bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defining the transcriptomic landscape ofCandida glabrataby RNA-Seq
Authors: Linde Jörg , Duggan Seána , Weber Michael , Horn Fabian , Sieber Patricia , Hellwig Daniela , Riege Konstantin , Marz Manja , Martin Ronny , Guthke Reinhard , Kurzai Oliver 
Published: January 2015

AbstractCandida glabrata is the second most common pathogenic Candida species and has emerged as a leading cause of nosocomial fungal infections. Its reduced susceptibility to antifungal drugs and its close relationship to Saccharomyces cerevisiae make it an interesting research focus. Although its genome sequence was published in 2004, little is known about its transcriptional dynamics. Here, we provide a detailed RNA-Seq-based analysis of the transcriptomic landscape of C. glabrata in nutrient-rich media, as well as under nitrosative stress and during pH shift. Using RNA-Seq data together with state-of-the-art gene prediction tools, we refined the annotation of the C. glabrata genome and predicted 49 novel protein-coding genes. Of these novel genes, 14 have homologs in S. cerevisiae and six are shared with other Candida species. We experimentally validated four novel protein-coding genes of which two are differentially regulated during pH shift and interaction with human neutrophils, indicating a potential role in host–pathogen interaction. Furthermore, we identified 58 novel non-protein-coding genes, 38 new introns and condition-specific alternative splicing. Finally, our data suggest different patterns of adaptation to pH shift and nitrosative stress in C. glabrata, Candida albicans and S. cerevisiae and thus further underline a distinct evolution of virulence in yeast.
Concomitant Grafting of Both Postbifurcation Internal Thoracic Artery Branches
Authors: Sahar Gideon , Wolak Arik , Matsa Menachem , Shelef Ilan , Raichel Lior , Ishay Yaron , Lev-Ran Oren 
Published: January 2015

Objective We aimed to assess the clinical outcome and graft patency after concomitant grafting of both postbifurcation internal thoracic artery (ITA) branches. Methods Between 2007 and 2013, 17 patients (14 men; mean [SD] age, 60 [9.3] years) underwent skeletonized bifurcated ITA grafting. Respective targets were restricted to non–left anterior descending (LAD) area. in all patients, a complementary standard ITA was used to graft the LAD artery. Graft patency was assessed by standard coronary angiography or serial multidetector computed tomography. Results Of the bifurcated conduits, 94% were right ITA. Respective right ITA target sets were first and second obtuse marginal arteries (M1-M2) (n = 12), ramus-M1 (n = 2), and distal right coronary artery–posterior descending artery (n = 2). Right ITAs were mobilized retroaortic (via the transverse sinus) in 14 patients (82%) (to circumflex artery targets). Circumflex artery targets comprised 88.2% of all anastomoses (30/34). There were no early mortalities, myocardial infarctions, or hypoperfusion syndromes. During median follow-up of 44 months (range, 3–63), there was no late mortality. Overall reintervention rate was 11.7%, and bifurcated ITA–related reintervention rate was 5.8%. At 5 years, freedom from major adverse cardiac or cerebrovascular event related to bifurcated ITA respective territory was 87% (Kaplan-Meier). Coronary imaging was achieved in 76% of the patients (elective multidetector computed tomography, n = 9; symptoms-directed coronary catheterization, n = 4). Bifurcation branch patency rate was 88.4% (23/26) at a median of 3.5 years. Conclusions Grafting both postbifurcation ITA branches is technically feasible and may be selectively considered. Current observations are valid for skeletonized conduits and limited to non-LAD targets. These preliminary findings should be corroborated by larger data sets.
Genome-Wide Analysis ofPHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE(PDAT) Genes in Plants Reveals the Eudicot-WidePDATGene Expansion and Altered Selective Pressures Acting on the Core EudicotPDATParalogs
Authors: Pan Xue , Peng Fred Y. , Weselake Randall J. 
Published: January 2015

AbstractPHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE (PDAT) is an enzyme that catalyzes the transfer of a fatty acyl moiety from the sn-2 position of a phospholipid to the sn-3-position of sn-1,2-diacylglyerol, thus forming triacylglycerol and a lysophospholipid. Although the importance of PDAT in triacylglycerol biosynthesis has been illustrated in some previous studies, the evolutionary relationship of plant PDATs has not been studied in detail. In this study, we investigated the evolutionary relationship of the PDAT gene family across the green plants using a comparative phylogenetic framework. We found that the PDAT candidate genes are present in all examined green plants, including algae, lowland plants (a moss and a lycophyte), monocots, and eudicots. Phylogenetic analysis revealed the evolutionary division of the PDAT gene family into seven major clades. The separation is supported by the conservation and variation in the gene structure, protein properties, motif patterns, and/or selection constraints. We further demonstrated that there is a eudicot-wide PDAT gene expansion, which appears to have been mainly caused by the eudicot-shared ancient gene duplication and subsequent species-specific segmental duplications. In addition, selection pressure analyses showed that different selection constraints have acted on three core eudicot clades, which might enable paleoduplicated PDAT paralogs to either become nonfunctionalized or develop divergent expression patterns during evolution. Overall, our study provides important insights into the evolution of the plant PDAT gene family and explores the evolutionary mechanism underlying the functional diversification among the core eudicot PDAT paralogs.
The Pransky interview: Dr Rodney Brooks, Robotics Entrepreneur, Founder and CTO of Rethink Robotics
Authors: Pransky Joanne 
Published: January 2015

Purpose
– This article, a “Q&A interview” conducted by Joanne Pransky of Industrial Robot Journal, aims to impart the combined technological, business, and personal experience of a prominent, robotic industry engineer-turned entrepreneur regarding the evolution, commercialization, and challenges of bringing a technological invention to market.

Design/methodology/approach
– The interviewee is Dr Rodney Brooks, the Panasonic Professor of Robotics (emeritus), Massachusetts Institute of Technology (MIT), Computer Science and Artificial Intelligence Lab; Founder, Chief Technical Officer (CTO) and Chairman of Rethink Robotics. Dr Brooks shares some of his underlying principles in technology, academia and business, as well as past and future challenges.

Findings
– Dr Brooks received degrees in pure mathematics from the Flinders University of South Australia and a PhD in computer science from Stanford University in 1981. He held research positions at Carnegie Mellon University and MIT, and a faculty position at Stanford before joining the faculty of MIT in 1984. He is also a Founder, Board Member and former CTO (1991-2008) of iRobot Corp (Nasdaq: IRBT). Dr Brooks is the former Director (1997-2007) of the MIT Artificial Intelligence Laboratory and then the MIT Computer Science & Artificial Intelligence Laboratory. He founded Rethink Robotics (formerly Heartland Robotics) in 2008.

Originality/value
– While at MIT, in 1988, Dr Brooks built Genghis, a hexapodal walker, designed for space exploration (which was on display for ten years in the Smithsonian National Air and Space Museum in Washington, D.C.). Genghis was one of the first robots that utilized Brooks’ pioneering subsumption architecture. Dr Brooks’ revolutionary behavior-based approach underlies the autonomous robots of iRobot, which has sold more than 12 million home robots worldwide, and has deployed more than 5,000 defense and security robots; and Rethink Robotics’ Baxter, the world’s first interactive production robot. Dr Brooks has won the Computers and Thought Award at the 1991 International Joint Conference on Artificial Intelligence, the 2008 IEEE Inaba Technical Award for Innovation Leading to Production, the 2014 Robotics Industry Association’s Engelberger Robotics Award for Leadership and the 2015 IEEE Robotics and Automation Award.
Outsourcing of facilities management (FM) services in public hospitals
Authors: Ikediashi Dubem , Ekanem Anyiekere M 
Published: January 2015

Purpose
– The purpose of this paper is to extend the body of knowledge on health care facilities management (FM) by investigating the extent to which public hospitals in Nigeria have fared in terms of outsourced FM services.

