bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large‐scale maps of variable infection efficiencies in aquatic Bacteroidetes phage‐host model systems
Authors: Holmfeldt Karin , Solonenko Natalie , Howard‐Varona Cristina , Moreno Mario , Malmstrom Rex R. , Blow Matthew J. , Sullivan Matthew B. 
Published: May 2016

SummaryMicrobes drive ecosystem functioning and their viruses modulate these impacts through mortality, gene transfer and metabolic reprogramming. Despite the importance of virus‐host interactions and likely variable infection efficiencies of individual phages across hosts, such variability is seldom quantified. Here, we quantify infection efficiencies of 38 phages against 19 host strains in aquatic Cellulophaga (Bacteroidetes) phage‐host model systems. Binary data revealed that some phages infected only one strain while others infected 17, whereas quantitative data revealed that efficiency of infection could vary 10 orders of magnitude, even among phages within one population. This provides a baseline for understanding and modeling intrapopulation host range variation. Genera specific host ranges were also informative. For example, the Cellulophaga Microviridae, showed a markedly broader intra‐species host range than previously observed in Escherichia coli systems. Further, one phage genus, Cba41, was examined to investigate nonheritable changes in plating efficiency and burst size that depended on which host strain it most recently infected. While consistent with host modification of phage DNA, no differences in nucleotide sequence or DNA modifications were detected, leaving the observation repeatable, but the mechanism unresolved. Overall, this study highlights the importance of quantitatively considering replication variations in studies of phage–host interactions.
Organization and mode of action of two component system signaling circuits from the various kingdoms of life
Authors: Alvarez Adrian F. , Barba‐Ostria Carlos , Silva‐Jiménez Hortencia , Georgellis Dimitris 
Published: May 2016

SummaryTwo‐component system (TCS) signaling circuits regulate numerous cellular processes in response to environmental cues in both prokaryotic and eukaryotic cells. These signaling circuits are all based on phosphoryl‐group transfers between histidine and aspartate containing modules of sensor kinase and response regulator proteins. Curiously, the architecture and organization of prokaryotic and eukaryotic two‐component systems reveal notable variations, raising the question of whether the input‐response specificity that governs the majority of prokaryotic TCSs also governs the eukaryotic ones. In this review, we contrast the TCS architecture and signaling circuits of prokaryotes and eukaryotes, and discuss their possible consequences on signaling specificity.
Physiological adjustments and transcriptome reprogramming are involved in the acclimation to salinity gradients in diatoms
Authors: Bussard Adrien , Corre Erwan , Hubas Cédric , Duvernois‐Berthet Evelyne , Le Corguillé Gildas , Jourdren Laurent , Coulpier Fanny , Claquin Pascal , Lopez Pascal Jean 
Published: May 2016

SummarySalinity regimes in estuaries and coastal areas vary with river discharge patterns, seawater evaporation, the morphology of the coastal waterways and the dynamics of marine water mixing. Therefore, microalgae have to respond to salinity variations at time scales ranging from daily to annual cycles. Microalgae may also have to adapt to physical alterations that induce the loss of connectivity between habitats and the enclosure of bodies of water. Here, we integrated physiological assays and measurements of morphological plasticity with a functional genomics approach to examine the regulatory changes that occur during the acclimation to salinity in the estuarine diatom Thalassiosira weissflogii. We found that cells exposed to different salinity regimes for a short or long period presented adjustments in their carbon fractions, silicon pools, pigment concentrations and/or photosynthetic parameters. Salinity‐induced alterations in frustule symmetry were observed only in the long‐term (LT) cultures. Whole transcriptome analyses revealed a down‐regulation of nuclear and plastid encoded genes during the LT response and identified only a few regulated genes that were in common between the ST and LT responses. We propose that in diatoms, one strategy for acclimating to salinity gradients and maintaining optimal cellular fitness could be a reduction in the cost of transcription.
Surface area–volume ratios in insects
Authors: Kühsel Sara , Brückner Adrian , Schmelzle Sebastian , Heethoff Michael , Blüthgen Nico 
Published: May 2016

