bluuebunny/crossref_metadata_2025 huggingface dataset:
Drivers of aquatic macroinvertebrate richness in spring fens in relation to habitat specialization and dispersal mode
Authors: Horsák Michal , Rádková Vanda , Syrovátka Vít , Bojková Jindřiška , Křoupalová Vendula , Schenková Jana , Zajacová Jana
Published: July 2015

Aims

The aim was to identify the main drivers of aquatic macroinvertebrate species richness in spring‐fen habitats (i.e. groundwater seepage wetlands) because these habitats are among the most threatened temperate biodiversity hotspots.

Location

Isolated spring fens in the western Carpathian Mountains.

Methods

Assemblages of Tricladida, Clitellata, Mollusca, Ephemeroptera, Plecoptera, Trichoptera and Diptera were sampled at 48 fens distributed evenly along a gradient of water mineral richness and grouped according to habitat specialization and dispersal mode. Several physicochemical parameters that have been reported to be the main drivers of species distribution were recorded for each site, along with radiocarbon measurements of the absolute age of the sites. The numbers of species in the taxonomic groups analysed were modelled as a function of the predictors via multiple linear regressions.

Results

We achieved a notably higher sampling efficiency than had been used in previous spring aquatic macroinvertebrate studies. In total, we collected and identified 255 species within 331 taxa from > 235,000 individuals. The number of species in all taxonomic groups increased with water discharge but the highest predictive power was obtained with water redox potential, which explained as much as 55.7% of the specialist species richness variance. We found contrasting and systematic differences in the importance of predictors related mainly to the level of species habitat specialization. Species richness of spring‐fen specialists was strongly determined by the main environmental gradient of change in groundwater chemistry, while generalists primarily reflected habitat stability linked to higher water discharge, habitat size and absolute age.

Main conclusion

Isolated island‐like spring fens can harbour unusually species‐rich assemblages of aquatic macroinvertebrates, the species richness of which is shaped by contrasting mechanisms dependent mainly on habitat specialization and also partly on dispersal mode. The richness of habitat specialist species seen at calcareous fens indicates their conservation priority.
Does vocal learning accelerate acoustic diversification? Evolution of contact calls in Neotropical parrots
Authors: Medina‐García A. , Araya‐Salas M. , Wright T. F.
Published: July 2015

Learning has been traditionally thought to accelerate the evolutionary change of behavioural traits. We evaluated the evolutionary rate of learned vocalizations and the interplay of morphology and ecology in the evolution of these signals. We examined contact calls of 51 species of Neotropical parrots from the tribe Arini. Parrots are ideal subjects due to their wide range of body sizes and habitats, and their open‐ended vocal learning that allows them to modify their calls throughout life. We estimated the evolutionary rate of acoustic parameters of parrot contact calls and compared them to those of morphological traits and habitat. We also evaluated the effect of body mass, bill length, vegetation density and species interactions on acoustic parameters of contact calls while controlling for phylogeny. Evolutionary rates of acoustic parameters did not differ from those of our predictor variables except for spectral entropy, which had a significantly slower rate of evolution. We found support for correlated evolution of call duration, and fundamental and peak frequencies with body mass, and of fundamental frequency with bill length. The degree of sympatry between species did not have a significant effect on acoustic parameters. Our results suggest that parrot contact calls, which are learned acoustic signals, show evolutionary rates similar to those of morphological traits. This is the first study to our knowledge to provide evidence that change through cultural evolution does not necessarily accelerate the evolutionary rate of traits acquired through life‐long vocal learning.
Liking the good guys: amplifying local adaptation via the evolution of condition‐dependent mate choice
Authors: Veen T. , Otto S. P.
Published: July 2015

Local adaptation can be strengthened through a diversity of mechanisms that reduce gene flow between contrasting environments. Recent work revealed that mate choice could enhance local adaptation when females preferentially mate with locally adapted males and that such female preferences readily evolve, but the opposing effects of recombination, migration and costs of female preferences remain relatively unexplored. To investigate these effects, we develop a two‐patch model with two genes, one influencing an ecological trait and one influencing female preferences, where both male signals and female preferences are allowed to depend on the match between an individual's ecological trait and the local environment (condition). Because trait variation is limited when migration is rare and the benefits of preferential mating are short‐lived when migration is frequent, we find that female preferences for males in high condition spread most rapidly with intermediate levels of migration. Surprisingly, we find that preferences for locally adapted males spread fastest with higher recombination rates, which contrasts with earlier studies. This is because a stronger preference allele for locally adapted males can only get uncoupled from maladapted ecological alleles following migration through recombination. The effects of migration and recombination depend strongly on the condition of the males being chosen by females, but only weakly on the condition of the females doing the choosing, except when it comes to the costs of preference. Although costs always impede the spread of female preferences for locally adapted males, the impact is substantially lessened if costs are borne primarily by females in poor condition. The abundance of empirical examples of condition‐dependent mate choice combined with our theoretical results suggests that the evolution of mate choice could commonly facilitate local adaptation in nature.
Sex‐biased dispersal, kin selection and the evolution of sexual conflict
Authors: Faria Gonçalo S. , Varela Susana A. M. , Gardner Andy
Published: July 2015

