bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contemporary Patterns and Survival Outcome of Adjuvant Systemic Therapy for Localized Gastrointestinal Stromal Tumors
Authors: Sineshaw Helmneh M. , Jemal Ahmedin , Lin Chun Chieh , McGinnis LaMar S. , Ward Elizabeth M. 
Published: January 2015

Objectives:
To describe contemporary patterns of and factors associated with adjuvant therapy use and survival outcome after resection of localized gastrointestinal stromal tumors (GISTs) using a large contemporary clinical database.

Methods:
We queried the National Cancer Data Base to identify localized GIST cases diagnosed from 2004 to 2011, and used descriptive and logistic regression analyses to determine patterns of and factors associated with adjuvant therapy. Kaplan-Meier and Cox proportional-hazard model were utilized to generate survival probabilities and hazard ratios (HRs).

Results:
Of 4694 patients, 73.5% received surgery alone, and 26.5% received adjuvant therapy during 2004 to 2011. Receipt of adjuvant therapy more than doubled between 2006 (13.2%) and 2007 (30.5%), peaked to 37.9% in 2009, and then decreased to 25.6% in 2011 (P for trend<0.0001). Receipt of adjuvant therapy monotonically decreased with older age (P for trend<0.0001), and was higher in patients with larger tumor size (>10 cm) than those with smaller tumor size (≤5 cm) (44.1% vs. 15.8%; P<0.0001). Patients who received adjuvant therapy had 46% lower risk of death than those who received surgery alone (HR=0.55; 95% confidence interval, 0.37-0.79; P<0.001); survival benefit was statistically significant for GISTs with >10 cm tumor size (HR=0.42; 95% confidence interval, 0.20-0.89; P=0.02).

Conclusions:
In a large nationwide dataset, we showed that the use of adjuvant therapy for localized GISTs has significantly increased over time and patients treated with adjuvant therapy have better survival than patients treated with surgery alone.
Oral Platelet Gel Supernatant Plus Supportive Medical Treatment Versus Supportive Medical Treatment in the Management of Radiation-induced Oral Mucositis
Authors: Bonfili Pierluigi , Gravina Giovanni L. , Marampon Francesco , Rughetti Anna , Di Staso Mario , Dell’Orso Luigi , Vittorini Francesca , Moro Roberto , La Verghetta Maria E. , Parente Silvia , Reale Marilisa , Ruggieri Valeria , Franzese Pietro , Tombolini Vincenzo , Masciocchi Carlo , Di Cesare Ernesto 
Published: January 2015

Objectives:
In this active control trial, the rate of radio-induced WHO grade 3/4 oral mucositis and the change in quality of life, assessed by OMWQ-HN, were measured in subjects with head and neck cancer treated by platelet gel supernatant (PGS) and supportive medical treatment versus subjects treated by supportive medical treatment alone.

Materials and Methods:
Eighty patients with nonmetastatic head and neck cancer underwent curative or adjuvant radiotherapy. All patients underwent supportive medical treatment and/or PGS at the beginning and during radiotherapy. Sixteen patients received PGS in association with supportive medical treatment. To obtain 2 groups virtually randomized for important clinical characteristics subjects were matched, by propensity analysis, with a group of subjects (64 patients) treated with supportive medical treatment alone.

Results:
Subjects treated with standard supportive treatment experienced significant higher WHO grade 3/4 toxicity (55%; 35/64) than subjects treated by PGS (13%; 3/16). The reduced toxicity found in PGS group paralleled with the evidence that they developed later symptoms with respect to controls. The Cox proportional hazard model indicated that patients treated with standard supportive medical treatment experienced 2.7-fold increase (hazard ratio=2.7; 95% confidence interval, 1.3-5.7) in the occurrence of WHO grade 3/4 toxicity. PGS group significantly experienced higher quality of life than control groups as measured by OMWQ-HN. A significant decrease in the opioid analgesics usage was found in the PGS group.