AbstractBody mass, volume and surface area are important for many aspects of the physiology and performance of species. Whereas body mass scaling received a lot of attention in the literature, surface areas of animals have not been measured explicitly in this context. We quantified surface area–volume (SA/V) ratios for the first time using 3D surface models based on a structured light scanning method for 126 species of pollinating insects from 4 orders (Diptera, Hymenoptera, Lepidoptera, and Coleoptera). Water loss of 67 species was measured gravimetrically at very dry conditions for 2 h at 15 and 30 °C to demonstrate the applicability of the new 3D surface measurements and relevance for predicting the performance of insects. Quantified SA/V ratios significantly explained the variation in water loss across species, both directly or after accounting for isometric scaling (residuals of the SA/V ∼ mass2/3 relationship). Small insects with a proportionally larger surface area had the highest water loss rates. Surface scans of insects to quantify allometric SA/V ratios thus provide a promising method to predict physiological responses, improving the potential of body mass isometry alone that assume geometric similarity.
Metatranscriptome of the protistan community in Reticulitermes flaviceps
Authors: Liu Xiao‐Jing , Che Min , Xie Lei , Zhan Shuai , Zhou Zhi‐Hua , Huang Yong‐Ping , Wang Qian 
Published: May 2016

AbstractThe hindgut of lower termites harbors various symbiotic protists, which perform varied functions in lignocellulose decomposition. As termites are social insects, the species and numbers of these flagellated protists in the termite gut vary among the different castes. Juvenile hormones (JHs) can regulate caste differentiation in termites. In this study, we used the juvenile hormone analog fenoxycarb to induce termite workers (Reticulitermes flaviceps) to differentiate into pre‐soldiers. A metatranscriptomic investigation of the protistan community was then performed by 454 pyrosequencing. From a thorough analysis based on 597 312 generated reads, we found that the starch and sucrose metabolism pathway was the most abundant pathway across the metatranscriptome. The current study demonstrates that the metatranscriptome of the protistan community in termites contains an abundance of lignocellulase, which plays a vital role in termite nutrition.
Survival analysis of veteran patients with pancreatic cancer
Authors: Kim David , Zhu Hong , Nassri Ammar , Mokdad Ali , Kukreja Sachin , Polanco Patricio , Huerta Sergio , Ramzan Zeeshan 
Published: May 2016

ObjectiveFor patients with pancreatic cancer, the identification of reliable predictors of their outcomes could be invaluable for directing the managements. This study aimed to identify clinical and laboratory factors that could be used to predict early (≤6 months) or late (>6 months) mortality.MethodsMedical records of patients diagnosed with pancreatic cancer in the VA North Texas Health Care System from 2005 to 2010 were retrospectively reviewed. Univariate and multivariate analyses (MVA) were performed and the utility of cancer antigen 19‐9 (CA19‐9) test was explored.ResultsAltogether 109 patients with pancreatic cancer, 89.0% of whom were with adenocarcinoma, were divided into early (n = 62) and late (n = 47) mortality groups. Kaplan–Meier analysis revealed a median survival of 154 days [95% confidence interval (CI) 93–194 days]. On MVA, abdominal pain (OR = 10.6, P = 0.009) and large tumor size (OR = 2.4, P = 0.028) were significantly associated with early mortality, while palliative chemotherapy (OR = 0.048, P = 0.001) and neuroendocrine tumor (OR = 0.009, P = 0.024) were significantly associated with late mortality. Subgroup analyses of adenocarcinoma and late‐stage patients revealed similar results. Serum CA19‐9 performed poorly as a prognostic indicator in both groups (P = 0.43), in metastatic disease at diagnosis (P = 0.32) and after treatment (P = 0.65).ConclusionsAbdominal pain and large tumor size portends a poor prognosis in patients with pancreatic cancer. Palliative chemotherapy and surgical intervention may prolong the patient's survival. CA19‐9 is not universally reliable for predicting metastasis, survival, or the responses to chemotherapy.
Lessons from genome skimming of arthropod‐preserving ethanol
Authors: Linard B. , Arribas P. , Andújar C. , Crampton‐Platt A. , Vogler A. P. 
Published: May 2016

