bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bursaphelenchus xylophilus and B. mucronatus secretomes: a comparative proteomic analysis
Authors: Cardoso Joana M. S. , Anjo Sandra I. , Fonseca Luís , Egas Conceição , Manadas Bruno , Abrantes Isabel 
Published: December 2016

AbstractThe pinewood nematode, Bursaphelenchus xylophilus, recognized as a worldwide major forest pest, is a migratory endoparasitic nematode with capacity to feed on pine tissues and also on fungi colonizing the trees. Bursaphelenchus mucronatus, the closest related species, differs from B. xylophilus on its pathogenicity, making this nematode a good candidate for comparative analyses. Secretome profiles of B. xylophilus and B. mucronatus were obtained and proteomic differences were evaluated by quantitative SWATH-MS. From the 681 proteins initially identified, 422 were quantified and compared between B. xylophilus and B. mucronatus secretomes and from these, 243 proteins were found differentially regulated: 158 and 85 proteins were increased in B. xylophilus and B. mucronatus secretomes, respectively. While increased proteins in B. xylophilus secretome revealed a strong enrichment in proteins with peptidase activity, the increased proteins in B. mucronatus secretome were mainly related to oxidative stress responses. The changes in peptidases were evaluated at the transcription level by RT-qPCR, revealing a correlation between the mRNA levels of four cysteine peptidases with secretion levels. The analysis presented expands our knowledge about molecular basis of B. xylophilus and B. mucronatus hosts interaction and supports the hypothesis of a key role of secreted peptidases in B. xylophilus pathogenicity.
A nomogram improves AJCC stages for colorectal cancers by introducing CEA, modified lymph node ratio and negative lymph node count
Authors: Zhang Zhen-yu , Gao Wei , Luo Qi-feng , Yin Xiao-wei , Basnet Shiva , Dai Zhen-ling , Ge Hai-yan 
Published: December 2016

AbstractLymph node stages (pN stages) are primary contributors to survival heterogeneity of the 7th AJCC staging system for colorectal cancer (CRC), indicating spaces for modifications. To implement the modifications, we selected eligible CRC patients from the Surveillance Epidemiology and End Results (SEER) database as participants in a training (n = 6675) and a test cohort (n = 6760), and verified tumor deposits to be metastatic lymph nodes to derive modified lymph node count (mLNC), lymph node ratio (mLNR), and positive lymph node count (mPLNC). After multivariate Cox regression analyses with forward stepwise elimination of the mLNC and mPLNC for the training cohort, a nomogram was constructed to predict overall survival (OS) via incorporating preoperative carcinoembryonic antigen, pT stages, negative lymph node count, mLNR and metastasis. Internal validations of the nomogram showed concordance indexes (c-index) of 0.750 (95% CI, 0.736–0.764) and 0.749 before and after corrections for overfitting. Serial performance evaluations indicated that the nomogram outperformed the AJCC stages (c-index = 0.725) with increased accuracy, net benefits, risk assessment ability, but comparable complexity and clinical validity. All the results were reproducible in the test cohort. In summary, the proposed nomogram may serve as an alternative to the AJCC stages. However, validations with longer follow-up periods are required.
In vitro effects of the small-molecule protein kinase C agonists on HIV latency reactivation
Authors: Brogdon Jessica , Ziani Widade , Wang Xiaolei , Veazey Ronald S. , Xu Huanbin 
Published: December 2016