Design/methodology/approach
– The paper relied on two strands of methodology common with pragmatic research. Questionnaire survey (QS) used data from 74 respondents representing 74 hospitals, while 3 of the 74 hospitals involved in the QS were selected based on their willingness to enter the case study interview. Data collected were analysed using descriptive statistics (QS) and using narrative techniques by discussing themes, sub-themes and interconnecting themes through a chronology of events, as in grounded theory.

Findings
– Findings revealed that most public hospitals do not have a policy framework for outsourcing in general and FM services in particular, giving room for duplication of functions and non-establishment of functional FM units to handle FM activities, while six FM services are outsourced in all the hospitals. Cleaning, security and catering services received the highest satisfaction ratings, while plant maintenance services, however, received the least satisfaction rating.

Originality/value
– The paper provides the first ever survey based on empirical evidence about the state of FM services outsourced in Nigeria’s public hospitals. The survey suggests a relatively low level of usage of outsourcing for its services, as only a handful of FM services are outsourced in most of the hospitals.
Simulation analysis for managing and improving productivity
Authors: El-Khalil Raed 
Published: January 2015

Purpose
– The current economic crisis increased the demand on management to improve process efficiency. The purpose of this paper is to identify and resolve inefficiencies within the car assembly system utilizing discrete simulation modeling and analysis in order to improve productivity at one of the original equipment manufacturers (OEM) body shops in North America.

Design/methodology/approach
– This research was driven by a manager’s recommendation from one of the Big Three (GM, Ford, Chrysler LLC) companies in order to improve operational performance. The data utilized in creating the simulation model was obtained from one of the assembly facilities that produce three different vehicles over a period of one year. All model simulation, inputs and outputs were discussed and agreed upon by facility management.

Findings
– The established base model was verified and validated to mimic the actual facility outputs indicating all process bottlenecks. Two model scenarios were considered: the first scenario focussed on the top bottleneck processes flexibility with a ROI of 497 percent, while the second considered changing the model mix percentage leading to a cost improvement of $1.6 million/annually.

Research limitations/implications
– The model only considered management decision on buffer sizes, batch size and the top bottleneck station alternatives to make improvements. Simulating improvements in labor efficiency, robots uptime, scrap root cause, and maintenance response to downtime where not considered.

Practical implications
– This paper indicated the importance of discrete simulation modeling in providing alternatives for improving process efficiency under certain financial limitations. Given the similarity of the automotive manufacturing processes among the various companies, the findings for this particular facility remain valid for other facilities.

Originality/value
– Investment cost and process improvement are currently the two biggest challenges facing operations managers in the manufacturing industry. This study allows managers to gain a broader perspective on discrete simulation ability to simulate complicated systems and present different process improvement alternatives.
The effect of trap colour and trap‐flower distance on prey and pollinator capture in carnivorous Drosera species
Authors: Jürgens Andreas , Witt Taina , Sciligo Amber , El‐Sayed Ashraf M. 
Published: January 2015

Summary

The functional features of carnivorous plants’ traps have been mostly interpreted as adaptations to capture prey. Carnivorous plants that feed on insects, however, run the risk that increasing trapping effectiveness might in turn reduce reproductive success through capture of pollinators. Such a pollinator–prey conflict might play an important role in the evolution of trap features. In carnivorous plants with sticky leaves (e.g. Drosera, Pinguicula), both spatial distance between traps and flowers and their visual signals (e.g. colour, display size) likely play a role in attracting prey but it has also been suggested that they affect the risk of potential pollinators landing on a trap. It has been reported, for example, that red pigmentation in carnivorous plants may lure insect prey to traps. This idea remains controversial, however, because colour vision of most insects does not extend very far into the red part of the spectrum.

We tested an alternative hypothesis, namely that red pigmentation of the trapping leaves may reduce the risk of a pollinator–prey conflict. Experiments were conducted in a natural habitat of Drosera arcturi and D. spatulata in the Southern Alps of New Zealand. Using sticky model traps similar in shape to Drosera leaf traps and flowers, we investigated the effect of colour (green vs. red vs. white) and flower‐trap distance (flower stalk length and leaf arrangement, that is upright as in D. arcturi vs. flat ground rosette as in D. spatulata) on composition and abundance of insects landing and being trapped.