AbstractField‐collected specimens of invertebrates are regularly killed and preserved in ethanol, prior to DNA extraction from the specimens, while the ethanol fraction is usually discarded. However, DNA may be released from the specimens into the ethanol, which can potentially be exploited to study species diversity in the sample without the need for DNA extraction from tissue. We used shallow shotgun sequencing of the total DNA to characterize the preservative ethanol from two pools of insects (from a freshwater habitat and terrestrial habitat) to evaluate the efficiency of DNA transfer from the specimens to the ethanol. In parallel, the specimens themselves were subjected to bulk DNA extraction and shotgun sequencing, followed by assembly of mitochondrial genomes for 39 of 40 species in the two pools. Shotgun sequencing from the ethanol fraction and read‐matching to the mitogenomes detected ~40% of the arthropod species in the ethanol, confirming the transfer of DNA whose quantity was correlated to the biomass of specimens. The comparison of diversity profiles of microbiota in specimen and ethanol samples showed that ‘closed association’ (internal tissue) bacterial species tend to be more abundant in DNA extracted from the specimens, while ‘open association’ symbionts were enriched in the preservative fluid. The vomiting reflex of many insects also ensures that gut content is released into the ethanol, which provides easy access to DNA from prey items. Shotgun sequencing of DNA from preservative ethanol provides novel opportunities for characterizing the functional or ecological components of an ecosystem and their trophic interactions.
Sex determination in the wild: a field application of loop‐mediated isothermal amplification successfully determines sex across three raptor species
Authors: Centeno‐Cuadros A. , Abbasi I. , Nathan R. 
Published: May 2016

AbstractPCR‐based methods are the most common technique for sex determination of birds. Although these methods are fast, easy and accurate, they still require special facilities that preclude their application outdoors. Consequently, there is a time lag between sampling and obtaining results that impedes researchers to take decisions in situ and in real time considering individuals’ sex. We present an outdoor technique for sex determination of birds based on the amplification of the duplicated sex‐chromosome‐specific gene Chromo‐Helicase‐DNA binding protein using a loop‐mediated isothermal amplification (LAMP). We tested our method on Griffon Vulture (Gyps fulvus), Egyptian Vulture (Neophron percnopterus) and Black Kite (Milvus migrans) (family Accipitridae). We introduce the first fieldwork procedure for sex determination of animals in the wild, successfully applied to raptor species of three different subfamilies using the same specific LAMP primers. This molecular technique can be deployed directly in sampling areas because it only needs a voltage inverter to adapt a thermo‐block to a car lighter and results can be obtained by the unaided eye based on colour change within the reaction tubes. Primers and reagents are prepared in advance to facilitate their storage at room temperature. We provide detailed guidelines how to implement this procedure, which is simpler (no electrophoresis required), cheaper and faster (results in c. 90 min) than PCR‐based laboratory methods. Our successful cross‐species application across three different raptor subfamilies posits our set of markers as a promising tool for molecular sexing of other raptor families and our field protocol extensible to all bird species.
A high‐throughput detection method for invasive fruit fly (Diptera:Tephritidae) species based on microfluidic dynamic array
Authors: Jiang Fan , Fu Wei , Clarke Anthony R. , Schutze Mark Kurt , Susanto Agus , Zhu Shuifang , Li Zhihong 
Published: May 2016

AbstractInvasive species can be detrimental to a nation's ecology, economy and human health. Rapid and accurate diagnostics are critical to limit the establishment and spread of exotic organisms. The increasing rate of biological invasions relative to the taxonomic expertise available generates a demand for high‐throughput,DNA‐based diagnostics methods for identification. We designed species‐specificqPCRprimer and probe combinations for 27 economically important tephritidae species in six genera (Anastrepha,Bactrocera,Carpomya,Ceratitis,DacusandRhagoletis) based on 935COI DNAbarcode haplotypes from 181 fruit fly species publically available inBOLD, and then tested the specificity for each primer pair and probe throughqPCRof 35 of those species. We then developed a standardization reaction system for detecting the 27 target species based on a microfluidic dynamic array and also applied the method to identify unknown immature samples from port interceptions and field monitoring. This method led to a specific and simultaneous detection for all 27 species in 7.5 h, using only 0.2 μL of reaction system in each reaction chamber. The approach successfully discriminated among species within complexes that had genetic similarities of up to 98.48%, while it also identified all immature samples consistent with the subsequent results of morphological examination of adults which were reared from larvae of cohorts from the same samples. We present an accurate, rapid and high‐throughput innovative approach for detecting fruit flies of quarantine concern. This is a new method which has broad potential to be one of international standards for plant quarantine and invasive species detection.
State‐and‐transition simulation models: a framework for forecasting landscape change
Authors: Daniel Colin J. , Frid Leonardo , Sleeter Benjamin M. , Fortin Marie‐Josée 
Published: May 2016