Conclusions:
These preliminary data should be interpreted with caution and could serve as a framework around which to design future trials.
Surgery and Adjuvant Radiation for High-risk Skin Adnexal Carcinoma of the Head and Neck
Authors: Wang Lora S. , Handorf Elizabeth A. , Wu Hong , Liu Jeffrey C. , Perlis Clifford S. , Galloway Thomas J. 
Published: January 2015

Objectives:
Skin adnexal carcinoma (SAC) is a rare cutaneous malignancy that arises from sebaceous and sweat glands. These carcinomas are believed to behave more aggressively than cutaneous squamous cell carcinomas (SCC) with a propensity for local recurrence. The role of adjuvant radiotherapy in SAC is undefined.

Methods:
We retrospectively reviewed all cases of head and neck SAC treated with surgery and adjuvant radiation from 2000 to 2012 at a single institution.

Results:
Nine cases were identified. Median age was 67 (range, 52 to 88) years. The histologies were: adnexal carcinoma (n=1), adnexal carcinoma with sebaceous differentiation (n=1), adnexal carcinoma with squamous differentiation (n=1), skin appendage carcinoma (n=1), sclerosing sweat duct carcinoma (n=1), mucinous carcinoma (n=1), ductal eccrine adenocarcinoma (n=1), porocarcinoma (n=1), and trichilemmal carcinoma (n=1). All tumors were reviewed by a dermatopathologist to confirm the SAC diagnosis.
All patients had undergone surgery. Indications for adjuvant radiation included involved lymph nodes (n=4), perineural invasion (n=2), nodal extracapsular extension (n=2), positive margin (n=1), high-grade histology (n=6), multifocal disease (n=2), and/or recurrent disease (n=5). Radiation was delivered to the primary site alone (n=3), to the draining lymphatics alone (n=2), or to both (n=4). One patient received concurrent cisplatin. Median dose to the primary site was 60 Gy and to the neck was 50 Gy.
Median follow-up was 4.0 years (range, 0.6 to 11.4 y). Locoregional control was 100%. Five-year progression-free survival was 89%. There was 1 acute grade 3 toxicity and no greater than or equal to grade 2 late toxicities were recorded.

Conclusions:
Surgery and adjuvant radiation for high-risk SAC offers excellent locoregional control with acceptable toxicity.
Notification of changes in taxonomic opinion previously published outside the IJSEM
Authors: Oren Aharon , Garrity George M. 
Published: January 2015

The Bacteriological Code deals with the nomenclature of prokaryotes. This may include existing names (the Approved Lists of Bacterial Names) as well as new names and new combinations. In this sense the Code is also dealing indirectly with taxonomic opinions. However, as with most codes of nomenclature there are no mechanisms for formally recording taxonomic opinions that do not involve the creation of new names or new combinations. In particular, it would be desirable for taxonomic opinions resulting from the creation of synonyms or emended descriptions to be made widely available to the public. In 2004, the Editorial Board of the International Journal of Systematic and Evolutionary Microbiology (IJSEM) agreed unanimously that it was desirable to cover such changes in taxonomic opinions (i.e. the creation of synonyms or the emendation of circumscriptions) previously published outside the IJSEM, and to introduce a List of Changes in Taxonomic Opinion [Notification of changes in taxonomic opinion previously published outside the IJSEM; Euzéby et al. (2004). Int J Syst Evol Microbiol
54, 1429-1430]. Scientists wishing to have changes in taxonomic opinion included in future lists should send one copy of the pertinent reprint or a photocopy or a PDF file thereof to the IJSEM Editorial Office or to the Lists Editor.
It must be stressed that the date of proposed taxonomic changes is the date of the original publication not the date of publication of the list. Taxonomic opinions included in the List of Changes in Taxonomic Opinion cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission. The names that are to be used are those that are the ‘correct names’ (in the sense of Principle 6) in the opinion of the bacteriologist, with a given circumscription, position and rank. A particular name, circumscription, position and rank does not have to be adopted in all circumstances. Consequently, the List of Changes in Taxonomic Opinion must be considered as a service to bacteriology and it has no ‘official character’, other than providing a centralized point for registering/indexing such changes in a way that makes them easily accessible to the scientific community.
Septic thrombophlebitis of the internal jugular and subclavian veins treated with percutaneous mechanical thrombolysis
Authors: Ashraf Muna , Laurich Chad , Huntington Mark K. 
Published: January 2015

Introduction:
Treatment of septic thrombophlebitis of the jugular vein may include both medical and surgical interventions. Historically, the goal of surgical interventions was not the restoration of blood flow through the affected vessel.

