bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cystoscopic placement of transurethral stent in a fetus with urethral stenosis
Authors: Ruano R. , Yoshizaki C. T. , Giron A. M. , Srougi M. , Zugaib M. 
Published: December 2013

ABSTRACTWe report the case of a fetus with severe megabladder, displaying the ‘keyhole’ sign on ultrasound imaging, that underwent cystoscopy at 22 weeks' gestation. There was a familial history of mild urethral atresia. Fetal cystoscopy revealed congenital urethral atresia. A guide wire was advanced through the fetal urethra and a transurethral vesicoamniotic stent was placed successfully. The fetus was delivered at 36 weeks' gestation and postnatal cystoscopy confirmed the absence of posterior urethral valves or urethral atresia. The infant was 5 years old with normal renal function at the time of writing. We conclude that fetal cystoscopic placement of a transurethral stent for congenital urethral stenosis is feasible. Copyright © 2013 ISUOG. Published by John Wiley & Sons Ltd
Effects of a forest pathogen on habitat selection and quality for the endangered golden‐cheeked warbler
Authors: Stewart Laura R. , Morrison Michael L. , Hutchinson Mark R. , Appel David N. , Wilkins R. Neal 
Published: December 2013

ABSTRACTOak wilt is a fatal forest disease caused by the fungus Ceratocystis fagacearum. Loss or degradation of habitat caused by oak wilt may negatively affect forest songbirds, including the federally endangered golden‐cheeked warbler (Setophaga chrysoparia), a species that breeds exclusively in the Ashe juniper–oak woodlands (Juniperus ashei–Quercus spp.) of central Texas, USA. During 2010 and 2011, we investigated the influence of oak wilt on golden‐cheeked warbler habitat selection and quality at 25 study sites that each contained forest affected by oak wilt and unaffected forest. We assessed habitat selection in terms of use versus availability at 2 scales: within the patch and within the territory. We also assessed post‐breeding use of affected forest by comparing detection densities in affected and unaffected forest. To assess the influence of oak wilt on habitat quality, we compared the reproductive outcome of territories in unaffected and affected areas. We assessed within‐patch habitat selection for 67 territories and found that golden‐cheeked warblers used affected forest significantly less than its availability. We found use of affected forest to be variable within the 14 territories that contained affected forest in >10% of their area. Post‐breeding use of affected forest was also variable. Pairing success was 27% lower for males whose territories contained >10% affected forest but fledging success was not affected. Our results suggest that the presence of oak wilt negatively influences habitat selection and quality for golden‐cheeked warblers, likely due to reduced canopy cover in susceptible oak species. © 2013 The Wildlife Society.
Lung uptake on I-131 therapy and short-term outcome in patients with lung metastasis from differentiated thyroid cancer
Authors: Okamoto Shozo , Shiga Tohru , Uchiyama Yuko , Manabe Osamu , Kobayashi Kentaro , Yoshinaga Keiichiro , Tamaki Nagara 
Published: December 2013

Abstract

Objective
It is sometimes difficult to assess I-131 lung uptake at the initial I-131 therapy because of strong artifacts from I-131 uptake in the thyroid bed. The aim of this study was to analyze the lung uptake at the second I-131 therapy for lung metastasis in patients who did not have lung uptake at the initial therapy from differentiated thyroid carcinoma (DTC). Then, we also analyzed the relationship between the initial lung uptake and short-term outcome after I-131 therapies.

Methods
This study included 62 DTC patients with lung metastasis. The patients were classified into 2 groups according to the lung uptake at the initial I-131 therapy such as patients with lung uptake (positive uptake group n = 31) and those without lung uptake (negative uptake group n = 31). The lung uptake was analyzed at the second therapy in both groups. The short-term outcome was also analyzed based on the CT findings of lung metastasis size and serum thyroglobulin level between the two groups.

Results
The positive uptake group showed positive lung uptake at the second therapy in 23 patients (74 %), whereas none of negative uptake group showed any lung uptake at the second therapy (P < 0.01). The positive uptake group significantly decreased in the size of lung metastasis from the initial therapy to the second therapy (20.0 ± 11.7 to 16.6 ± 9.6 mm, P < 0.01) with further decrease after the second therapy (P < 0.05). The serum thyroglobulin level was also significantly decreased from the initial therapy to the second therapy (4348 ± 7011 to 2931 ± 4484 ng/ml, P < 0.05). In contrast, the negative uptake group significantly increased in the size of lung metastasis from the initial therapy to the second therapy (17.3 ± 12.2 to 19.9 ± 14.3 mm, P < 0.01) with further increase after the second therapy (P < 0.01).