There is growing interest in resolving the curious disconnect between the fields of kin selection and sexual selection. Rankin's (2011, J. Evol. Biol. 24, 71–81) theoretical study of the impact of kin selection on the evolution of sexual conflict in viscous populations has been particularly valuable in stimulating empirical research in this area. An important goal of that study was to understand the impact of sex‐specific rates of dispersal upon the coevolution of male‐harm and female‐resistance behaviours. But the fitness functions derived in Rankin's study do not flow from his model's assumptions and, in particular, are not consistent with sex‐biased dispersal. Here, we develop new fitness functions that do logically flow from the model's assumptions, to determine the impact of sex‐specific patterns of dispersal on the evolution of sexual conflict. Although Rankin's study suggested that increasing male dispersal always promotes the evolution of male harm and that increasing female dispersal always inhibits the evolution of male harm, we find that the opposite can also be true, depending upon parameter values.
No evidence of trade‐offs in the evolution of sperm numbers and sperm size in mammals
Authors: Tourmente M. , Delbarco Trillo J. , Roldan E. R. S.
Published: July 2015

Post‐copulatory sexual selection, in the form sperm competition, has influenced the evolution of several male reproductive traits. However, theory predicts that sperm competition would lead to trade‐offs between numbers and size of spermatozoa because increased costs per cell would result in a reduction of sperm number if both traits share the same energetic budget. Theoretical models have proposed that, in large animals, increased sperm size would have minimal fitness advantage compared with increased sperm numbers. Thus, sperm numbers would evolve more rapidly than sperm size under sperm competition pressure. We tested in mammals whether sperm competition maximizes sperm numbers and size, and whether there is a trade‐off between these traits. Our results showed that sperm competition maximizes sperm numbers in eutherian and metatherian mammals. There was no evidence of a trade‐off between sperm numbers and sperm size in any of the two mammalian clades as we did not observe any significant relationship between sperm numbers and sperm size once the effect of sperm competition was taken into account. Maximization of both numbers and size in mammals may occur because each trait is crucial at different stages in sperm's life; for example size‐determined sperm velocity is a key determinant of fertilization success. In addition, numbers and size may also be influenced by diverse energetic budgets required at different stages of sperm formation.
Neutrophil gelatinase‐associated lipocalin regulates gut microbiota of mice
Authors: Mori Katsuya , Suzuki Takeshi , Minamishima Shizuka , Igarashi Toru , Inoue Kei , Nishimura Daisuke , Seki Hiroyuki , Yamada Takashige , Kosugi Shizuko , Katori Nobuyuki , Hashiguchi Saori , Morisaki Hiroshi
Published: July 2015

Background and Aim:

Because neutrophil gelatinase‐associated lipocalin (NGAL) is known to provide significant bacteriostatic effects during infectious conditions, we tested the hypothesis that this protein is up‐regulated and secreted into the intraluminal cavity of the gut under critically ill conditions and is thus responsible for the regulation of bacterial overgrowth.

Methods:

With our institutional approval, male C57BL/6J mouse (6–7 weeks) were enrolled and applied for lipopolysaccharide or peritonitis model compared with naïve control. We assessed NGAL protein concentrations in intestinal lumen and up‐regulation of NGAL expression in intestinal tissues in in vivo as well as ex vivo settings. Simultaneously, we examined the effects of NGAL protein administration on the growth of Escherichia coli (E. coli) in in vivo and in vitro experimental settings. The localization of NGAL in intestinal tissues and lumen was also assessed by immunohistological approach using NGAL antibody.

Results:

Both lipopolysaccharide and peritonitis insults evoked the marked up‐regulation of NGAL mRNA and protein levels in gut tissues such as crypt cells. In addition, the administration of NGAL protein significantly inhibited the outgrowth of enteric E. coli under both in vitro and in vivo conditions, accompanied by histological evidence.

Conclusion:

Neutrophil gelatinase‐associated lipocalin protein accompanied by apparent bacteriostatic action accumulated in the intestinal wall and streamed into the mucosal layer during critically ill state, thereby possibly shaping microbiota homeostasis in the gut.
Structure, function and toxicity of alpha‐synuclein: the Bermuda triangle in synucleinopathies
Authors: Villar‐Piqué Anna , Lopes da Fonseca Tomás , Outeiro Tiago Fleming
Published: July 2015

Parkinson's disease belongs to a group of currently incurable neurodegenerative disorders characterized by the misfolding and accumulation of alpha‐synuclein aggregates that are commonly known as synucleinopathies. Clinically, synucleinopathies are heterogeneous, reflecting the somewhat selective neuronal vulnerability characteristic of each disease. The precise molecular underpinnings of synucleinopathies remain unclear, but the process of aggregation of alpha‐synuclein appears as a central event. However, there is still no consensus with respect to the toxic forms of alpha‐synuclein, hampering our ability to use the protein as a target for therapeutic intervention. To decipher the molecular bases of synucleinopathies, it is essential to understand the complex triangle formed between the structure, function and toxicity of alpha‐synuclein. Recently, important steps have been undertaken to elucidate the role of the protein in both physiological and pathological conditions. Here, we provide an overview of recent findings in the field of alpha‐synuclein research, and put forward a new perspective over paradigms that persist in the field. Establishing whether alpha‐synuclein has a causative role in all synucleinopathies will enable the identification of targets for the development of novel therapeutic strategies for this devastating group of disorders.

image

Alpha‐synuclein is the speculated cornerstone of several neurodegenerative disorders known as Synucleinopathies. Nevertheless, the mechanisms underlying the pathogenic effects of this protein remain unknown. Here, we review the recent findings in the three corners of alpha‐synuclein biology – structure, function and toxicity – and discuss the enigmatic roads that have accompanied alpha‐synuclein from the beginning.

