bluuebunny/crossref_metadata_2025_split huggingface dataset:
CpG-mediated augmentation of CD8+ T-cell responses in mice is attenuated by a water-in-oil emulsion (Montanide ISA-51) but enhanced by an oil-in-water emulsion (IDRI SE)
Authors: Makinen Shawn R. , Zhu Qin , Davis Heather L. , Weeratna Risini D. 
Published: April 2016

AbstractAdjuvants are a key component in enhancing immunogenicity of vaccines and play a vital role in facilitating the induction of the correct type of immunity required for each vaccine to be optimally efficacious. Several different adjuvants are found in licensed vaccines, and many others are in pre-clinical or clinical testing. Agonists for TLRs are potent activators of the innate immune system and some, such as CpG (TLR9 agonist), are particularly good for promoting cellular immunity because of the induction of Th1 cytokines. Emulsions that have both delivery and adjuvant properties are classified as water-in-oil (W/O) or oil-in-water (O/W) formulations. The W/O emulsion Montanide ISA-51, often combined with CpG, has been widely tested in cancer vaccine clinical trials. Squalene-based O/W emulsions are in licensed influenza vaccines, and T-cell responses have been assessed pre-clinically. No clinical study has compared the two types of emulsions, and the continued use of W/O with CpG in cancer vaccines may be because the lack of single adjuvant controls has masked the interference issue. These findings may have important implications for the development of vaccines where T-cell immunity is considered essential, such as those for cancer and chronic infections. Using particulate (hepatitis B surface antigen) and soluble protein (ovalbumin) antigen, we show in mice that a W/O emulsion (ISA-51) abrogates CpG-mediated augmentation of CD8+ T-cell responses, whereas a squalene-based O/W emulsion significantly enhanced them.
Complex heterochrony underlies the evolution of hermaphrodite self-fertility and sex allocation in experimentalC. eleganspopulations
Authors: Poullet Nausicaa , Vielle Anne , Gimond Clotilde , Carvalho Sara , Teotónio Henrique , Braendle Christian 
Published: April 2016

AbstractHermaphroditic organisms are common both in plants and animals, and have served as key models to study the evolution of sex allocation. Despite extensive past research, the specific developmental mechanisms by which hermaphrodite sex allocation can evolve remain largely unknown. To address this problem, we here use experimental evolution ofCaenorhabditis eleganshermaphrodite-male populations to directly quantify changes in germline and somatic development that underlie adaptive shifts in hermaphrodite sex allocation associated with the evolution of improved self-fertility. Specifically, we test whether the evolution of hermaphrodite sex allocation is due to heterochrony, i.e. evolutionary changes in the relative timing of developmental processes.We show that the experimental evolution of improved hermaphrodite self-fertility occurred through complex modification of a suite of developmental and reproductive traits: increased sperm production, accelerated oogenesis and ovulation rates, and increased embryo retentionin utero. The experimental evolution of increased sperm production delayed entry into oogenesis – as expected, given the sequentially coupled production of spermatogenesis and oogenesis. Surprisingly, however, delayed oogenesis onset did not delay reproductive maturity, nor did it trade-off with gamete or embryo size. Comparing developmental dynamics of germline and soma indicates that the evolution of increased sperm production did not delay reproductive maturity due to a globally accelerated larval development during the period of spermatogenesis.We conclude that the integration of multiple heterochronic events in gametogenesis and soma can explain the experimental evolution of hermaphrodite sex allocation and self-fertility. Our results thus support the idea that heterochrony can represent a specific mechanism that explains the maintenance of partial selfing in natural populations with mixed reproduction modes and different forms of hermaphroditism. More generally, our results provide a quantitative perspective on how natural selection can operate on developmental characters – and their integration – during the evolution of life history at the population level.
Insights into telomerase action from high-throughput sequencing ofS. pombetelomeres
Authors: Bennett Henrietta W. , Liu Na , Hu Yan , King Megan C. 
Published: April 2016

AbstractWe have developed a high-throughput sequencing approach that enables us to determine terminal telomere sequences from tens of thousands of individualSchizosaccharomyces pombetelomeres. This method provides unprecedented coverage of telomeric sequence complexity in fission yeast.S. pombetelomeres are composed of modular degenerate repeats that can be explained by variation in usage of the TER1 RNA template during reverse transcription. Taking advantage of this deep sequencing approach, we find that “like” repeat modules are highly correlated within individual telomeres. Moreover, repeat module preference varies with telomere length, suggesting that existing repeats promote the incorporation of like repeats and/or that specific conformations of the telomerase holoenzyme efficiently and/or processively add repeats of like nature. After the loss of telomerase activity, this sequencing and analysis pipeline defines a population of telomeres with altered sequence content. This approach should be adaptable to study telomeric repeats in other organisms and can provide new insights into telomere sequence content at high density.
SLICER: Inferring Branched, Nonlinear Cellular Trajectories from Single Cell RNA-seq Data
Authors: Welch Joshua D. , Hartemink Alexander , Prins Jan F. 
Published: April 2016