Summary

A wide range of spatially explicit simulation models have been developed to forecast landscape dynamics, including models for projecting changes in both vegetation and land use. While these models have generally been developed as separate applications, each with a separate purpose and audience, they share many common features.

We present a general framework, called a state‐and‐transition simulation model (STSM), which captures a number of these common features, accompanied by a software product, called ST‐Sim, to build and run such models. The STSM method divides a landscape into a set of discrete spatial units and simulates the discrete state of each cell forward as a discrete‐time‐inhomogeneous stochastic process. The method differs from a spatially interacting Markov chain in several important ways, including the ability to add discrete counters such as age and time‐since‐transition as state variables, to specify one‐step transition rates as either probabilities or target areas, and to represent multiple types of transitions between pairs of states.

We demonstrate the STSM method using a model of land‐use/land‐cover (LULC) change for the state of Hawai'i, USA. Processes represented in this example include expansion/contraction of agricultural lands, urbanization, wildfire, shrub encroachment into grassland and harvest of tree plantations; the model also projects shifts in moisture zones due to climate change. Key model output includes projections of the future spatial and temporal distribution of LULC classes and moisture zones across the landscape over the next 50 years.

State‐and‐transition simulation models can be applied to a wide range of landscapes, including questions of both land‐use change and vegetation dynamics. Because the method is inherently stochastic, it is well suited for characterizing uncertainty in model projections. When combined with the ST‐Sim software, STSMs offer a simple yet powerful means for developing a wide range of models of landscape dynamics.
Stability of the Effect of a Standardized Meal on QTc
Authors: Täubel Jörg , Fernandes Sara , Ferber Georg 
Published: May 2016

BackgroundThe assessment of QTc changes after the intake of a standardized meal has been proposed as an alternative approach to prove assay sensitivity when the proarrhythimic potential of a drug is to be excluded in either TQT or intensive Phase I QT studies.MethodsIn this article, an analysis of the food effect at baseline across periods in two different studies is presented to support the robustness of the method.ResultsThe results show that the time‐effect attributed to food is stable over different study periods demonstrating consistency of the physiological response triggered by food.ConclusionsStability and reproducibility of the effect is comparable with moxifloxacin.
Functional and clinical outcomes following anterior hip replacement: a 5‐year comparative study versus posterior approach
Authors: Balasubramaniam Umatheepan , Dowsey Michelle , Ma Francis , Dunin Anthony , Choong Peter 
Published: May 2016

BackgroundWith the evolution of total hip joint replacement techniques, there has been a trend towards minimally invasive surgery. The anterior approach (AA) to total hip arthroplasty has been widely associated with less soft tissue damage. The aim of our study was to compare clinical and 1‐year functional outcomes for AA hip arthroplasty versus a posterior approach (PA).MethodWe retrospectively reviewed 92 (50 anterior and 42 posterior) total hip replacements performed at our centre between 2006 and 2011. Clinical outcomes were recorded from hospital medical records and clinical audit system. Range of motion analysis, Harris hip score (HHS) and Short Form‐12 score were recorded pre‐operatively and at the 12‐month follow‐up marks. Additionally, we reviewed operative time, length of stay, discharge destination, complications, return to theatre and readmission rates.ResultsThe results of our study revealed significantly shorter average hospital length of stay for the AA versus PA (4.2 versus 6.0 days, P = 0.004). Interestingly, our study also showed significantly shorter operating time with the AA (83.0 versus 91.8 min, P = 0.048) and lower return to theatre rates (0 versus 9.5%, P = 0.026). Finally, multivariate analysis showed AA to be associated with higher HHS and pre‐operative body mass index to be associated with lower HHS at 12‐month post‐operation (P = 0.02 and <0.001, respectively).ConclusionsOur study showed improved HHS at 12 months as well as reduced hospital length of stay, operating time and return to theatre with an AA when compared with a PA.
Variance components in confocal scanning laser tomography measurements of neuro‐retinal rim area and the effect of repeated measurements on the power to detect loss over time
Authors: Sandberg Melin Camilla , Nuija Eva , Alm Albert , Yu Zhaohua , Söderberg Per G. 
Published: May 2016