This article is part of aspecial issue on Parkinson disease.
Interferon gamma induces protective non‐canonical signaling pathways in primary neurons
Authors: O'Donnell Lauren A. , Henkins Kristen M. , Kulkarni Apurva , Matullo Christine M. , Balachandran Siddharth , Pattisapu Anil K. , Rall Glenn F.
Published: July 2015

The signal transduction molecule, Stat1, is critical for the expression of type I and II interferon (IFN)‐responsive genes in most cells; however, we previously showed that primary hippocampal mouse neurons express low basal Stat1, with delayed and attenuated expression of IFN‐responsive genes. Moreover, IFNγ‐dependent resolution of a neurotropic viral challenge in permissive mice is Stat1‐independent. Here, we show that exogenous IFNγ has no deleterious impact on neuronal viability, and staurosporine‐induced apoptosis in neurons is significantly blunted by the addition of IFNγ, suggesting that IFNγ confers a pro‐survival signal in neurons. To identify the pathways induced by IFNγ in neurons, the activation of alternative signal transducers associated with IFNγ signaling was assessed. Rapid and pronounced activation of extracellular signal regulated kinase (Erk1/2) was observed in neurons, compared to a modest response in fibroblasts. Moreover, the absence of Stat1 in primary fibroblasts led to enhanced Erk activation following IFNγ addition, implying that the cell‐specific availability of signal transducers can diversify the cellular response following IFN engagement.

image

Interferon gamma (IFNγ) signaling varies depending upon cell type and the inflammatory milieu. In neurons, IFNγ activates extracellular regulated kinase‐1/2 (Erk‐1/2) in the context of low expression of the classical IFNγ signaling molecule Signal Transducers and Activators of Transcription‐1 (STAT1). We propose that such alternative signaling pathways could protect against inflammation, and may be dictated by basal expression of intracellular signal transducers.
Dialogic Accountings for Stakeholders: On Opening Up and Closing Down Participatory Governance
Authors: Brown Judy , Dillard Jesse
Published: July 2015

Interpretivist and critical accounting researchers have long challenged the shareholder focus of conventional accounting, calling for new approaches that promote accountability to stakeholders and participatory governance. One proposal is for dialogic accountings that take pluralism seriously and enable critical reflection on organizational practices from diverse socio‐political perspectives. Dialogic accounting aims to counter narrow managerialist framings and address constituencies poorly served by traditional accounting. However, those favouring pluralist approaches face significant challenges in addressing entrenched ideologies and power relations. Rather than trying to address these challenges solely from within accounting, much can be learned from disciplinary fields that demonstrate sustained interest in pluralistic analysis and engagement. Here, we focus on the insights science and technology studies (STS) provides on opening up and closing down participatory governance, understanding knowledge‐power dynamics and implications for stakeholder value creation.
Topography and climate are more important drivers of long‐term, post‐fire vegetation assembly than time‐since‐fire in the Sonoran Desert, US
Authors: Shryock Daniel F. , Esque Todd C. , Chen Felicia C.
Published: July 2015

Questions

Do abiotic environmental filters or time‐since‐fire (TSF) explain more variability in post‐fire vegetation assembly? Do these influences vary between vegetation structure and composition, and across spatial scales?

Location

Sonoran Desert of southwestern Arizona, US.

Methods

We measured perennial vegetation in a chronosequence of 13 fires (8–33 yr TSF) spanning a broad regional gradient. The relative influence of environmental filters (topography and climate) and TSF were compared as predictors of long‐term, post‐fire vegetation assembly. Analyses considered different measures of vegetation structure (cover, height and density) and scales of community organization (species composition, structure and landscape).

Results

Species and growth form composition did not exhibit directional responses with increasing TSF, but sorted along abiotic gradients. Differences in vegetation cover and height between burned and unburned control areas were attributed primarily to gradients of topography and climate. In contrast, vegetation density initially increased in burned areas but declined to pre‐burn levels with increasing TSF. The strongest predictors of landscape‐scale recovery of vegetation cover, height and density were elevation, post‐fire precipitation and average annual precipitation, respectively. Recovery of vegetation height was positively correlated with precipitation in the first year following fire, suggesting that abiotic conditions of the immediate post‐fire environment may drive long‐term variability in vegetation structure.

