bluuebunny/crossref_metadata_2025_split huggingface dataset:
Library preparation methodology can influence genomic and functional predictions in human microbiome research
Authors: Jones Marcus B. , Highlander Sarah K. , Anderson Ericka L. , Li Weizhong , Dayrit Mark , Klitgord Niels , Fabani Martin M. , Seguritan Victor , Green Jessica , Pride David T. , Yooseph Shibu , Biggs William , Nelson Karen E. , Venter J. Craig 
Published: October 2015

Significance
The field of microbiome research is moving from 16S rDNA gene sequencing to metagenomic sequencing of complete communities, which clearly gives a more comprehensive genomic and functional representation of the organisms present. Here we describe, quantify, and compare biases associated with four currently available next-generation sequencing library preparation methods using a synthetic DNA mock community and an extraction spike-in control of microbial cells. Our study highlights a critical need for consistency in protocols and data analysis procedures, especially when attempting to interpret human microbiome data for human health.
Basal autophagy maintains pancreatic acinar cell homeostasis and protein synthesis and prevents ER stress
Authors: Antonucci Laura , Fagman Johan B. , Kim Ju Youn , Todoric Jelena , Gukovsky Ilya , Mackey Mason , Ellisman Mark H. , Karin Michael 
Published: October 2015

Significance
This work identifies autophagy as an essential homeostatic process that maintains pancreatic acinar cell function. By preventing endoplasmic reticulum stress, reactive oxygen species accumulation, and DNA damage, basal autophagy preserves the high rates of protein synthesis that characterize the exocrine pancreas. Conversely, loss of autophagy can result in progressive loss of pancreatic function, which leads to development of pancreatitis as well as regenerative responses that may increase the risk of pancreatic cancer.
Comparison of Two Length‐Based Estimators of Total Mortality: A Simulation Approach
Authors: Then Amy Y. , Hoenig John M. , Gedamke Todd , S. Ault Jerald 
Published: October 2015

AbstractLength‐based methods for estimating the total mortality rate, Z, are appealing due to their potential application in data‐poor situations, particularly when assessing tropical and invertebrate fisheries where age composition data are lacking. We evaluated two length‐based estimators attributed to Beverton and Holt (1956) and to Ehrhardt and Ault (1992) for precision and accuracy when applied to simulated length data generated under varying combinations of Z rates, growth rates, variability in length at age, and the degree of length truncation imposed by the data analyst. The Beverton–Holt method generally overestimated Z, with bias ranging from −5% to +40%, when the abundance of the oldest age‐groups is less than that associated with a constant mortality rate. The bias in the Ehrhardt–Ault method ranged from −80% to +140%, depending on the combinations of Z and the von Bertalanffy growth coefficient K, the degree of imposed length truncation, and the method for mean length calculation. In general, the Ehrhardt–Ault estimator exhibited complex behavior, which made it difficult to summarize the direction and magnitude of the bias and the mean square error. The best length truncation to impose on the length samples to apply the Ehrhardt–Ault method often did not coincide with the “true” length of truncation especially with more realistic scenarios of variability in length at age. The Beverton–Holt method has the advantage of having known directional biases and predictable behavior. Use of the Ehrhardt–Ault estimator should be accompanied by a case‐specific evaluation of its likely performance.
Anti‐Glypican 3, a Novel Ancillary Maker in the Histological Assessment of Hirschsprung's Disease
Authors: Ludwig Kathrin , Volpe Andrea , Guzzardo Vincenza , Santoro Luisa , Midrio Paola , Gamba Piergiorgio , Alaggio Rita 
Published: October 2015