AbstractThe persistence of latently HIV-infected cellular reservoirs represents the major obstacle to virus eradication in patients under antiretroviral therapy (ART). Cure strategies to eliminate these reservoirs are thus needed to reactivate proviral gene expression in latently infected cells. In this study, we tested optimal concentrations of PKC agonist candidates (PEP005/Ingenol-3-angelate, prostratin, bryostatin-1, and JQ1) to reactivate HIV latency in vitro, and examined their effects on cell survival, activation and epigenetic histone methylation after treatment alone or in combination in cell line and isolated CD4 T cells from SIV-infected macaques. The results showed that PKC agonists increased cell activation with different degrees of latency reactivation, concomitant with reduced levels of histone methylation. With increasing concentrations, prostratin and byrostain-1 treatment rapidly reduced cell survival and cell activation. The PKC agonist combinations, or in combination with JQ1, led to modest levels of synergistic reactivation of HIV. Remarkably, PEP005 treatment alone caused marked reactivation of HIV latency, similar to PMA stimulation. These findings suggested that PEP005 alone, as indicated its lower cytotoxicity and lower effective dose inducing maximal reactivation, might be a candidate for effectively reactivating HIV latency as part of a therapeutic strategy for HIV infection.
Choroidal fissure acts as an overflow device in cerebrospinal fluid drainage: morphological comparison between idiopathic and secondary normal-pressure hydrocephalus
Authors: Yamada Shigeki , Ishikawa Masatsune , Iwamuro Yasushi , Yamamoto Kazuo 
Published: December 2016

AbstractTo clarify the pathogenesis of two different types of adult-onset normal-pressure hydrocephalus (NPH), we investigated cerebrospinal fluid distribution on the high-field three-dimensional MRI. The subarachnoid spaces in secondary NPH were smaller than those in the controls, whereas those in idiopathic NPH were of similar size to the controls. In idiopathic NPH, however, the basal cistern and Sylvian fissure were enlarged in concurrence with ventricular enlargement towards the z-direction, but the convexity subarachnoid space was severely diminished. In this article, we provide evidence that the key cause of the disproportionate cerebrospinal fluid distribution in idiopathic NPH is the compensatory direct CSF communication between the inferior horn of the lateral ventricles and the ambient cistern at the choroidal fissure. In contrast, all parts of the subarachnoid spaces were equally and severely decreased in secondary NPH. Blockage of CSF drainage from the subarachnoid spaces could cause the omnidirectional ventricular enlargement in secondary NPH.
Is There an Ideal Low-Density Lipoprotein Cholesterol Level? Confusion regarding Lipid Guidelines, Low-Density Lipoprotein Cholesterol Targets, and Medical Management
Authors: Whayne Thomas 
Published: December 2016

AbstractThere are multiple guidelines for managing patients with high-risk cardiovascular disease, and unfortunately for the practicing clinician, these guidelines are quite variable. Some are fairly specific whereas others are not, resulting in a great deal of confusion regarding whether management of low-density lipoprotein cholesterol (LDL-C) should be tailored only, targeted only, or managed by a combination of both. In the management of cardiovascular disease, favorable cardiovascular outcomes can be obtained by simply lowering the LDL-C in the absence of any other medications. The advent of statins, the most potent LDL-C–lowering medication yet when developed, provided benefits augmented by the presence of multiple pleiotropic effects. Tailoring and/or targeting the decrease in LDL-C is also an issue of concern. Then, in 2016, the new proprotein convertase sutilisin-like/kexin type 9 (PCSK9) inhibitors appeared, providing a solution to patients with high-risk cardiovascular disease with statin intolerance and those who did not attain a desired LDL-C level while on a high-dose statin. These new PCSK9 inhibitors necessitate a determination of how low the LDL-C can and should go, most likely safely down to a beneficial level of 25 mg/dL for the highest-risk patient. These issues are documented and discussed with an attempt to help the reader make an informed risk management decision.
Minimally Invasive Approach for Resection of Parameningeal Rhabdomyosarcoma
Authors: Wertz Aileen , Tillman Brittny , Brinkmeier Jennifer , Glazer Tiffany , Kroeker Andrew , Sullivan Steven , McKean Erin 
Published: December 2016