Conclusions

We find substantial evidence that environmental filters, rather than TSF, drive the majority of variability in long‐term, post‐fire vegetation assembly within the Sonoran Desert. Careful consideration of spatial variability in abiotic conditions may benefit post‐fire vegetation modelling, as well as fire management and restoration strategies.
Beyond the achievement of sustained virological response after liver transplantation
Authors: Lens Sabela , Mariño Zoe , Forns Xavier
Published: July 2015

See Articles on Page 2433 and 2442
VEGF Pathways in the Lymphatics of Healthy and Diseased Heart
Authors: Dashkevich Alexey , Hagl Christian , Beyersdorf Friedhelm , Nykänen Antti I. , Lemström Karl B.
Published: July 2015

Cardiac lymphatic system is a rare focus of the modern cardiovascular research. Nevertheless, the growing body of evidence is depicting lymphatic endothelium as an important functional unit in healthy and diseased myocardium. Since the discovery of angiogenic VEGF‐A in 1983 and lymphangiogenic VEGF‐C in 1997, an increasing amount of knowledge has accumulated on the essential roles of VEGF ligands and receptors in physiological and pathological angiogenesis and lymphangiogenesis. Tissue adaptation to several stimuli such as hypoxia, pathogen invasion, degenerative process and inflammation often involves coordinated changes in both blood and lymphatic vessels. As lymphatic vessels are involved in the initiation and resolution of inflammation and regulation of tissue edema, VEGF family members may have important roles in myocardial lymphatics in healthy and in cardiac disease. We will review the properties of VEGF ligands and receptors concentrating on their lymphatic vessel effects first in normal myocardium and then in cardiac disease.
Randomized placebo‐controlled trial of zonisamide in patients with Parkinson's disease
Authors: Murata Miho , Hasegawa Kazuko , Kanazawa Ichiro , Shirakura Kenji , Kochi Kenji , Shimazu Rieko ,   The Zonisamide PD Study Group
Published: July 2015

Background

We previously showed that zonisamide significantly improved parkinsonian symptoms by a multicenter, double‐blind clinical trial.

Aim

To confirm the efficacy of zonisamide on Parkinson's disease, a phase 3, randomized, placebo‐controlled, multicenter, double‐blind trial was carried out in Japan.

Methods

Participants had advanced Parkinson's disease taking L‐dopa with at least one other antiparkinson drug, but were developing a deterioration of response to L‐dopa therapy. The trial consisted of a 2‐week initial phase (single‐blind, with administration of placebo) and a 12‐week treatment phase (double‐blind, with patients randomly assigned to either placebo, or zonisamide 25 or 50 mg/day). Patients were evaluated using the Unified Parkinson's Disease Rating Scale (UPDRS).

Results

A total of 185 patients (mean age 64.8 years; mean duration 7.5 years) were included in the efficacy analysis (placebo, zonisamide 25 mg, 50 mg; 63, 61, 61 patients, respectively). When compared with the placebo group, the UPDRS Part III total score at final assessment (the primary end‐point for efficacy) significantly improved (P = 0.029) in the zonisamide 25 mg group. After 12 weeks of therapy, the UPDRS Part III total score significantly improved in both the zonisamide 25 mg (P = 0.038) and 50 mg groups (P = 0.049), compared with the placebo group. Neither the zonisamide 25 mg nor 50 mg group differed significantly from the placebo group in the incidence of adverse events (P = 0.363 and P = 0.713, respectively).

Conclusion

These findings confirmed that zonisamide is well tolerated and efficacious in the treatment of advanced Parkinson's disease.
Endoscopic delivery of enteric neural stem cells to treat Hirschsprung disease
Authors: Cheng L. S. , Hotta R. , Graham H. K. , Nagy N. , Goldstein A. M. , Belkind‐Gerson J.
Published: July 2015

Background

Transplantation of enteric neural stem cells (ENSC) holds promise as a potential therapy for enteric neuropathies, including Hirschsprung disease. Delivery of transplantable cells via laparotomy has been described, but we propose a novel, minimally invasive endoscopic method of cell delivery.

Methods

Enteric neural stem cells for transplantation were cultured from dissociated gut of postnatal donor mice. Twelve recipient mice, including Ednrb−/− mice with distal colonic aganglionosis, underwent colonoscopic injection of ENSC under direct vision using a 30‐gauge Hamilton needle passed through a rigid cystoureteroscope. Cell engraftment, survival, and neuroglial differentiation were studied 1–4 weeks after the procedure.

Key Results

All recipient mice tolerated the procedure without complications and survived to sacrifice. Transplanted cells were found within the colonic wall in 9 of 12 recipient mice with differentiation into enteric neurons and glia.

Conclusions & Inferences

Endoscopic injection of ENSC is a safe and reliable method for cell delivery, and can be used to deliver a large number of cells to a specific area of disease. This minimally invasive endoscopic approach may prove beneficial to future human applications of cell therapy for neurointestinal disease.
Blur, eye movements and performance on a driving visual recognition slide test
Authors: Lee Samantha Sze‐Yee , Wood Joanne M. , Black Alexander A.
Published: July 2015

Purpose

Optical blur and ageing are known to affect driving performance but their effects on drivers' eye movements are poorly understood. This study examined the effects of optical blur and age on eye movement patterns and performance on the DriveSafe slide recognition test which is purported to predict fitness to drive.

Methods

Twenty young (27.1 ± 4.6 years) and 20 older (73.3 ± 5.7 years) visually normal drivers performed the DriveSafe under two visual conditions: best‐corrected vision and with +2.00 DS blur. The DriveSafe is a Visual Recognition Slide Test that consists of brief presentations of static, real‐world driving scenes containing different road users (pedestrians, bicycles and vehicles). Participants reported the types, relative positions and direction of travel of the road users in each image; the score was the number of correctly reported items (maximum score of 128). Eye movements were recorded while participants performed the DriveSafe test using a Tobii TX300 eye tracking system.