Case presentation:
We present a case of a 19‐year‐old male with septic thrombophlebitis who, despite appropriate antibiotic treatment, experienced symptomatic thrombus progression. Percutaneous thrombolytic procedures were performed, successfully restoring blood flow without triggering clinically significant bacteraemia or septic emboli.

Conclusion:
Thrombolysis may have a role in select patients, especially those with co‐existent thrombophilia or progressive thrombus development despite medical treatment.
Homology- and coevolution-consistent structural models of bacterial copper-tolerance protein CopM support a ‘metal sponge’ function and suggest regions for metal-dependent protein-protein interactions
Authors: Abriata Luciano A. 
Published: January 2015

AbstractCopper is essential for life but toxic, therefore all organisms control tightly its intracellular abundance. Bacteria have indeed whole operons devoted to copper resistance, with genes that code for efflux pumps, oxidases, etc. Recently, the CopM protein of the CopMRS operon was described as a novel important element for copper tolerance inSynechocystis. This protein consists of a domain of unknown function, and was proposed to act as a periplasmic/extracellular copper binder. This work describes a bioinformatic study of CopM including structural models based on homology modeling and on residue coevolution, to help expand on its recent biochemical characterization. The protein is predicted to be periplasmic but membrane-anchored, not secreted. Two disordered regions are predicted, both possibly involved in protein-protein interactions. The 3D models disclose a 4-helix bundle with several potential copper-binding sites, most of them largely buried inside the bundle lumen. Some of the predicted copper-binding sites involve residues from the disordered regions, suggesting they could gain structure upon copper binding and thus possibly modulate the interactions they mediate. All models are provided as PDB files in the Supporting Information and can be visualized online athttp://lucianoabriata.altervista.org/modelshome.htmlNote (January 2017):Recent X-ray structures of apo, copper- and silver-bound CopM are < 3Å RMSD away from the models, and reveal metal-dependent structural flexibility (Zhao et alActa Crystallogr D Struct Biol.2016)
Extracorporeal Photoimmunotherapy for Circulating Tumor Cells
Authors: Kim Gwangseong , Gaitas Angelo 
Published: January 2015

AbstractIt is believed that metastasis through the cardiovascular system is primarily caused by circulating tumor cells (CTCs). We report an approach to eliminate circulating tumor cells from the blood stream by flowing the blood though an extracorporeal tube and applying photodynamic therapy (PDT). Chlorin e6 (Ce6), a photosensizer, was conjugated to antibody CD44 in order to target PC-3, a prostate cancer cell line. PC-3 cells were successfully stained by the Ce6-CD44 antibody conjugate. PDT was performed on whole blood spiked with stained PC-3 cells. As the blood circulated through a transparent medical tube, it was exposed to light of a specific wavelength generated by an LED array. A 2 minute exposure was sufficient to achieve selective cancer cell necrosis. Control studies showed no cell death.
In plants, decapping prevents RDR6-dependent production of small interfering RNAs from endogenous mRNAs
Authors: de Alba Angel Emilio Martínez , Moreno Ana Beatriz , Gabriel Marc , Mallory Allison C. , Christ Aurélie , Bounon Rémi , Balzergue Sandrine , Aubourg Sebastien , Gautheret Daniel , Crespi Martin D. , Vaucheret Hervé , Maizel Alexis 
Published: January 2015