Conclusion
No patients without lung uptake at the initial I-131 therapy showed lung uptake at the second therapy, or showed treatment effect. Therefore, second I-131 therapy for these patients with initially negative lung uptake should be considered cautiously.
Phylogeny-based classification of microbial communities
Authors: Tanaseichuk Olga , Borneman James , Jiang Tao 
Published: December 2013

Abstract
Motivation: Next-generation sequencing coupled with metagenomics has led to the rapid growth of sequence databases and enabled a new branch of microbiology called comparative metagenomics. Comparative metagenomic analysis studies compositional patterns within and between different environments providing a deep insight into the structure and function of complex microbial communities. It is a fast growing field that requires the development of novel supervised learning techniques for addressing challenges associated with metagenomic data, e.g. sensitivity to the choice of sequence similarity cutoff used to define operational taxonomic units (OTUs), high dimensionality and sparsity of the data and so forth. On the other hand, the natural properties of microbial community data may provide useful information about the structure of the data. For example, similarity between species encoded by a phylogenetic tree captures the relationship between OTUs and may be useful for the analysis of complex microbial datasets where the diversity patterns comprise features at multiple taxonomic levels. Even though some of the challenges have been addressed by learning algorithms in the literature, none of the available methods take advantage of the inherent properties of metagenomic data.
Results: We proposed a novel supervised classification method for microbial community samples, where each sample is represented as a set of OTU frequencies, which takes advantage of the natural structure in microbial community data encoded by a phylogenetic tree. This model allows us to take advantage of environment-specific compositional patterns that may contain features at multiple granularity levels. Our method is based on the multinomial logistic regression model with a tree-guided penalty function. Additionally, we proposed a new simulation framework for generating 16S ribosomal RNA gene read counts that may be useful in comparative metagenomics research. Our experimental results on simulated and real data show that the phylogenetic information used in our method improves the classification accuracy.
Availability and implementation: http://www.cs.ucr.edu/∼tanaseio/metaphyl.htm.
Contact: tanaseio@cs.ucr.edu or jiang@cs.ucr.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Improving computational efficiency and tractability of protein design using a piecemeal approach. A strategy for parallel and distributed protein design
Authors: Pitman Derek J. , Schenkelberg Christian D. , Huang Yao-Ming , Teets Frank D. , DiTursi Daniel , Bystroff Christopher 
Published: December 2013

Abstract
Motivation: Accuracy in protein design requires a fine-grained rotamer search, multiple backbone conformations, and a detailed energy function, creating a burden in runtime and memory requirements. A design task may be split into manageable pieces in both three-dimensional space and in the rotamer search space to produce small, fast jobs that are easily distributed. However, these jobs must overlap, presenting a problem in resolving conflicting solutions in the overlap regions.
Results: Piecemeal design, in which the design space is split into overlapping regions and rotamer search spaces, accelerates the design process whether jobs are run in series or in parallel. Large jobs that cannot fit in memory were made possible by splitting. Accepting the consensus amino acid selection in conflict regions led to non-optimal choices. Instead, conflicts were resolved using a second pass, in which the split regions were re-combined and designed as one, producing results that were closer to optimal with a minimal increase in runtime over the consensus strategy. Splitting the search space at the rotamer level instead of at the amino acid level further improved the efficiency by reducing the search space in the second pass.
Availability and implementation: Programs for splitting protein design expressions are available at www.bioinfo.rpi.edu/tools/piecemeal.html.
Contact: bystrc@rpi.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
tasiRNAdb: a database of ta-siRNA regulatory pathways
Authors: Zhang Changqing , Li Guangping , Zhu Shinong , Zhang Shuo , Fang Jinggui 
Published: December 2013