Results

There was a significant main effect of blur on DriveSafe scores (best‐corrected: 114.9 vs blur: 93.2; p < 0.001). There was also a significant age and blur interaction on the DriveSafe scores (p < 0.001) such that the young drivers were more negatively affected by blur than the older drivers (reductions of 22% and 13% respectively; p < 0.001): with best‐corrected vision, the young drivers performed better than the older drivers (DriveSafe scores: 118.4 vs 111.5; p = 0.001), while with blur, the young drivers performed worse than the older drivers (88.6 vs 95.9; p = 0.009). For the eye movement patterns, blur significantly reduced the number of fixations on road users (best‐corrected: 5.1 vs blur: 4.5; p < 0.001), fixation duration on road users (2.0 s vs 1.8 s; p < 0.001) and saccade amplitudes (7.4° vs 6.7°; p < 0.001). A main effect of age on eye movements was also found where older drivers made smaller saccades than the young drivers (6.7° vs 7.4°; p < 0.001).

Conclusions

Blur reduced DriveSafe scores for both age groups and this effect was greater for the young drivers. The decrease in number of fixations and fixation duration on road users, as well as the reduction in saccade amplitudes under the blurred condition, highlight the difficulty experienced in performing the task in the presence of optical blur, which suggests that uncorrected refractive errors may have a detrimental impact on aspects of driving performance.
Modulation of Melanogenesis and Antioxidant Status of Melanocytes in Response to Phototoxic Action of Doxycycline
Authors: Rok Jakub , Buszman Ewa , Beberok Artur , Delijewski Marcin , Otręba Michał , Wrześniok Dorota
Published: July 2015

Doxycycline is a commonly used tetracycline antibiotic showing the broad spectrum of antibacterial action. However, the use of this antibiotic is often connected with the risk of phototoxic reactions that lead to various skin disorders. One of the factors influencing the photosensitivity reactions is the melanin content in melanocytes. In this study, the impact of doxycycline and UVA irradiation on cell viability, melanogenesis and antioxidant defense system in cultured normal human epidermal melanocytes (HEMn‐DP) was examined. The exposure of cells to doxycycline and UVA radiation resulted in concentration‐dependent loss in melanocytes viability and induced melanin biosynthesis. Significant changes were stated in cellular antioxidant enzymes activity: SOD, CAT and GPx, which indicates alterations of antioxidant defense system. The results obtained in vitro may explain the mechanisms of phototoxic reactions that occur in normal human epidermal melanocytes in vivo after exposure of skin to doxycycline and UVA radiation.
Model for Optimization of the UV‐A/Riboflavin Strengthening (cross‐linking) of the Cornea: Percolation Threshold
Authors: Semchishen Anton , Mrochen Michael , Semchishen Vladimir
Published: July 2015

To achieve the maximum level of collagen strengthening within the shortest treatment time possible, we have developed a mathematical model which is used to optimize the process of corneal cross‐linking. This model is able to predict the temporal and spatial distribution of generated cross‐links within the corneal stroma and hence the increase in the elasticity modulus. Theory predicts corneal strengthening at low radiation intensities and the absence of the strengthening effect at radiation intensities above the threshold level, which agrees with the experimental results. The model takes account of the initial riboflavin concentration and bleaching, light intensity and time of illumination.
Activation of the General Stress Response of Bacillus subtilis by Visible Light
Authors: van der Steen Jeroen B. , Hellingwerf Klaas J.
Published: July 2015

A key challenge for microbiology is to understand how evolution has shaped the wiring of regulatory networks. This is amplified by the paucity of information of power‐spectra of physicochemical stimuli to which microorganisms are exposed. Future studies of genome evolution, driven by altered stimulus regimes, will therefore require a versatile signal transduction system that allows accurate signal dosing. Here, we review the general stress response of Bacillus subtilis, and its upstream signal transduction network, as a candidate system. It can be activated by red and blue light, and by many additional stimuli. Signal integration therefore is an intricate function of this system. The blue‐light response is elicited via the photoreceptor YtvA, which forms an integral part of stressosomes, to activate expression of the stress regulon of B. subtilis. Signal transfer through this network can be assayed with reporter enzymes, while intermediate steps can be studied with live‐cell imaging of fluorescently tagged proteins. Different parts of this system have been studied in vitro, such that its computational modeling has made significant progress. One can directly relate the microscopic characteristics of YtvA with activation of the general stress regulon, making this system a very well‐suited system for network evolution studies.
Work Design and Integration Glitches in Globally Distributed Technology Projects
Authors: Mishra Anant , Sinha Kingshuk K.
Published: July 2015