ABSTRACTObjectives:Hirschsprung's disease (HSCR) results from a malformation of the enteric nervous system. A congenital absence of intrinsic ganglion cells from the distal rectum and a variable length of the contiguous bowel is the required diagnostic feature of Hirschsprung's disease and total colonic aganglionosis (TCA). We evaluated the utility of a monoclonal antibody directed against glypican 3 (GPC‐3), a membrane bound protein involved in regulation of the signaling of Wingless‐types (WNTs), Hedgehogs (Hh), Fibroblast Growth Factors (FGFs), and Bone Morphogenetic Proteins (BMPs), in the detection of ganglion cells in formalin‐fixed, paraffin‐embedded tissue sections.Methods:The presence/absence of ganglion cells was evaluated retrospectively by immunohistochemical staining for calretinin and GPC‐3 in tissue specimens; a total of 15 patients who underwent colectomy (total or sub‐total) for histologically proven aganglionosis (14 HSCR, 1 TCA) and 5 rectal suction biopsies (4HSCR‐B, 1 TCA‐B) were considered. Of the 20 considered cases, a total of 60 tissue specimens (3 for each patient) were selected. A total of 30 additional normal (N) colonic mucosa biopsy samples were also included.Results:GPC‐3 constantly identified ganglion cell bodies in all but 2 normal biopsies (with normal presentation of ganglion cells on hematoxylin and eosin (H&E) stain), and was negative in all 60 aganglionotic biopsies; these results were reflective of calretinin staining pattern.Conclusions:The present study indicates that monoclonal anti‐GPC‐3 might prove to be useful immunohistochemical marker in the identification of ganglion cells in paraffin‐embedded rectal tissue specimens and suction biopsies. Further studies in larger series will contribute to demonstrate its utility as an ancillary marker in the histological assessment of HSCR aganglionosis.
Augmentation of nonsense mediated decay by rapamycin
Authors: Martinez-Nunez Rocio Teresa , Coyne Doyle , Jansson Linnea , Rush Miles , Ennajdaoui Hanane , Sanchez-Elsner Tilman , Sanford Jeremy R. 
Published: October 2015

ABSTRACTRNA surveillance by the Nonsense Mediated Decay (NMD) pathway eliminates potentially deleterious transcripts containing Premature Termination Codons (PTCs). The transition from a pioneering round of translation to steady state translation is hypothesized to be a major checkpoint in this process. One hallmark of mRNAs licensed for translation is the exchange of 7-methylguanosine cap binding proteins. However, mRNAs undergoing steady state translation are also NMD substrates, raising mechanistic questions about the NMD checkpoint. To test the role of cap binding proteins in NMD, we modulated the protein composition of cytoplasmic messenger ribonucleoprotein particles (mRNPs) with the naturally occurring macrolide rapamycin. We demonstrate that despite well-documented attenuation of cap-dependent mRNA translation, rapamycin can augment NMD. Rapamycin-treatment significantly reduces the levels of endogenous and exogenous PTC-containing mRNA isoforms in a dose- and UPF1- dependent manner. PTC-containing transcripts exhibit a shorter half-life upon rapamacyin-treatment as compared to non-PTC isoforms. Rapamycin also causes depletion of PTC-containing mRNA isoforms from polyribosomes, suggesting that actively translating ribosomes can transition between low and high NMD states. Importantly, mRNPs show depletion of eIF4E and retention of the nuclear Cap Binding Complex (CBC) in rapamycin-treated cells. Our data demonstrate that rapamycin potentiates pioneer-like mRNP context thereby decreasing NMD evasion.
Hydraulic conductance and the maintenance of water balance in flowers
Authors: Roddy Adam B. , Brodersen Craig R. , Dawson Todd E. 
Published: October 2015

AbstractFlowers face desiccating conditions, yet little is known about their ability to transport water. We quantified variability in floral hydraulic conductance (Kflower) for 20 species from 10 families and related it to traits hypothesized to be associated with liquid and vapor phase water transport. Basal angiosperm flowers had trait values associated with higher water and carbon costs than monocot and eudicot flowers.Kflowerwas coordinated with water supply (vein length per area,VLA) and loss (minimum epidermal conductance,gmin) traits among the magnoliids, but was insensitive to variation in these traits among the monocots and eudicots. Phylogenetic independent contrast (PIC) correlations revealed that few traits had undergone coordinated evolution. However,VLAand the desiccation time (Tdes), the quotient of water content andgmin, had significant trait and PIC correlations. The near absence of stomata from monocot and eudicot flowers may have been critical in minimizing water loss rates among these clades. Early-divergent, basal angiosperm flowers maintain higherKflowerdue to traits associated with high rates water loss and water supply, while monocot and eudicot flowers employ a more conservative strategy of limiting water loss and may rely on stored water to maintain turgor and delay desiccation.
Removing “invisible” barriers: opening paths towards the future of accessible tourism
Authors: Portales Rafael Cruces 
Published: October 2015