Flower‐trap distance had no significant effect on the risk of pollinators being trapped but model flowers higher above the ground received more pollinator landings. Across all model traps, the number of trapped potential pollinators was significantly lower in traps with red leaves compared to green ones.

The results suggest that the typical red pigmentation of the trapping leaves in Drosera may be a way to protect pollinators from being attracted and captured. However, our data also suggest that pollinator protection via red traps may come with a trade‐off since total prey capture was also significantly reduced.
Loss of phylogenetic and functional originalities of woody cerrado species in simulated extinction scenarios
Authors: Rosatti Natalia Bianca , Silva Danilo Muniz , Batalha Marco Antônio 
Published: January 2015

AbstractOriginality measures how different a given species is from all other co‐occurring species regarding either their phylogenetic history or functional traits. Since it is important to preserve the various aspects of diversity and original species carry more phylogenetic or functional information, originality may be used to assign conservation priorities. Our goal was to evaluate the relationships between phylogenetic and functional originalities, and their simulated losses under extinction scenarios based on abundance, fire tolerance and habitat preference. We placed 100 plots in a cerrado reserve located in central Brazil, sampled all woody plants species within the plots, measured 14 functional traits and measured fire history. We assembled a phylogenetic tree and a functional dendrogram, with which we calculated the originalities. Phylogenetic‐ and functional‐based originalities were correlated. However, the loss of functional originality was different from random extinctions on the abundance and fire tolerance scenarios, whereas the loss of phylogenetic originality was not. When compared with phylogenetic originality, functional originality brought more information to be used in conservation strategies because it was sensitive to differences in species abundance and fire tolerance. Thus, the extinction of rare or fire‐sensitive species would result in important functional changes due to loss of distinctive traits.
The Pyrazolobenzothiazine Core as a New Chemotype of p38 Alpha Mitogen‐Activated Protein Kinase Inhibitors
Authors: Sabatini Stefano , Manfroni Giuseppe , Barreca Maria Letizia , Bauer Silke M. , Gargaro Marco , Cannalire Rolando , Astolfi Andrea , Brea Jose , Vacca Carmine , Pirro Matteo , Massari Serena , Tabarrini Oriana , Loza Maria Isabel , Fallarino Francesca , Laufer Stefan A. , Cecchetti Violetta 
Published: January 2015

The identification, synthesis, biological activity, and binding mode prediction of a series of pyrazolobenzothiazines as novel p38α MAPK inhibitors are reported. Some of these compounds showed interesting activity in both p38α MAPK and TNF‐α release assays. Derivative 6 emerged as the most interesting compound with IC50 (p38α) = 0.457 μm, IC50 (TNF‐α) = 0.5 μm and a promising kinase selectivity profile. The obtained results strongly indicate the pyrazolobenzothiazine core as a new p38α inhibitor chemotype worthy of future chemical optimization efforts directed toward identifying a new generation of anti‐inflammatory agents.
Nutritional ecology beyond the individual: a conceptual framework for integrating nutrition and social interactions
Authors: Lihoreau Mathieu , Buhl Camille , Charleston Michael A. , Sword Gregory A. , Raubenheimer David , Simpson Stephen J. 
Published: January 2015

AbstractOver recent years, modelling approaches from nutritional ecology (known as Nutritional Geometry) have been increasingly used to describe how animals and some other organisms select foods and eat them in appropriate amounts in order to maintain a balanced nutritional state maximising fitness. These nutritional strategies profoundly affect the physiology, behaviour and performance of individuals, which in turn impact their social interactions within groups and societies. Here, we present a conceptual framework to study the role of nutrition as a major ecological factor influencing the development and maintenance of social life. We first illustrate some of the mechanisms by which nutritional differences among individuals mediate social interactions in a broad range of species and ecological contexts. We then explain how studying individual‐ and collective‐level nutrition in a common conceptual framework derived from Nutritional Geometry can bring new fundamental insights into the mechanisms and evolution of social interactions, using a combination of simulation models and manipulative experiments.
Imaging suppurative infections of the central nervous system in horses
Authors: Cardwell J. , Scrivani P. V. 
Published: January 2015