In a technology project, project integration represents the pooling together of complete, interdependent task modules to form a physical product or software delivering a desired functionality. This study develops and tests a conceptual framework that examines the interrelationships between the elements of work design, project integration challenges, and project performance. We identify two distinct elements of work design in technology projects: (i) the type of project organization based on whether a technology project spans a firm boundary ( Domestic‐Outsourcing) or a country boundary ( Offshore‐Insourcing) or both boundaries ( Offshore‐Outsourcing) or no boundaries ( Domestic‐Insourcing), and (ii) the joint coordination practices among key stakeholders in a technology project—namely, Onsite Ratio and Joint‐Task Ownership. Next, we measure the effectiveness of project integration using integration glitches that capture the incompatibility among interdependent task modules during project integration. Based on analysis of data from 830 technology projects, the results highlight the differential effects of distributed project organizations on integration glitches. Specifically, we find that project organizations that span both firm and country boundaries (Offshore‐Outsourcing) experience significantly higher levels of integration glitches compared to domestic project organizations (Domestic‐Outsourcing and Domestic‐Insourcing). The results further indicate that the relationship between project organization type and integration glitches is moderated by the extent of joint coordination practices in a project. That is, managers can actively lower integration glitches by increasing the levels of onsite ratio and by promoting higher levels of joint‐task ownership, particularly in project organization types that span both firm and country boundaries (Offshore‐Outsourcing). Finally, the results demonstrate the practical significance of studying integration glitches by highlighting its significant negative effect on project performance.
Temporary Hubs for the Global Vehicle Supply Chain in Humanitarian Operations
Authors: Stauffer Jon M. , Pedraza‐Martinez Alfonso J. , Van Wassenhove Luk N.
Published: July 2015

We model the global vehicle supply chain of an International Humanitarian Organization (IHO) with a dynamic hub location model across monthly periods. We use actual vehicle data from the International Federation of the Red Cross to feed our model and provide insights into IHO secondary support demand. We find that secondary support demand for items such as vehicles is different from primary beneficiary demand for items such as water and food. When considering disaster response and development program demand simultaneously (disaster cycle management), our results illustrate that keeping a lean centralized hub configuration with an option for temporary hubs in mega disaster locations can reduce overall supply chain costs over a long time horizon. We also show that it is possible to structure a supply chain to take operational advantage of earmarked funding. This research lays the groundwork for using optimization models to analyze disaster cycle management.
Effects of postharvest onion curing parameters on bulb rot caused by Pantoea agglomerans, Pantoea ananatis and Pantoea allii in storage
Authors: Vahling‐Armstrong C. , Dung J. K. S. , Humann J. L. , Schroeder B. K.
Published: July 2015

Crop loss of onion bulbs during storage carries an exceptionally high economic impact because a large portion of the production expenses has been expended before storage. Because of this, it is important to define practices that can reduce onion bulb losses caused by storage rots. This study investigates the impact of various curing parameters on disease development resulting from infection by Pantoea agglomerans, P. ananatis and P. allii on onion bulb cultivars Vaquero and Redwing, during storage. Overall, both the incidence and mean rot severity were similar amongst the bulbs under comparable conditions regardless of the species of Pantoea inoculated, although a significant difference was detected between the two onion bulb cultivars. In addition, a significant reduction of storage rot was observed when curing temperatures were ≤35°C. At temperatures >35°C, a shorter curing duration (2 days vs 14 days) decreased the severity of bulb rot due to Pantoea. This increased understanding of the inter‐relationships between the parameters used for curing, and the incidence and severity of bulb rot caused by Pantoea helps provide guidance towards using the curing process as a means to reduce the level of damage resulting from post‐harvest storage rot.
The development of a population of 4D pediatric XCAT phantoms for imaging research and optimization
Authors: Segars W. P. , Norris Hannah , Sturgeon Gregory M. , Zhang Yakun , Bond Jason , Minhas Anum , Tward Daniel J. , Ratnanather J. T. , Miller M. I. , Frush D. , Samei E.
Published: July 2015

Purpose:

We previously developed a set of highly detailed 4D reference pediatric extended cardiac‐torso (XCAT) phantoms at ages of newborn, 1, 5, 10, and 15 yr with organ and tissue masses matched to ICRP Publication 89 values. In this work, we extended this reference set to a series of 64 pediatric phantoms of varying age and height and body mass percentiles representative of the public at large. The models will provide a library of pediatric phantoms for optimizing pediatric imaging protocols.

Methods:

High resolution positron emission tomography‐computed tomography data obtained from the Duke University database were reviewed by a practicing experienced radiologist for anatomic regularity. The CT portion of the data was then segmented with manual and semiautomatic methods to form a target model defined using nonuniform rational B‐spline surfaces. A multichannel large deformation diffeomorphic metric mapping algorithm was used to calculate the transform from the best age matching pediatric XCAT reference phantom to the patient target. The transform was used to complete the target, filling in the nonsegmented structures and defining models for the cardiac and respiratory motions. The complete phantoms, consisting of thousands of structures, were then manually inspected for anatomical accuracy. The mass for each major tissue was calculated and compared to linearly interpolated ICRP values for different ages.

Results:

Sixty four new pediatric phantoms were created in this manner. Each model contains the same level of detail as the original XCAT reference phantoms and also includes parameterized models for the cardiac and respiratory motions. For the phantoms that were 10 yr old and younger, we included both sets of reproductive organs. This gave them the capability to simulate both male and female anatomy. With this, the population can be expanded to 92. Wide anatomical variation was clearly seen amongst the phantom models, both in organ shape and size, even for models of the same age and sex. The phantoms can be combined with existing simulation packages to generate realistic pediatric imaging data from different modalities.

