary data are available at Bioinformatics online.
The telomeric protein Pot1 from Schizosaccharomyces pombe binds ssDNA in two modes with differing 3′ end availability
Authors: Dickey Thayne H. , Wuttke Deborah S. 
Published: July 2014

Abstract
Telomere protection and length regulation are important processes for aging, cancer and several other diseases. At the heart of these processes lies the single-stranded DNA (ssDNA)-binding protein Pot1, a component of the telomere maintenance complex shelterin, which is present in species ranging from fission yeast to humans. Pot1 contains a dual OB-fold DNA-binding domain (DBD) that fully confers its high affinity for telomeric ssDNA. Studies of S. pombe Pot1-DBD and its individual OB-fold domains revealed a complex non-additive behavior of the two OB-folds in the context of the complete Pot1 protein. This behavior includes the use of multiple distinct binding modes and an ability to form higher order complexes. Here we use NMR and biochemical techniques to investigate the structural features of the complete Pot1-DBD. These experiments reveal one binding mode characterized by only subtle alternations to the individual OB-fold subdomain structures, resulting in an inaccessible 3′ end of the ssDNA. The second binding mode, which has equivalent affinity, interacts differently with the 3′ end, rendering it available for interaction with other proteins. These findings suggest a structural switch that contributes to telomere end-protection and length regulation.
Cortical Bone Trajectory for Thoracic Pedicle Screws
Authors: Matsukawa Keitaro , Yato Yoshiyuki , Hynes Richard A. , Imabayashi Hideaki , Hosogane Naobumi , Asazuma Takashi , Matsui Toshiyasu , Kobayashi Yasushi , Nemoto Koichi 
Published: July 2014

Study Design:
A morphometric measurement of new thoracic pedicle screw trajectory using computed tomography and a biomechanical study on cadaveric thoracic vertebrae using insertional torque.

Objective:
To introduce a new thoracic pedicle screw trajectory which maximizes engagement with denser bone.

Summary of Background Data:
Cortical bone trajectory (CBT) which maximizes the thread contact with cortical bone provides enhanced screw purchase. Despite the increased use of CBT screws in the lumbar spine, no study has yet reported the insertional technique for thoracic CBT.

Methods:
First, the computed tomography scans of 50 adults were studied for morphometric measurement of lower thoracic CBT. The starting point was determined to be the intersection of the lateral two thirds of the superior articular process and the inferior border of the transverse process. The trajectory was straight forward in the axial plane angulated cranially targeting the posterior third of the superior endplate. The maximum diameter, length, and the cephalad angle were investigated. Next, the insertional torque of pedicle screws using this new technique was measured and compared with that of the traditional technique on 24 cadaveric thoracic vertebrae.

Results:
All morphometric parameters of thoracic CBT increased from T9 to T12 (the mean diameter: from 5.8 mm at T9 to 8.5 mm at T12; the length: from 29.7 mm at T9 to 32.0 mm at T12; and the cephalad angle: from 21.4 degrees at T9 to 27.6 degrees at T12). The mean maximum insertional torque of CBT screws and traditional screws were 1.02±0.25 and 0.66±0.15 Nm, respectively. The new technique demonstrated average 53.8% higher torque than the traditional technique (P<0.01).

Conclusions:
The detailed morphometric measurement and favorable screw fixation stability of thoracic CBT are reported. The insertional torque using thoracic CBT technique was 53.8% higher than that of the traditional technique.
Above‐ground carbon assessment in theKom‐Mengamé forest conservation complex,SouthCameroon: Exploring the potential of managing forests for biodiversity and carbon
Authors: Fongnzossie Evariste Fedoung , Sonwa Denis Jean , Kemeuze Victor , Auzel Phillipe , Nkongmeneck Bernard‐Aloys 
Published: July 2014

AbstractProtected areas are important for biodiversity conservation and the maintenance of ecosystem services, including climate regulation through carbon storage. Yet, there is little knowledge of their carbon storage potential. This study assesses the above‐ground carbon stock and the congruence between carbon stock and tree diversity in theKom‐Mengamé forest conservation complex (KMFCC) inSouth‐Cameroon, based on an inventory of trees withDBH≥ 10 cm in 1,366 plots (100 × 5 m each) covering 63.8 ha, established in different land use types (terra firma forest, swamp forest and cultivated areas). Above‐ground carbon was estimated using generic allometric equation and species‐specific wood density derived from wood density databases. Results showed high carbon stock inKMFCCwith values ranging from 143.29 ± 124.37 Mg/ha‐1 in swamp areas to 240 ± 204.35 Mg/ha‐1 in terra firma forests. Mean carbon stock in managed areas differed from that of terra firma forests. Petersianthus macrocarpus showed the greatest carbon stock. The study demonstrates the need for integrated approaches for carbon management in secondary forests where agroforests might be important to maintain biodiversity associated with high carbon storage. These approaches are particularly relevant to theCongo basin region where protected areas are threatened by poor management of their periphery.
Impact of Essential Oils on the Taste Acceptance of Tomato Juice, Vegetable Soup, or Poultry Burgers
Authors: Espina Laura , García‐Gonzalo Diego , Pagán Rafael 
Published: July 2014

AbstractDespite the vast body of available literature on the possibilities of essential oils (EOs) as food preservatives or functional ingredients, the sensory impact of their addition to foods has barely been approached. This work focuses on the hedonic taste acceptance of 3 food products (tomato juice, vegetable soup, and poultry burgers) when they are incorporated with potentially antimicrobial concentrations (20 to 200 μL/L) of 6 selected EOs (lemon, pennyroyal mint, thyme, and rosemary) and individual compounds (carvacrol, p‐cymene). Although addition of 20 μL/L of pennyroyal mint or lemon EO did not change the taste acceptance of tomato juice, higher concentrations of these compounds or any concentration of the other 4 compounds did. In vegetable soup, the tolerance limit for rosemary EO, thyme EO, carvacrol, or p‐cymene was 20 μL/L, while the addition of 200 μL/L of lemon EO was accepted. Tolerance limits in poultry burgers were established in 20 μL/L for carvacrol and thyme EOs, 100 μL/L for pennyroyal mint EO and p‐cymene, and 200 μL/L for lemon and rosemary EOs. Moreover, incorporation of pennyroyal mint EO to tomato juice or poultry burgers, and enrichment of vegetable soup with lemon EO, could contribute to the development of food products with an improved sensory appeal.
Colonization by endophytic Ochrobactrum anthropi Mn1 promotes growth of Jerusalem artichoke
Authors: Meng Xianfa , Yan Dekai , Long Xiaohua , Wang Changhai , Liu Zhaopu , Rengel Zed 
Published: July 2014

SummaryThe Ochrobactrum anthropi Mn1 strain, taxonomically identified using 16S ribosomal DNA sequence, was isolated from roots of Jerusalem artichoke. Its endophytic colonization was investigated microscopically using green fluorescent protein introduced by vector pHC60. The strain entered Jerusalem artichoke tissues through the root, and was localized in the roots and stems. The plant growth‐promoting (PGP) effects of O. anthropi Mn1 were assessed in greenhouse as well as field trials with different nitrogen supplies. Only under moderate to ample nitrogen supply, could O. anthropi Mn1 promoted growth of host plant. The PGP effects of the strain were symbiotic nitrogen fixation, root morphological optimization and enhanced nutrient uptake. We hypothesize that the symbiotic interspecies interaction might be quorum sensing related.