SummarySuppurative infections are typically caused by pyogenic bacteria, and are characterised by the formation of purulent exudates (pus). These infections may occur anywhere in the body and are particularly life‐threatening when pertaining to the central nervous system (CNS). Suppurative infections of the CNS may be due to trauma, local extension of disease, and haematogenous spread. In horses, suppurative infections are an important cause of morbidity and mortality, but only infrequently involve the CNS. The gross morphology of suppurative inflammation is described as phlegmon, abscess and empyema, with each form having characteristic morphological features that may be identified during advanced imaging of the CNS. In horses with known or suspected suppurative infection of the CNS, imaging may be performed to reduce diagnostic uncertainty, determine prognosis, or to describe the character and extent of the disease to guide case management.
Consumer‐driven nutrient dynamics in freshwater ecosystems: an introduction
Authors: Capps Krista A. , Atkinson Carla L. , Rugenski Amanda T. 
Published: January 2015

Summary

Over the past decade, studies of the effects of consumer‐driven nutrient dynamics have become more common. This work has demonstrated that animals can function as sources and sinks of elements, but few studies have broadly compared these processes among organisms and across ecosystems.
Collectively, the articles in this special issue elucidate the important roles that organisms can play in nutrient dynamics in lotic, lentic and wetland ecosystems. These papers show how species‐specific traits, such as body stoichiometry and trophic ecology, and abiotic variables, including ambient water chemistry, govern the net impacts of consumer‐driven nutrient dynamics in freshwater ecosystems.
Globally, the introduction of non‐native species and the loss of native biodiversity compromise the functional integrity of freshwater ecosystems. The work featured in this issue will help ecologists and conservation biologists integrate species‐specific traits with ecosystem‐specific conditions to understand the potential effects of changing biodiversity on ecosystem function in fresh waters.
Convergent changes in the trophic ecology of extremophile fish along replicated environmental gradients
Authors: Tobler Michael , Scharnweber Kristin , Greenway Ryan , Passow Courtney N. , Arias‐Rodriguez Lenin , García‐De‐León Francisco J. 
Published: January 2015

Summary

Divergent selection along environmental gradients connecting locally restricted extreme habitats and adjacent benign habitats can shape convergent evolution of traits involved in coping with physiochemical stressors and can drive speciation. At the same time, the presence of such stressors alters aspects of the biotic environment, including resource availability and competitive regimes. However, it remains unclear whether and how the ecology of populations occurring in both extreme and benign environments varies in a predictable fashion.

We investigated the trophic ecology of live‐bearing fishes of the genus Poecilia that have independently colonised multiple springs containing toxic hydrogen sulphide in southern Mexico. Sulphide spring fish are adapted to the unique environmental conditions and are reproductively isolated from ancestral populations in adjacent non‐sulphidic habitats. We used gut content analyses to test whether colonisation of extreme habitats was accompanied by shifts of trophic resource use and expansions of trophic niche width. Furthermore, we tested whether dietary shifts were reflected in trophic morphology by comparing intestinal tract lengths among populations using both wild‐caught and common garden‐raised individuals.

Gut content analyses revealed that fish inhabiting toxic springs expanded their trophic niche width and changed their dietary resource use from detritus and algae to sulphide bacteria and invertebrates. This dietary shift was paralleled by changes in intestinal tract morphology, whereby sulphide spring fish had shorter intestines than fish from adjacent non‐sulphidic habitats. Analysis of common garden‐raised fish indicated that morphological differences between sulphidic and non‐sulphidic populations are at least in part due to genetic differentiation. Both patterns of trophic resource use and differentiation in trophic morphology were consistent across replicated pairs of sulphidic and non‐sulphidic populations, although the magnitude of differentiation varied among river drainages.

Our results suggest that colonisation of and adaptation to sulphide springs in southern Mexico was paralleled by convergent changes in trophic ecology. This highlights the complexity of environmental gradients and the necessity of considering multiple sources of selection when studying the evolution of complex phenotypes.