AbstractCytoplasmic degradation of endogenous RNAs is an integral part of RNA quality control (RQC) and often relies on the removal of the 5′ cap structure and their subsequent 5’ to 3’ degradation in cytoplasmic processing (P-)bodies. In parallel, many eukaryotes degrade exogenous and selected endogenous RNAs through post-transcriptional gene silencing (PTGS). In plants, PTGS depends on small interfering (si)RNAs produced after the conversion of single-stranded RNAs to double-stranded RNAs by the cellular RNA DEPENDENT RNA POLYMERASE 6 (RDR6) in cytoplasmic siRNA-bodies. PTGS and RQC compete for transgene-derived RNAs, but it is unknown whether this competition also occurs for endogenous transcripts. We show that the lethality of decapping mutants is suppressed by impairing RDR6 activity. We establish that upon decapping impairment hundreds of endogenous mRNAs give rise to a new class of rqc-siRNAs, that over-accumulate when RQC processes are impaired, a subset of which depending on RDR6 for their production. We observe that P- and siRNA-bodies often are dynamically juxtaposed, potentially allowing for crosstalk of the two machineries. Our results suggest that the decapping of endogenous RNA limits their entry into the PTGS pathway. We anticipate that the rqc-siRNAs identified in decapping mutants represent a subset of a larger ensemble of endogenous siRNAs.
MultiMeta: an R package for meta-analysing multi-phenotype genome-wide association studies
Authors: Vuckovic D. , Gasparini P. , Soranzo N. , Iotchkova V. 
Published: January 2015

AbstractSummaryAs new methods for multivariate analysis of Genome Wide Association Studies (GWAS) become available, it is important to be able to combine results from different cohorts in a meta-analysis. The R packageMultiMetaprovides an implementation of the inverse-variance based method for meta-analysis, generalized to an n-dimensional setting.AvailabilityThe R packageMultiMetacan be downloaded from CRAN Contact:dragana.vuckovic@burlo.trieste.it
Dissecting phylogenetic signal and accounting for bias in whole-genome data sets: a case study of the Metazoa
Authors: Borowiec Marek L. , Lee Ernest K. , Chiu Joanna C. , Plachetzki David C. 
Published: January 2015

AbstractTranscriptome-enabled phylogenetic analyses have dramatically improved our understanding of metazoan phylogeny in recent years, although several important questions remain. The branching order near the base of the tree is one such outstanding issue. To address this question we assemble a novel data set comprised of 1,080 orthologous loci derived from 36 publicly available genomes and dissect the phylogenetic signal present in each individual partition. The size of this data set allows for a closer look at the potential biases and sources of non-phylogenetic signal. We assessed a range of measures for each data partition including information content, saturation, rate of evolution, long-branch score, and taxon occupancy and explored how each of these characteristics impacts phylogeny estimation. We then used these data to prepare a reduced set of partitions that fit an optimal set of criteria and are amenable to the most appropriate and computationally intensive analyses using site-heterogeneous models of sequence evolution. We also employed several strategies to examine the potential for long-branch attraction to bias our inferences. All of our analyses support Ctenophora as the sister lineage to other Metazoa, although support for this relationship varies among analyses. We find no support for the traditional view uniting the ctenophores and Cnidaria (jellies, anemones, corals, and kin). We also examine phylogenetic placement of myriapods (centipedes and millipedes) and find it more sensitive to the type of analysis and data used. Our study provides a workflow for minimizing systematic bias in whole genome-based phylogenetic analyses.
ECERIFERUM2-LIKE Proteins Have Unique Biochemical and Physiological Functions in Very-Long-Chain Fatty Acid Elongation
Authors: Haslam Tegan M. , Haslam Richard , Thoraval Didier , Pascal Stéphanie , Delude Camille , Domergue Frédéric , Fernández Aurora Mañas , Beaudoin Frédéric , Napier Johnathan A. , Kunst Ljerka , Joubès Jérôme 
Published: January 2015