Background About one-third of rhabdomyosarcomas arise in the head and neck, with parameningeal primaries accounting for half of these. Principles of management involve chemotherapy, radiation, or both, in addition to surgical biopsy, debulking, and complete or near-complete resection. In the head and neck, diagnostic biopsies have historically been performed without attempt at resection due to proximity to critical structures and cosmetic considerations.
Methods Retrospective chart review of three cases of rhabdomyosarcoma at the cranial base managed through minimally invasive endoscopic surgical resection and adjuvant therapy.
Results Three patients were identified as having undergone endoscopic surgical debulking or margin-negative resection of a rhabdomyosarcoma of the cranial base. Two of three patients had complete resection based on intraoperative margin control. All three patients underwent adjuvant therapy within 1 month of diagnosis. Follow-up time ranged from 5 months to 3 years with all patients disease-free at last follow-up.
Conclusion Skull base surgeons should routinely be involved in multidisciplinary treatment planning for parameningeal rhabdomyosarcomas, as surgical options have evolved to allow for potential endoscopic resection with low morbidity and no or minimal delay in additional treatment options.
Conserved Non-exonic Elements: A Novel Class of Marker for Phylogenomics
Authors: Edwards Scott V. , Cloutier Alison , Baker Allan J. 
Published: December 2016

AbstractNoncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved non-exonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species. Although they often include UCEs, CNEEs are distinct from UCEs because they are not ultraconserved, and, most importantly, the core region alone is analyzed, rather than both the core and its flanking regions. Using a data set of 16 birds plus an alligator outgroup, and ~3600 - ~3800 loci per marker type, we found that although CNEEs were less variable than UCEs or introns and in some cases exhibited a slower approach to branch resolution as determined by phylogenomic subsampling, the quality of CNEE alignments was superior to those of the other markers, with fewer gaps and missing species. Phylogenetic resolution using coalescent approaches was comparable among the three marker types, with most nodes being fully and congruently resolved. Comparison of phylogenetic results across the three marker types indicated that one branch, the sister group to the passerine+falcon clade, was resolved differently and with moderate (> 70%) bootstrap support between CNEEs and UCEs or introns. Overall, CNEEs appear to be promising as phylogenomic markers, yielding phylogenetic resolution as high as for UCEs and introns but with fewer gaps, less ambiguity in alignments and with patterns of nucleotide substitution more consistent with the assumptions of commonly used methods of phylogenetic analysis.
Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates
Authors: Baker Zachary , Schumer Molly , Haba Yuki , Bashkirova Lisa , Holland Chris , Rosenthal Gil G. , Przeworski Molly 
Published: December 2016

AbstractStudies of highly diverged species have revealed two mechanisms by which meiotic recombination is directed to the genome—through PRDM9 binding or by targeting promoter-like features—that lead to dramatically different evolutionary dynamics of hotspots. Here, we identify PRDM9 orthologs from genome and transcriptome data in 225 species. We find the complete PRDM9 ortholog across distantly related vertebrates but, despite this broad conservation, infer a minimum of six partial and three complete losses. Strikingly, taxa carrying the complete ortholog of PRDM9 are precisely those with rapid evolution of its predicted binding affinity, suggesting that all domains are necessary for directing recombination. Indeed, as we show, swordtail fish carrying only a partial but conserved ortholog share recombination properties with PRDM9 knock-outs.
Non Diaphanous Formin Delphilin Acts as a Barbed End Capping Protein
Authors: Dutta Priyanka , Maiti Sankar 
Published: December 2016

ABSTRACTFormins are important for actin polymerization. Delphilin is a unique formin having PDZ domains and FH1, FH2 domains at its N and C terminus respectively. In this study we observed that Delphilin binds to actin filaments, and have negligible actin filament polymerizing activity. Delphilin inhibits actin filament elongation like barbed end capping protein CapZ.In vitro,Delphilin stabilized actin filaments by inhibiting actin filament depolymerisation. Therefore, our study demonstrates Delphilin as an actin-filament capping protein.
Darwinian selection of host and bacteria supports emergence of Lamarckian-like adaptation of the system as a whole
Authors: Osmanovic Dino , Kessler David A , Rabin Yitzhak , Soen Yoav 
Published: December 2016