Purpose
The purpose of this paper is to contribute to the analysis and grasp of accessible tourism, from its present into a medium-term future. It provides a socio-anthropological approach.

Design/methodology/approach
This paper uses the scenarios-planning analysis framework proposing four scenarios arising from the interaction of aforementioned driving forces. The author also use a trilemma to both form and evaluate scenarios. The criteria for the trilemma were (stakeholders, cooperation and prejudice).

Findings
The strength of combining a new set of driving forces, namely, empathy, apathy, certainty in economic profits and fear of economic losses, which would enable to draw four plausible scenarios into the future of accessible tourism within a scenarios-planning framework. The significance is to provide “food for thought” to address the future through a range of different concepts.

Research limitations/implications
The main limitation is the difficulty to obtain honest answers about why the lack of development of accessible tourism.

Practical implications
Participant observation on both groups and individuals in vacation atmosphere. Also, in-depth interviews to different stakeholder representatives.

Social implications
To try to explain to the stakeholders their wasted economic benefits and, at the same time, the opportunity of getting social prestige.

Originality/value
The main value is about considering the interplay of social concepts as empathy, apathy, “aesthetic prejudice” and fear of losses or faith in profits.
Information reliability for academic research: review and recommendations
Authors: Colepicolo Eliane 
Published: October 2015

Purpose– The purpose of this paper is to provide to scientific researchers and academic students some subsidies related to information reliability that may be used during information search and retrieval for academic research based on the author’s experience as a university librarian and interdisciplinary researcher.Design/methodology/approach– The paper is composed of a brief conceptualization of the term information reliability, followed by a practical guide containing three processes for obtaining reliable information: knowledge of bibliometric indicators, evaluation of sources of information and analysis of the content of recovered publications.Findings– Currently, there are few publications about information reliability that target the practical and effective learning of academic researchers and students, based on the experience of librarians who work directly with bibliographic search and training based on scientific literature.Social implications– The great demand of questions submitted by academic users on how to obtain reliable information shows the need for a paper like this to clarify them.Originality/value– This paper shares best practices for search and discovery of information reliability, which are based on experiences that are not commonly addressed in the literature, and presents processes covering the bibliometric indicators, information sources and publication contents.
Art outreach toward STEAM and academic libraries
Authors: Arrieta Diane , Kern Jacqueline 
Published: October 2015

Purpose– The purpose of this paper is to examine science, technology, engineering, art and mathematics (STEAM) efforts at Florida Atlantic University’s (FAU) John D. MacArthur Campus Library (JDM) to share methodologies and ideas with other academic libraries. Recently, there has been an emphasis on and push for science, technology, engineering and mathematics (STEM) education in colleges and universities across the USA as a means for training future work forces and for remaining competitive in global job markets (Land, 2013). FAU in South Florida is a big proponent of STEM and STEAM education (Florida Atlantic University, 2012; Dorothy F. Schmidt College of Arts and Letters, 2013).Design/methodology/approach– As many librarians and outreach staff strive to remain relevant to their faculty and students with changing technologies (Drewes and Hoffman, 2010), the FAU JDM outreach staff have developed several novel programs that are geared toward the STEAM initiative.Findings– The Library Outreach Committee at FAU was committed to investigating how they could advance student success through visual arts programming. How can the library help contribute to STEAM education for the students and learning community as a whole? How can the library engage art students? Can the library promote dialogue in arts to the faculty and staff, regardless of their disciplines? This article will describe and discuss the various art outreach programs that the JDM has tested and their outcomes addressing goals toward STEAM education and academic libraries.Originality/value– The objective in sharing the experiences at the JDM is to spark new and successful program ideas at other academic libraries across the country and abroad and create knowledge in this relatively new area.
Multiple‐stressor effects on leaf litter decomposition and fungal decomposers in agricultural streams contrast between litter species
Authors: Bruder Andreas , Salis Romana K. , McHugh Nicola J. , Matthaei Christoph D. 
Published: October 2015