Abstract
The extension of very-long-chain fatty acids (VLCFAs) for the synthesis of specialized apoplastic lipids requires unique biochemical machinery. Condensing enzymes catalyze the first reaction in fatty acid elongation and determine the chain length of fatty acids accepted and produced by the fatty acid elongation complex. Although necessary for the elongation of all VLCFAs, known condensing enzymes cannot efficiently synthesize VLCFAs longer than 28 carbons, despite the prevalence of C28 to C34 acyl lipids in cuticular wax and the pollen coat. The eceriferum2 (cer2) mutant of Arabidopsis (Arabidopsis thaliana) was previously shown to have a specific deficiency in cuticular waxes longer than 28 carbons, and heterologous expression of CER2 in yeast (Saccharomyces cerevisiae) demonstrated that it can modify the acyl chain length produced by a condensing enzyme from 28 to 30 carbon atoms. Here, we report the physiological functions and biochemical specificities of the CER2 homologs CER2-LIKE1 and CER2-LIKE2 by mutant analysis and heterologous expression in yeast. We demonstrate that all three CER2-LIKEs function with the same small subset of condensing enzymes, and that they have different effects on the substrate specificity of the same condensing enzyme. Finally, we show that the changes in acyl chain length caused by each CER2-LIKE protein are of substantial importance for cuticle formation and pollen coat function.
Transcriptome and Metabolite Profiling of the Infection Cycle ofZymoseptoria triticion Wheat Reveals a Biphasic Interaction with Plant Immunity Involving Differential Pathogen Chromosomal Contributions and a Variation on the Hemibiotrophic Lifestyle Definition
Authors: Rudd Jason J. , Kanyuka Kostya , Hassani-Pak Keywan , Derbyshire Mark , Andongabo Ambrose , Devonshire Jean , Lysenko Artem , Saqi Mansoor , Desai Nalini M. , Powers Stephen J. , Hooper Juliet , Ambroso Linda , Bharti Arvind , Farmer Andrew , Hammond-Kosack Kim E. , Dietrich Robert A. , Courbot Mikael 
Published: January 2015

AbstractThe hemibiotrophic fungus Zymoseptoria tritici causes Septoria tritici blotch disease of wheat (Triticum aestivum). Pathogen reproduction on wheat occurs without cell penetration, suggesting that dynamic and intimate intercellular communication occurs between fungus and plant throughout the disease cycle. We used deep RNA sequencing and metabolomics to investigate the physiology of plant and pathogen throughout an asexual reproductive cycle of Z. tritici on wheat leaves. Over 3,000 pathogen genes, more than 7,000 wheat genes, and more than 300 metabolites were differentially regulated. Intriguingly, individual fungal chromosomes contributed unequally to the overall gene expression changes. Early transcriptional down-regulation of putative host defense genes was detected in inoculated leaves. There was little evidence for fungal nutrient acquisition from the plant throughout symptomless colonization by Z. tritici, which may instead be utilizing lipid and fatty acid stores for growth. However, the fungus then subsequently manipulated specific plant carbohydrates, including fructan metabolites, during the switch to necrotrophic growth and reproduction. This switch coincided with increased expression of jasmonic acid biosynthesis genes and large-scale activation of other plant defense responses. Fungal genes encoding putative secondary metabolite clusters and secreted effector proteins were identified with distinct infection phase-specific expression patterns, although functional analysis suggested that many have overlapping/redundant functions in virulence. The pathogenic lifestyle of Z. tritici on wheat revealed through this study, involving initial defense suppression by a slow-growing extracellular and nutritionally limited pathogen followed by defense (hyper) activation during reproduction, reveals a subtle modification of the conceptual definition of hemibiotrophic plant infection.
Prognostic analysis of defects in manufacturing
Authors: Chongwatpol Jongsawas 
Published: January 2015

Purpose
– Since works-in-process (WIPs) are highly vulnerable to defects because of the variety and complexity of manufacturing processes, the purpose of this paper is to describe how to utilize existing analytics techniques to reduce defects, improve production processes, and reduce the cost of operations.

Design/methodology/approach
– Three alternatives for diagnosing causes of defects and variations in the production process are presented in order to answer the following research question: “What are the most important factors to be included in prognostic analysis to prevent defects?”

Findings
– The key findings for the proposed alternatives help explain the characteristics of defects that have a great impact on manufacturing yield and the quality of products. Consequently, any corrective action and preventive maintenance addressing the common causes of defects and variations in the process can be regularly evaluated and monitored.

Research limitations/implications
– Although the focus of this study is on improving shop-floor operations by reducing defects, further experimentation with business analytics in other areas such as machine utilization and maintenance, process control, and safety evaluation remains to be done.

Practical implications
– This study has been validated with several scenarios in a manufacturing company, and the results demonstrate the practical validity of the approach, which is equally applicable to other manufacturing sub-sectors.

Originality/value
– This study is different from the others by providing alternatives for diagnosing the root causes of defects. Control charts, costs of defects, and clustering-based defect prediction scores are utilized to reduce defects. Additionally, the key contribution of this study is to demonstrate different methods for understanding WIP behaviors and identifying any irregularities in the production process.