Abstract
Summary: In plants, many trans-acting small interfering RNA (ta-siRNA) regulatory pathways have been identified as significant components of the gene networks involved in development, metabolism, responses to biotic and abiotic stresses and DNA methylation at the TAS locus. To obtain a more comprehensive understanding on the nature of ta-siRNA regulatory pathways, we developed a freely accessible resource, tasiRNAdb, to serve as a repository for the sequences of ta-siRNA regulatory pathway-related microRNAs, TASs, ta-siRNAs and ta-siRNA targets, and for the cascading relations among them. With 583 pathways from 18 species, tasiRNAdb is the largest resource for known ta-siRNA regulatory pathways currently available. tasiRNAdb also provides a tool named TasExpAnalysis that was developed to map user-submitted small RNA and degradome libraries to a stored/input TAS and to perform sRNA phasing analysis and TAS cleavage analysis.
Availability: The database of plant ta-siRNA regulatory pathways is available at http://bioinfo.jit.edu.cn/tasiRNADatabase/.
Contact: zhang_chq2002@sohu.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Assimilating genome-scale metabolic reconstructions with modelBorgifier
Authors: Sauls John T. , Buescher Joerg M. 
Published: December 2013

Abstract
Motivation: Genome-scale reconstructions and models, as collections of genomic and metabolic information, provide a useful means to compare organisms. Comparison requires that models are similarly notated to pair shared components.
Result: Matching and comparison of genome-scale reconstructions and models are facilitated by modelBorgifier. It reconciles models in light of different annotation schemes, allowing diverse models to become useful for synchronous investigation.
Availability and implementation: The modelBorgifier toolbox is freely available at http://www.brain-biotech.de/downloads/modelBorgifier.zip.
Contact: jrb@brain-biotech.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Seabed classification using surface backscattering strength versus acoustic frequency and incidence angle measured with vertical, split-beam echosounders
Authors: Cutter George R. , Demer David A. 
Published: December 2013

Abstract
The multifrequency biplanar interferometric imaging technique (MBI) is applied to data from vertical, split-beam echosounders to produce sub-beam estimates of seabed surface-backscattering strength (Ss), incidence angle (θ), and roughness (${\rm {\cal R}}$). A simple model is used to quantify the variation of Ss versus θ = {2–20°} and acoustic frequency, f = {18, 38, 70, 120 and 200 kHz}. The coefficients of the angle- and frequency-dependent terms of the model indicate seabed material properties, principally small- and large-scale roughness and hardness. These indices are combined with the estimates of θ and ${\rm {\cal R}}$ to classify the seabed using unsupervised cluster analysis. This technique is applied to data from the Forty-Three-Fathom Bank, a seamount in the Southern California Bight. The resulting seabed classifications are consistent with the surficial lithology and the spatial distribution of known rockfish (Sebastes spp.) habitat. The method should be generally applicable to seabed classification.
The effects of polymorphisms on human gene targeting
Authors: Deyle David R. , Li Li B. , Ren Gaoying , Russell David W. 
Published: December 2013

AbstractDNA mismatches that occur between vector homology arms and chromosomal target sequences reduce gene targeting frequencies in several species; however, this has not been reported in human cells. Here we demonstrate that even a single mismatched base pair can significantly decrease human gene targeting frequencies. In addition, we show that homology arm polymorphisms can be used to direct allele-specific targeting or to improve unfavorable vector designs that introduce deletions.
Sugar-modified G-quadruplexes: effects of LNA-, 2′F-RNA– and 2′F-ANA-guanosine chemistries on G-quadruplex structure and stability
Authors: Li Zhe , Lech Christopher Jacques , Phan Anh Tuân 
Published: December 2013

Abstract
G-quadruplex-forming oligonucleotides containing modified nucleotide chemistries have demonstrated promising pharmaceutical potential. In this work, we systematically investigate the effects of sugar-modified guanosines on the structure and stability of a (4+0) parallel and a (3+1) hybrid G-quadruplex using over 60 modified sequences containing a single-position substitution of 2′-O-4′-C-methylene-guanosine (LNAG), 2′-deoxy-2′-fluoro-riboguanosine (FG) or 2′-deoxy-2′-fluoro-arabinoguanosine (FANAG). Our results are summarized in two parts: (I) Generally, LNAG substitutions into ‘anti’ position guanines within a guanine-tetrad lead to a more stable G-quadruplex, while substitutions into ‘syn’ positions disrupt the native G-quadruplex conformation. However, some interesting exceptions to this trend are observed. We discover that a LNAG modification upstream of a short propeller loop hinders G-quadruplex formation. (II) A single substitution of either FG or FANAG into a ‘syn’ position is powerful enough to perturb the (3+1) G-quadruplex. Substitution of either FG or FANAG into any ‘anti’ position is well tolerated in the two G-quadruplex scaffolds. FANAG substitutions to ‘anti’ positions are better tolerated than their FG counterparts. In both scaffolds, FANAG substitutions to the central tetrad layer are observed to be the most stabilizing. The observations reported herein on the effects of LNAG, FG and FANAG modifications on G-quadruplex structure and stability will enable the future design of pharmaceutically relevant oligonucleotides.
A phylogenetic model for understanding the effect of gene duplication on cancer progression
Authors: Ma Qin , Reeves Jaxk H. , Liberles David A. , Yu Lili , Chang Zheng , Zhao Jing , Cui Juan , Xu Ying , Liu Liang 
Published: December 2013