Summary

Agricultural land use commonly exerts multiple stressors on the functioning of stream ecosystems, including leaf litter decomposition and the utilization of this resource in stream food webs. If stressors interact, their cumulative effects on biotic responses cannot be predicted from knowledge of individual stressor effects, posing challenges for management and restoration of ecosystems.

We examined the individual and interactive effects of four common agricultural stressors and the role of litter quality on leaf litter decomposition and fungal decomposers. In 128 outdoor, flow‐through mesocosms, we manipulated levels of nutrients, a nitrification inhibitor (dicyandiamide), deposited fine sediment and flow velocity. Interactions among these stressors can ensue because, for instance, they jointly affect physicochemical conditions around leaf litter colonized by fungi such as concentrations of dissolved oxygen and nutrients.

The two litter species used, deciduous birch and evergreen mahoe, showed contrasting decomposition dynamics, and these differences influenced their response to stressors. Fungi were important for birch litter decomposition but played a minor role for mahoe. Overall, flow velocity reduction and deposited fine sediment had the strongest, mainly negative effects on fungi and litter decomposition, probably as a consequence of reductions in dissolved oxygen available to fungi. However, fine sediment substantially increased mahoe litter mass loss, pointing at fungi‐independent processes being relevant for its decomposition.

Although interactions among stressors were uncommon, they showed effects of the same magnitude as stressor main effects. Potential mechanisms underlying interactions included reductions in dissolved oxygen and changes in microbial community composition.

Knowledge of the effects of multiple agricultural stressors and of litter quality on litter decomposition and litter‐associated fungi is crucial for management of forested riparian corridors, which have been shown to efficiently mitigate impacts of agricultural stressors on streams. The contrasting responses of the litter species used in our study warrant consideration of species composition of the riparian vegetation.
Invasive cutleaf coneflower seeds cached in nest boxes: possibility of dispersal by a native rodent
Authors: Suzuki Kei , Yamane Yutaka , Yanagawa Hisashi 
Published: October 2015

AbstractInvasive species present serious problems for ecosystems and economies. One such species, the invasive cutleaf coneflower (Rudbeckia laciniata L.), has several modes of seed dispersal, namely autochory, anemochory, epizoochory, myrmecochory and anthropochory. Because we found caches of this invasive plant's seeds in two nest boxes, suggesting the possibility of synzoochory, we report here the details of the caches. In one of the boxes, many of the seeds were cached in autumn and eaten during the winter. Automatic sensor cameras directed at the boxes revealed that three rodent species and two avian species visited the boxes. The characteristics of the caches and the nest‐box visitors suggested that the small Japanese field mouse (Apodemus argenteus Temm.) was the animal most likely to have cached the seeds in the boxes.
John Paul Jones: An Overlooked Autopsy Finding that May Explain His Terminal Illness
Authors: Hamrell Burt B. 
Published: October 2015

AbstractA finding in the autopsy of John Paul Jones, the American Revolutionary War naval hero, may explain his terminal illness. During his last 2 years, he had a persistent productive cough and dyspnea. Ten days before death, he developed rapidly progressive dependent edema and ascites. He died in France in 1792. His body, preserved in alcohol in a lead coffin, was, in 1905, removed to the United States. Glomerulonephritis was noted on an autopsy, performed in France, but there was no comment then or since about ventricular wall thickness being the same in both ventricles at 5–6 mm. Hypertrophy and dilatation with biventricular failure followed by tissue shrinkage during 113 years in alcohol could have resulted in these ventricular wall findings. Systemic hypertension and left ventricular failure are consistent with his respiratory symptoms complicated perhaps by pulmonary emboli, right ventricular failure with tricuspid regurgitation, peripheral congestion, and jaundice.
Analysis of Scientific Production in Food Science from 2003 to 2013
Authors: Guerrero‐Bote Vicente P. , Moya‐Anegón Félix 
Published: October 2015