AbstractSingle cell experiments provide an unprecedented opportunity to reconstruct a sequence of changes in a biological process from individual “snapshots” of cells. However, nonlinear gene expression changes, genes unrelated to the process, and the possibility of branching trajectories make this a challenging problem. We developed SLICER (Selective Locally Linear Inference of Cellular Expression Relationships) to address these challenges. SLICER can infer highly nonlinear trajectories, select genes without prior knowledge of the process, and automatically determine the location and number of branches and loops. SLICER more accurately recovers the ordering of points along simulated trajectories than existing methods. We demonstrate the effectiveness of SLICER on previously published data from mouse lung cells and neural stem cells.
Anti‐tumor necrosis factor‐alpha therapy improves endothelial function and arterial stiffness in patients with moderate to severe psoriasis: A 6‐month prospective study
Authors: Pina Trinitario , Corrales Alfonso , Lopez‐Mejias Raquel , Armesto Susana , Gonzalez‐Lopez Marcos A. , Gómez‐Acebo Ines , Ubilla Begoña , Remuzgo‐Martínez Sara , Gonzalez‐Vela M. Carmen , Blanco Ricardo , Hernández Jose L. , Llorca Javier , Gonzalez‐Gay Miguel A. 
Published: April 2016

AbstractThe aim of the present study was to determine if the use of the anti‐tumor necrosis factor (TNF)‐α monoclonal antibody adalimumab could improve endothelial function and arterial stiffness in patients with moderate to severe psoriasis. This was a prospective study on a series of consecutive patients with moderate to severe psoriasis who completed 6 months of therapy with adalimumab. Patients with history of cardiovascular events, diabetes mellitus, kidney disease, hypertension or body mass index of 35 kg/m2 or more were excluded. Assessment of endothelial function by brachial artery reactivity measuring flow‐mediated endothelial dependent vasodilatation (FMD%), and carotid arterial stiffness by pulse wave velocity (PWV) was performed at the onset of treatment (time 0) and at month 6. Twenty‐nine patients were studied. Anti‐TNF‐α adalimumab therapy yielded a significant improvement of endothelial function. The mean ± standard deviation (SD) FMD% values increased from 6.19 ± 2.44% at the onset of adalimumab to 7.46 ± 2.43% after 6 months of treatment with this biologic agent (P = 0.008). Likewise, following the use of adalimumab, PWV levels decreased from 6.28 ± 1.04 m/s at the onset of adalimumab to 5.69 ± 1.31 m/s at 6 months (P = 0.03). In conclusion, patients with moderate to severe psoriasis exhibit improvement of endothelial function and arterial stiffness following anti‐TNF‐α therapy. These findings are of potential relevance due to increased risk of cardiovascular disease in patients with severe psoriasis.
Research Note: Compact Depth from Extreme Points: a tool for fast potential field imaging
Authors: Baniamerian Jamaledin , Fedi Maurizio , Oskooi Behrooz 
Published: April 2016

ABSTRACTWe propose a fast method for imaging potential field sources. The new method is a variant of the “Depth from Extreme Points,” which yields an image of a quantity proportional to the source distribution (magnetization or density). Such transformed field is here transformed into source‐density units by determining a constant with adequate physical dimension by a linear regression of the observed field versus the field computed from the “Depth from Extreme Points” image. Such source images are often smooth and too extended, reflecting the loss of spatial resolution for increasing altitudes. Consequently, they also present too low values of the source density. We here show that this initial image can be improved and made more compact to achieve a more realistic model, which reproduces a field consistent with the observed one. The new algorithm, which is called “Compact Depth from Extreme Points” iteratively produces different source distributions models, with an increasing degree of compactness and, correspondingly, increasing source‐density values. This is done through weighting the model with a compacting function. The compacting function may be conveniently expressed as a matrix that is modified at any iteration, based on the model obtained in the previous step. At any iteration step the process may be stopped when the density reaches values higher than prefixed bounds based on known or assumed geological information. As no matrix inversion is needed, the method is fast and allows analysing massive datasets. Due to the high stability of the “Depth from Extreme Points” transformation, the algorithm may be also applied to any derivatives of the measured field, thus yielding an improved resolution. The method is investigated by application to 2D and 3D synthetic gravity source distributions, and the imaged sources are a good reconstruction of the geometry and density distributions of the causative bodies. Finally, the method is applied to microgravity data to model underground crypts in St. Venceslas Church, Tovacov, Czech Republic.
Phylogenetic ecology and the greening of cities
Authors: MacIvor James S. , Cadotte Marc W. , Livingstone Stuart W. , Lundholm Jeremy T. , Yasui Simone‐Louise E. 
Published: April 2016

Summary

Ecologists are increasingly involved in city‐making, especially in the development of green infrastructure and other designed plant communities.

Plant communities that are more phylogenetically related are more similar in functional traits and adaptations to their environment than distant relatives.