AbstractAs biotechnology advances rapidly, a tremendous amount of cancer genetic data has become available, providing an unprecedented opportunity for understanding the genetic mechanisms of cancer. To understand the effects of duplications and deletions on cancer progression, two genomes (normal and tumor) were sequenced from each of five stomach cancer patients in different stages (I, II, III and IV). We developed a phylogenetic model for analyzing stomach cancer data. The model assumes that duplication and deletion occur in accordance with a continuous time Markov Chain along the branches of a phylogenetic tree attached with five extended branches leading to the tumor genomes. Moreover, coalescence times of the phylogenetic tree follow a coalescence process. The simulation study suggests that the maximum likelihood approach can accurately estimate parameters in the phylogenetic model. The phylogenetic model was applied to the stomach cancer data. We found that the expected number of changes (duplication and deletion) per gene for the tumor genomes is significantly higher than that for the normal genomes. The goodness-of-fit test suggests that the phylogenetic model with constant duplication and deletion rates can adequately fit the duplication data for the normal genomes. The analysis found nine duplicated genes that are significantly associated with stomach cancer.
Inhibition of translation by IFIT family members is determined by their ability to interact selectively with the 5′-terminal regions of cap0-, cap1- and 5′ppp- mRNAs
Authors: Kumar Parimal , Sweeney Trevor R. , Skabkin Maxim A. , Skabkina Olga V. , Hellen Christopher U. T. , Pestova Tatyana V. 
Published: December 2013

AbstractRibosomal recruitment of cellular mRNAs depends on binding of eIF4F to the mRNA’s 5′-terminal ‘cap’. The minimal ‘cap0’ consists of N7-methylguanosine linked to the first nucleotide via a 5′-5′ triphosphate (ppp) bridge. Cap0 is further modified by 2′-O-methylation of the next two riboses, yielding ‘cap1’ (m7GpppNmN) and ‘cap2’ (m7GpppNmNm). However, some viral RNAs lack 2′-O-methylation, whereas others contain only ppp- at their 5′-end. Interferon-induced proteins with tetratricopeptide repeats (IFITs) are highly expressed effectors of innate immunity that inhibit viral replication by incompletely understood mechanisms. Here, we investigated the ability of IFIT family members to interact with cap1-, cap0- and 5′ppp- mRNAs and inhibit their translation. IFIT1 and IFIT1B showed very high affinity to cap-proximal regions of cap0-mRNAs (K1/2,app ∼9 to 23 nM). The 2′-O-methylation abrogated IFIT1/mRNA interaction, whereas IFIT1B retained the ability to bind cap1-mRNA, albeit with reduced affinity (K1/2,app ∼450 nM). The 5′-terminal regions of 5′ppp-mRNAs were recognized by IFIT5 (K1/2,app ∼400 nM). The activity of individual IFITs in inhibiting initiation on a specific mRNA was determined by their ability to interact with its 5′-terminal region: IFIT1 and IFIT1B efficiently outcompeted eIF4F and abrogated initiation on cap0-mRNAs, whereas inhibition on cap1- and 5′ppp- mRNAs by IFIT1B and IFIT5 was weaker and required higher protein concentrations.
An H2A histone isotype regulates estrogen receptor target genes by mediating enhancer-promoter-3′-UTR interactions in breast cancer cells
Authors: Su Chia-Hsin , Tzeng Tsai-Yu , Cheng Ching , Hsu Ming-Ta 
Published: December 2013