AbstractFood Science is an active discipline in scientific research. The improvements in Food Technology constitute a challenge for society to eradicate hunger, while achieving food safety. This work analyses the scientific production in Food Science of the 25 countries with the greatest output in this subject area in the period 2003 to 2013. The growth of China's production was striking, with the country becoming top‐ranked by the end of the period. Some developing countries (such as Nigeria) achieved a major increase in production but reducing their proportion of scientific collaboration and their works' impact. There appear to be 2 international collaboration networks that get good results—one European and the other Pacific.
Reasons for Thiomicrospira crunogena's recalcitrance towards previous attempts to detect its hydrogen consumption ability
Authors: Hansen Moritz , Perner Mirjam 
Published: October 2015

SummaryThe first Thiomicrospira species was isolated in 1972 and was described as a sulfur‐oxidizing chemolithoautotroph. Since then, several other Thiomicrospira species have been recovered from around the globe and have been classified as common sulfur oxidizers. In the past, attempts to demonstrate hydrogen consumption of a Thiomicrospira species have failed. However, recently, we showed that some Thiomicrospira strains can indeed consume hydrogen. Here, we discuss why Thiomicrospira species have likely resisted efforts to consume hydrogen under the offered conditions. It appears that their hydrogen consumption ability is closely tied to the concentration of nickel in the medium. Investigated carbonate and thiosulfate concentrations did not appear to be critical for hydrogen utilization under the tested conditions.
Non‐interest Income, Profit, and Risk Efficiencies: Evidence from Commercial Banks in China
Authors: Bian Wen‐Long , Wang Xiang‐Nan , Sun Qi‐Xiang 
Published: October 2015

AbstractChinese commercial banks are transforming their activities into more non‐interest income businesses under a highly regulated financial system. This paper investigates the effects of this transformation on profit and risk efficiencies. We find that commission and fee income significantly reduce risk efficiency due to the circumvention of the regulation on deposit interest rate and the assumption of risk that should have been borne by customers. In terms of trading income, it significantly reduces profit efficiency due to the upper limit of the loan‐deposit ratio, the lack of investment channels and low returns of bond markets. The regulatory authorities are supposed to further liberalize the banking industry and grant banks more rights.
Prevalence of bullying, discrimination and sexual harassment in surgery in Australasia
Authors: Crebbin Wendy , Campbell Graeme , Hillis David A. , Watters David A. 
Published: October 2015

AbstractBackgroundThe topic of discrimination, bullying and sexual harassment in surgery was raised in the Australian media earlier in 2015. This led the Royal Australasian College of Surgeons (RACS) to commission an Expert Advisory Group to investigate and advise the College on their prevalence in surgery in Australia and New Zealand. This paper reports the findings with respect to prevalence of these inappropriate behaviours.MethodsThe data in this paper were drawn from the published results of two quantitative surveys. One was an online survey sent to all RACS members. The other was an invited survey of hospitals, medical institutions and other related professional organizations including surgical societies.ResultsThe prevalence survey achieved a 47.8% response rate, representing 3516 individuals. Almost half of the respondents 1516 (49.2%) indicated that they had experienced one or more of the behaviours. This proportion was consistent across every specialty. Male surgical consultants were identified as the most likely perpetrators. More than 70% of the hospitals reported that they had instances in their organization of discrimination, bullying or sexual harassment by a surgeon within the last 5 years. Surgical directors or surgical consultants were by far the most frequently reported perpetrators (in 50% of hospitals).ConclusionsDiscrimination, bullying and sexual harassment are common in surgical practice and training in Australia and New Zealand. RACS needs to urgently address these behaviours in surgery. This will involve a change in culture, more education for fellows and trainees, and better processes around complaints including support for those who have suffered.