Conclusions:

This work provides a large cohort of highly detailed pediatric phantoms with 4D capabilities of varying age, height, and body mass. The population of phantoms will provide a vital tool with which to optimize 3D and 4D pediatric imaging devices and techniques in terms of image quality and radiation‐absorbed dose.
Engineered binding to erythrocytes induces immunological tolerance to
E. coli
asparaginase
Authors: Lorentz Kristen M. , Kontos Stephan , Diaceri Giacomo , Henry Hugues , Hubbell Jeffrey A.
Published: July 2015

Humoral immune tolerance to the therapeutic enzyme
E. coli
l
-asparaginase was induced by engineering the enzyme for in vivo erythrocyte binding.
Natural aerosols explain seasonal and spatial patterns of Southern Ocean cloud albedo
Authors: McCoy Daniel T. , Burrows Susannah M. , Wood Robert , Grosvenor Daniel P. , Elliott Scott M. , Ma Po-Lun , Rasch Phillip J. , Hartmann Dennis L.
Published: July 2015

Sulfate and organic mass in sea spray explain more than half of the variability in Southern Ocean cloud droplet concentration.
Local variations of HER2 dimerization in breast cancer cells discovered by correlative fluorescence and liquid electron microscopy
Authors: Peckys Diana B. , Korf Ulrike , de Jonge Niels
Published: July 2015

New microscopy method reveals local variations of functional state of membrane protein associated with cancer cell growth.
Controlling the metal-to-insulator relaxation of the metastable hidden quantum state in 1T-TaS
2
Authors: Vaskivskyi Igor , Gospodaric Jan , Brazovskii Serguei , Svetin Damjan , Sutar Petra , Goreshnik Evgeny , Mihailovic Ian A. , Mertelj Tomaz , Mihailovic Dragan
Published: July 2015

Revealing the relaxation mechanisms of hidden states in transition metal dichalcogenides leads to control of metastability.
A Complex Signaling Cascade Governs Pristinamycin Biosynthesis in Streptomyces pristinaespiralis
Authors: Mast Yvonne , Guezguez Jamil , Handel Franziska , Schinko Eva
Published: July 2015

Pristinamycin production in
Streptomyces pristinaespiralis
Pr11 is tightly regulated by an interplay between different repressors and activators. A γ-butyrolactone receptor gene (
spbR
), two TetR repressor genes (
papR3
and
papR5
), three SARP (

S

treptomyces
a
ntibiotic
r
egulatory
p
rotein) genes (
papR1
,
papR2
, and
papR4
), and a response regulator gene (
papR6
) are carried on the large 210-kb pristinamycin biosynthetic gene region of
Streptomyces pristinaespiralis
Pr11. A detailed investigation of all pristinamycin regulators revealed insight into a complex signaling cascade, which is responsible for the fine-tuned regulation of pristinamycin production in
S. pristinaespiralis
.
The Pathway-Specific Regulator ClaR of Streptomyces clavuligerus Has a Global Effect on the Expression of Genes for Secondary Metabolism and Differentiation
Authors: Martínez-Burgo Yolanda , Álvarez-Álvarez Rubén , Rodríguez-García Antonio , Liras Paloma
Published: July 2015

Streptomyces clavuligerus
claR
::
aph
is a
claR
-defective mutant, but in addition to its
claR
defect it also carries fewer copies of the resident linear plasmids pSCL2 and pSCL4 (on the order of 4 × 10
5
-fold lower than the wild-type strain), as shown by qPCR. To determine the function of ClaR without potential interference due to plasmid copy number, a new strain,
S. clavuligerus
Δ
claR
::
aac
, with
claR
deleted and carrying the wild-type level of plasmids, was constructed. Transcriptomic analyses were performed in
S. clavuligerus
Δ
claR
::
aac
and
S. clavuligerus
ATCC 27064 as the control strain. The new Δ
claR
mutant did not produce clavulanic acid (CA) and showed a partial expression of genes for the early steps of the CA biosynthesis pathway and a very poor expression (1 to 8%) of the genes for the late steps of the CA pathway. Genes for cephamycin C biosynthesis were weakly upregulated (1.7-fold at 22.5 h of culture) in the Δ
claR
mutant, but genes for holomycin biosynthesis were expressed at levels from 3- to 572-fold higher than in the wild-type strain, supporting the observed overproduction of holomycin by
S. clavuligerus
Δ
claR
::
aac
. Interestingly, three secondary metabolites produced by gene clusters SMCp20, SMCp22, and SMCp24, encoding still-cryptic compounds, had partially or totally downregulated their genes in the mutant, suggesting a regulatory role for ClaR wider than previously reported. In addition, the
amfR
gene was downregulated, and consequently, the mutant did not produce aerial mycelium. Expression levels of about 100 genes in the genome were partially up- or downregulated in the Δ
claR
mutant, many of them related to the upregulation of the sigma factor-encoding
rpoE
gene.
Degradation of Granular Starch by the Bacterium Microbacterium aurum Strain B8.A Involves a Modular α-Amylase Enzyme System with FNIII and CBM25 Domains
Authors: Valk Vincent , Eeuwema Wieger , Sarian Fean D. , van der Kaaij Rachel M. , Dijkhuizen Lubbert
Published: July 2015