Abstract
A replication-dependent histone H2A isotype, H2ac, is upregulated in MCF-7 cells and in estrogen receptor-positive clinical breast cancer tissues. Cellular depletion of this H2A isotype leads to defective estrogen signaling, loss of cell proliferation and cell cycle arrest at G0/G1 phase. H2ac mediates regulation of estrogen receptor target genes, particularly BCL2 and c-MYC, by recruiting estrogen receptor alpha through its HAR domain and facilitating the formation of a chromatin loop between the promoter, enhancer and 3′-untranslated region of the respective genes. These findings reveal a new role for histone isotypes in the regulation of gene expression in cancer cells, and suggest that these molecules may be targeted for anti-cancer drug discovery.
Using Mixed Methods to Examine the Role of Veterans’ Illness Perceptions on Depression Treatment Utilization and HEDIS Concordance
Authors: Elwy A. Rani , Glickman Mark E. , Bokhour Barbara G. , Dell Natalie S. , Mueller Nora M. , Zhao Shibei , Osei-Bonsu Princess E. , Rodrigues Stephanie , Coldwell Craig M. , Ngo Tu A. , Schlosser James , Vielhauer Melanie J. , Pirraglia Paul A. , Eisen Susan V. 
Published: December 2013

Background:
Although depression screening occurs annually in the Department of Veterans Affairs (VA) primary care, many veterans may not be receiving guideline-concordant depression treatment.

Objectives:
To determine whether veterans’ illness perceptions of depression may be serving as barriers to guideline-concordant treatment.

Research Design:
We used a prospective, observational design involving a mailed questionnaire and chart review data collection to assess depression treatment utilization and concordance with Healthcare Effectiveness Data and Information Set guidelines adopted by the VA. The Self-Regulation Model of Illness Behavior guided the study.

Subjects:
Veterans who screened positive for a new episode of depression at 3 VA primary care clinics in the US northeast.

Measures:
The Illness Perceptions Questionnaire-Revised, measuring patients’ perceptions of their symptoms, cause, timeline, consequences, cure or controllability, and coherence of depression and its symptoms, was our primary measure to calculate veterans’ illness perceptions. Treatment utilization was assessed 3 months after the positive depression screen through chart review. Healthcare Effectiveness Data and Information Set (HEDIS) guideline-concordant treatment was determined according to a checklist created for the study.

Results:
A total of 839 veterans screened positive for a new episode of depression from May 2009–June 2011; 275 (32.8%) completed the survey. Ninety-two (33.9%) received HEDIS guideline-concordant depression treatment. Veterans’ illness perceptions of their symptoms, cause, timeline, and controllability of depression predicted receiving guideline-concordant treatment.

Conclusions:
Many veterans are not receiving guideline-concordant treatment for depression. HEDIS guideline measures may not be assessing all aspects of quality depression care. Conversations about veterans’ illness perceptions and their specific needs are encouraged to ensure that appropriate treatment is achieved.
Sensitivity of Medicare Claims to Identify Cancer Recurrence in Elderly Colorectal and Breast Cancer Patients
Authors: Warren Joan L. , Mariotto Angela , Melbert Danielle , Schrag Deborah , Doria-Rose Paul , Penson David , Yabroff K. Robin 
Published: December 2013

Background:
Researchers are increasingly interested in using observational data to evaluate cancer outcomes following treatment, including cancer recurrence and disease-free survival. Because population-based cancer registries do not collect recurrence data, recurrence is often imputed from health claims, primarily by identifying later cancer treatments after initial treatment. The validity of this approach has not been established.

Research Design:
We used the linked Surveillance, Epidemiology, and End Results-Medicare data to assess the sensitivity of Medicare claims for cancer recurrence in patients very likely to have had a recurrence. We selected newly diagnosed stage II/III colorectal (n=6910) and female breast cancer (n=3826) patients during 1994–2003 who received initial cancer surgery, had a treatment break, and then died from cancer in 1994–2008. We reviewed all claims from the treatment break until death for indicators of recurrence. We focused on additional cancer treatment (surgery, chemotherapy, radiation therapy) as the primary indicator, and used multivariate logistic regression analysis to evaluate patient factors associated with additional treatment. We also assessed metastasis diagnoses and end-of-life care as recurrence indicators.

Results:
Additional treatment was the first indicator of recurrence for 38.8% of colorectal patients and 35.2% of breast cancer patients. Patients aged 70 and older were less likely to have additional treatment (P < 0.05), in adjusted analyses. Over 20% of patients either had no recurrence indicator before death or had end-of-life care as their first indicator.

Conclusions:
Identifying recurrence through additional cancer treatment in Medicare claims will miss a large percentage of patients with recurrences; particularly those who are older.