AbstractPurposeTo estimate the variation in measurements of neuro‐retinal rim area (NRA) determined by confocal scanning laser tomography and consequences for clinical follow‐up.MethodsAltogether, 24 healthy subjects were randomized on –320 μm, Moorfields and Standard NRA plane strategies. Additionally, NRA was measured in 32 glaucoma subjects. Variance components for subjects, visits and measurements were estimated with analysis of variance. Sample sizes required to detect a 6.0 × 10−2 mm2 NRA change were estimated assuming a significance level of 0.05 and a power of 0.8. Consequences for independent group, and paired comparison design, respectively, were analysed. Further, precision in estimates within subjects over time was investigated.ResultsThe variation of NRA among subjects was considerably larger than the variation among visits and measurements. For glaucoma subjects, the variation among visits and measurements were of the same order but larger than in healthy subjects. It was found that independent group comparisons require inconveniently large sample sizes. Within‐subject paired comparisons over time require sample sizes of below 15 subjects. The estimated variations for glaucoma subjects imply that 54 months of follow‐up is required for detection of change from baseline.ConclusionsThe variance for subjects is substantial in relation to those for visits and measurements. Cross‐sectional independent group comparisons of levels of NRA are unsuitable, due to considerable subject variation. Levels of NRA differences within subjects between visits can be estimated with acceptable precision. Neuro‐retinal rim area (NRA) measurement can be used for long‐term follow‐up of glaucoma progression.
The role of corneal endothelial morphology in graft assessment and prediction of endothelial cell loss during organ culture of human donor corneas
Authors: Hermel Martin , Salla Sabine , Fuest Matthias , Walter Peter 
Published: May 2016

AbstractPurposeEndothelial assessment is crucial in the release of corneas for grafting. We retrospectively analysed the role of endothelial morphology parameters in predicting endothelial cell loss during organ culture.MethodsHuman donor corneas were cultured in minimal essential medium with 2% fetal calf serum and antibiotics. Initial endothelial morphology was assessed microscopically using score parameters polymegethism (POL), pleomorphism (PLE), granulation (GRA), vacuolization (VAC), segmentation of cell membranes (SEG), Descemet's folds (DF), trypan blue‐positive cells (TBPC) and endothelial cell‐free areas (ECFA). Some corneas were primarily rejected based on endothelial assessment. Endothelial cell density (ECD) was assessed at the beginning (I‐ECD) and end of culture. Corneas were then placed in dehydration medium (as above + 5% dextran 500). In a subgroup, ECD was reassessed after dehydration. Endothelial cell loss during culture (ECL@Culture) and culture+dehydration (ECL‐Culture&Dehydration) were calculated. Data were given as mean ± SD and analysed using multiple linear and logistic regression. Odds ratios (OR) and 95% confidence intervals (CI) were calculated.ResultI‐ECD was 2812 ± 360/mm2 (n = 2356). The decision to reject a cornea due to endothelial assessment was associated negatively with I‐ECD (OR = 0.77/100 cells, CI 0.7–0.82) and positively with ECFA (OR = 2.7, CI 1.69–4.35), SEG (OR =1.3, CI 1.01–1.68) and donor age (OR = 1.26/decade, CI 1.33–1.41). ECL@Culture was 153 ± 201/mm2 (n = 1277), ECL@Culture&Dehydration was 169 ± 183/mm2 (n = 918). ECL@Culture was associated positively with donor age, I‐ECD, GRA and TBPC, and negatively with PLE, and DF. ECL@Culture&Dehydration was associated positively with age, sex, initial ECD, POL, PLE, VAC and TBPC.ConclusionMorphological parameters displayed associations with the exclusion of corneas from culture and with endothelial cell loss. Appropriate parameter selection for screening purposes may help improve graft quality.