AbstractBackgroundThe relatively fast selection of symbiotic bacteria within hosts and the potential transmission of these bacteria across generations of hosts raise the question of whether interactions between host and bacteria support emergent adaptive capabilities beyond those of germ-free hosts.ResultsTo investigate possibilities for emergent adaptations that may distinguish composite host-microbiome systems from germ-free hosts, we introduce a population genetics model of a host-microbiome system with vertical transmission of bacteria. The host and its bacteria are jointly exposed to a toxic agent, creating a toxic stress that can be alleviated by selection of resistant individuals and by secretion of a detoxification agent (“detox”). We show that toxic exposure in one generation of hosts leads to selection of resistant bacteria, which in turn, increases the toxic tolerance of the host’s offspring. Prolonged exposure to toxin over many host generations promotes additional form of emergent adaptation due to selection of hosts based on detox capabilities of their bacterial community as a whole (as opposed to properties of individual bacteria).ConclusionsThese findings show that interactions between pure Darwinian selections of host and its bacteria can give rise to emergent adaptive capabilities, including Lamarckian-like adaptation of the host-microbiome system.
Historian: accurate reconstruction of ancestral sequences and evolutionary rates
Authors: Holmes Ian 
Published: December 2016

AbstractReconstruction of ancestral sequence histories, and estimation of parameters like indel rates, are improved by using explicit evolutionary models and summing over uncertain alignments. The previous best tool for this purpose (according to simulation benchmarks) was ProtPal, but this tool was too slow for practical use. Historian combines an efficient reimplementation of the ProtPal algorithm with performance-improving heuristics from other alignment tools. Simulation results on fidelity of rate estimation via ancestral reconstruction, along with evaluations on the structurally-informed alignment dataset BAliBase 3.0, recommend Historian over other alignment tools for evolutionary applications. Historian is available athttps://github.com/ihh/indelhistorianunder the Creative Commons Attribution 3.0 US license. Contact: Ian Holmesihholmes+historian@gmail.com.
Implementation of ISO 9001 in the Spanish tourism industry
Authors: Djofack Sidonie , Camacho Marco Antonio Robledo 
Published: December 2016

Purpose
Although many studies have concentrated on analyzing the impact of the implementation of ISO 9001 certification, there is still a clear need for research in specific sectors. The purpose of this paper is to focus on the implementation of this international management system standard in the tourism industry, and in particular the motivations conducting to its adoption and the satisfaction derived from it.

Design/methodology/approach
A questionnaire survey was conducted among 120 ISO 9001-certified Spanish tourism companies. Confirmatory factor analysis tests were used to verify the scales validity and reliability. The logit model was utilized to investigate the statistical effects of ISO certification.

Findings
The paper findings showed that the certified companies in the tourism industry implement ISO 9001 more for internal reasons, like improving processes and procedures or products and/or services, than for external reasons, like the image of the company or promotional or sales tools. The variables size, age and use of a consultant affect the cost and time factors for the implementation of a quality system. In addition, the certification process generated three categories of benefits, with the organizational and control benefits being the more relevant. These benefits are correlated to the antiquity of the certificate. In the final analysis, results show that tourism companies are generally satisfied with the ISO 9001 certificate.

Originality/value
The ISO 9001 quality management system is part of the modern management tools. The paper contributes to a better understanding of the motivations and benefits for implementing the ISO 9001 certification and to the analysis of its application in a particular industry as important as the tourism industry in Spain, a country that is recognized for its leadership in tourism.
Getting acquainted with social networks and apps: Gotta catch them all? Augmented reality gaming apps
Authors: Anderson Katie Elson 
Published: December 2016

Purpose
This past summer marked the release of a record-breaking mobile app, an app that had more downloads during its first week of release on the Apple App store than any other app before it (Vanian, 2016).