The bacterium
Microbacterium aurum
strain B8.A, originally isolated from a potato plant wastewater facility, is able to degrade different types of starch granules. Here we report the characterization of an unusually large, multidomain
M. aurum
B8.A α-amylase enzyme (MaAmyA). MaAmyA is a 1,417-amino-acid (aa) protein with a predicted molecular mass of 148 kDa. Sequence analysis of MaAmyA showed that its catalytic core is a family GH13_32 α-amylase with the typical ABC domain structure, followed by a fibronectin (FNIII) domain, two carbohydrate binding modules (CBM25), and another three FNIII domains. Recombinant expression and purification yielded an enzyme with the ability to degrade wheat and potato starch granules by introducing pores. Characterization of various truncated mutants of MaAmyA revealed a direct relationship between the presence of CBM25 domains and the ability of MaAmyA to form pores in starch granules, while the FNIII domains most likely function as stable linkers. At the C terminus, MaAmyA carries a 300-aa domain which is uniquely associated with large multidomain amylases; its function remains to be elucidated. We concluded that
M. aurum
B8.A employs a multidomain enzyme system to initiate degradation of starch granules via pore formation.
The Role of the Microbiome of Truffles in Aroma Formation: a Meta-Analysis Approach
Authors: Vahdatzadeh Maryam , Deveau Aurélie , Splivallo Richard
Published: July 2015

Truffles (
Tuber
spp.) are ascomycete subterraneous fungi that form ectomycorrhizas in a symbiotic relationship with plant roots. Their fruiting bodies are appreciated for their distinctive aroma, which might be partially derived from microbes. Indeed, truffle fruiting bodies are colonized by a diverse microbial community made up of bacteria, yeasts, guest filamentous fungi, and viruses. The aim of this minireview is two-fold. First, the current knowledge on the microbial community composition of truffles has been synthesized to highlight similarities and differences among four truffle (
Tuber
) species (
T. magnatum
,
T. melanosporum
,
T. aestivum
, and
T. borchii
) at various stages of their life cycle. Second, the potential role of the microbiome in truffle aroma formation has been addressed for the same four species. Our results suggest that on one hand, odorants, which are common to many truffle species, might be of mixed truffle and microbial origin, while on the other hand, less common odorants might be derived from microbes only. They also highlight that bacteria, the dominant group in the microbiome of the truffle, might also be the most important contributors to truffle aroma not only in
T. borchii
, as already demonstrated, but also in
T. magnatum
,
T. aestivum
, and
T. melanosporum
.
Three of a Kind: Genetically Similar Tsukamurella Phages TIN2, TIN3, and TIN4
Authors: Dyson Zoe A. , Tucci Joseph , Seviour Robert J. , Petrovski Steve
Published: July 2015

Three
Tsukamurella
phages, TIN2, TIN3, and TIN4, were isolated from activated sludge treatment plants located in Victoria, Australia, using conventional enrichment techniques. Illumina and 454 whole-genome sequencing of these
Siphoviridae
viruses revealed that they had similar genome sequences, ranging in size between 76,268 bp and 76,964 bp. All three phages shared 74% nucleotide sequence identity to the previously described
Gordonia
phage GTE7. Genome sequencing suggested that phage TIN3 had suffered a mutation in one of its lysis genes compared to the sequence of phage TIN4, to which it is genetically very similar. Mass spectroscopy data showed the unusual presence of a virion structural gene in the DNA replication module of phage TIN4, disrupting the characteristic modular genome architecture of
Siphoviridae
phages. All three phages appeared highly virulent on strains of
Tsukamurella inchonensis
and
Tsukamurella paurometabola
.
Involvement of Coat Proteins in Bacillus subtilis Spore Germination in High-Salinity Environments
Authors: Nagler Katja , Setlow Peter , Reineke Kai , Driks Adam , Moeller Ralf
Published: July 2015

The germination of spore-forming bacteria in high-salinity environments is of applied interest for food microbiology and soil ecology. It has previously been shown that high salt concentrations detrimentally affect
Bacillus subtilis
spore germination, rendering this process slower and less efficient. The mechanistic details of these salt effects, however, remained obscure. Since initiation of nutrient germination first requires germinant passage through the spores' protective integuments, the aim of this study was to elucidate the role of the proteinaceous spore coat in germination in high-salinity environments. Spores lacking major layers of the coat due to chemical decoating or mutation germinated much worse in the presence of NaCl than untreated wild-type spores at comparable salinities. However, the absence of the crust, the absence of some individual nonmorphogenetic proteins, and the absence of either CwlJ or SleB had no or little effect on germination in high-salinity environments. Although the germination of spores lacking GerP (which is assumed to facilitate germinant flow through the coat) was generally less efficient than the germination of wild-type spores, the presence of up to 2.4 M NaCl enhanced the germination of these mutant spores. Interestingly, nutrient-independent germination by high pressure was also inhibited by NaCl. Taken together, these results suggest that (i) the coat has a protective function during germination in high-salinity environments; (ii) germination inhibition by NaCl is probably not exerted at the level of cortex hydrolysis, germinant accessibility, or germinant-receptor binding; and (iii) the most likely germination processes to be inhibited by NaCl are ion, Ca
2+
-dipicolinic acid, and water fluxes.