Design/methodology/approach
With 7.2 million downloads in its first week, Pokémon Go became an overnight sensation (Mac, 2016) and has continued to grow since the initial release.

Findings
News about this app was hard to avoid during the summer months, especially in the USA where it was reported that one in ten Americans was using Pokémon Go (Mac, 2016).

Originality/value
The download numbers have continued to grow to an impressive 500 million as of September 2016, and the app continues to increase its worldwide audience and is currently available in 100 countries (Skipper, 2016). What is this app that has captured such large international audiences? Why has it become so popular? And most importantly, what does it have to do with libraries?
What’s trending in libraries from the internet cybersphere – alternate technology use – 03 – 2016
Authors: Oyelude Adetoun A. 
Published: December 2016

Purpose
This last edition of the column begins with the disadvantages of sleeping in the library and ends with 60-year-old overdue loans, but in between are alternate ways of using different technology to access information!

Design/methodology/approach
Sleeping in the library is trending on the internet, not because it is a nice pastime, but because it is one of the most viral trends of the year.

Findings
The real advice is that falling asleep in public places such as libraries is not good. A lot of wild reactions to the picture of a girl sleeping in a university library has caused all sorts, as “photo-shoppers”have had a field day, putting the sleeper in all sorts of situations – in Drake’s “Hotline Bling” music video, dancing with Michael Jackson and more.

Social implications
Derrick Lewis on 26th August reported that an Orange County library had made wi-fi devices available for rural internet users.

Originality/value
It is helping rural families make faster connections, and it is free to try the device which can be borrowed for 3 weeks and renewed twice if no one else has booked to use it.
Modes of Variability of Annual and Seasonal Rainfall in Mexico
Authors: Alvarez‐Olguin Gabriela , Escalante‐Sandoval Carlos 
Published: December 2016

AbstractThe aim of this study is to identify temporal and spatial variability patterns of annual and seasonal rainfall in Mexico. A set of 769 weather stations located in Mexico was examined. The country was divided into 12 homogeneous rainfall regions via principal component analysis. A Pettitt test was conducted to perform a homogeneity analysis for detecting abrupt changes in mean rainfall levels, and a Mann‐Kendall test was conducted to examine the presence of monotonically increasing/decreasing patterns in the data. In total, 14.4% of the annual series was deemed nonstationary. Fourteen percent of the samples were nonstationary in the winter and summer, and 9% were nonstationary in the spring and autumn. According to the results, the nonstationarity of some seasonal rainfall series may be associated with the presence of atmospheric phenomena (e.g., El Niño/Southern Oscillation, Pacific Decadal Oscillation, Atlantic Multidecadal Oscillation, and North Atlantic Oscillation). A rainfall frequency analysis was performed for the nonstationary annual series, and significant differences in the return levels can be expected for the scenarios analyzed. The identification of areas that are more susceptible to changes in rainfall levels will improve water resource management plans in the country, and it is expected that these plans will take into account nonstationary theory.
Resource Allocation and Priority Setting in Health Care: A Multi‐criteria Decision Analysis Problem of Value?
Authors: Angelis Aris , Kanavos Panos , Montibeller Gilberto 
Published: December 2016

AbstractA methodological approach is needed for allocating health care resources in an efficient and fair way that gives legitimacy to decisions. Currently, most priority setting approaches tend to focus on single or limited benefit dimensions, even though the value of new health care interventions is multi‐dimensional. Explicit elicitation of social value trade‐offs is usually not possible and decision‐makers often adopt intuitive or heuristic modes for simplification purposes as part of an ad hoc decision‐making process which might diminish the reasonableness and credibility of the decisions. In this paper, we suggest that multi‐criteria decision analysis could provide a more comprehensive and transparent approach in health care to systematically capture decision‐makers’ concerns, compare value trade‐offs and elicit their value preferences. We conclude that such methods could inform the development of a decision support system in health care, contributing towards more efficient, rational and legitimate resource allocation decisions.