Knowledge of how evolutionary relationships among plant species influence ecosystem functions could be applied to green infrastructure to improve benefits such as urban cooling, habitat creation and stormwater management.

The intended outcomes of manipulations of phylogenetic diversity (PD) may vary depending on project goals, particularly when considering the trade‐offs between multiple ecosystem functions. For instance, constraining PD could improve survival and performance in stressful environments or short growing seasons. Increasing PD could improve habitat diversity, aesthetics and other direct human benefits.

Synthesis and applications. Given the potential benefits of considering phylogenetic relationships of plant communities in green infrastructure, we recommend that ecologists work with landscape architects and other design professionals to test how ecophylogenetics – the application of phylogenies in ecology – might aid in achieving desired outcomes for green infrastructure.
Priority effects: natives, but not exotics, pay to arrive late
Authors: Stuble Katharine L. , Souza Lara 
Published: April 2016

Summary

Assembly history can determine ecosystem structure and function by influencing the relative abundances of species. Priority effects (impacts associated with early arrival) likely promote the success of exotic invaders, which often arrive at larger propagule sizes and germinate earlier than native species and tend to grow more quickly. However, the potential for exotic species to tolerate late arrival is unknown.

Using a suite of native and exotic old‐field plant species, we established a mesocosm experiment varying the order of species arrival to address the following question: Does plant origin influence a species' response to priority effects?

We found that, while all plant groups benefited from arriving early to a similar extent, arriving late came at a lower cost for exotic species.

Synthesis. We suggest that, when exploring assembly mechanisms in community ecology, the costs associated with late arrival may be as important as the benefits of arriving early. These priority effects may ultimately play a role in promoting the local success and overall distribution of exotic invaders.
Exotic invasive plants increase productivity, abundance of ammonia‐oxidizing bacteria and nitrogen availability in intermountain grasslands
Authors: McLeod Morgan Luce , Cleveland Cory C. , Lekberg Ylva , Maron John L. , Philippot Laurent , Bru David , Callaway Ragan M. 
Published: April 2016

Summary

Exotic plant invasion is often associated with dramatic increases in above‐ground net primary productivity and soil nitrogen. However, most evidence for these increases comes from correlative studies of single species, leaving open the question of whether invasive plants drive these processes and whether they are consistent among invaders.

We combined field surveys and measurements within experimental plantings to examine how plant productivity, soil nitrogen and the abundance of ammonia‐oxidizing bacteria (AOB) change in response to invasions by four exotic species.

The relationship between plant productivity and soil nitrate differed among native and invasive species, suggesting a fundamental disparity in the effects of natives and invaders on ecosystem processes. In field surveys, dense patches of all invasive species had higher abundances of AOB than native‐dominated sites. Three of the four invasive species had higher productivity, soil nitrate concentrations and rates of potential nitrification as compared to nearby native‐dominated communities. In our experimental plantings, we found that two invasive species drove increases in soil nitrate and one invader caused increased productivity after a single season.

Synthesis. Our results highlight the importance of the N cycling soil microbial community in how exotic invasive plants alter ecosystem function and show that shifts in function can occur rapidly.
Could everyday technology improve access to assessments? A pilot study on the feasibility of screening cognition in people with Parkinson's disease using the Montreal Cognitive Assessment via Internet videoconferencing
Authors: Stillerova Tereza , Liddle Jacki , Gustafsson Louise , Lamont Robyn , Silburn Peter 
Published: April 2016

BackgroundThe distances and distribution of people, and pressures on the health system in Australia mean that access to services for people living with a neurodegenerative condition may be inadequate. Telehealth may offer ways to provide timely and efficient monitoring and support. People with Parkinson's disease require regular screening of their symptoms and needs, but may have limited access to health professionals. Cognitive changes can impact on occupational performance, thus timely monitoring of cognition is important for informing occupational therapy interventions.AimTo evaluate the feasibility of screening cognition in people with Parkinson's disease using available technology in their homes.MethodEleven participants with Parkinson's disease completed the Montreal Cognitive Assessment face‐to‐face and then via videoconferencing one week later using the technology available at their home. Participants and assessors provided feedback on their experience.ResultsAll Montreal Cognitive Assessment items could be completed over videoconference (e.g. Skype), with a median difference of 2 (IQR: 1–2.5) between face‐to‐face and videoconference scores. Higher scores were not favoured by either mode of assessment. Three participants received inconsistent cognitive classifications between the two assessment methods. Participant and assessor feedback indicated reported benefits including convenience as well as technological limitations.ConclusionsGiven the pressures on the health system and the apparent acceptability to consumers, occupational therapists may explore the utility of readily accessible technology to enable timely monitoring of cognition for people with Parkinson's disease. Further research is needed to develop and demonstrate the reliability and validity of this approach.
Role of Simvastatin on fracture healing and osteoporosis: a systematic review onin vivoinvestigations
Authors: Moshiri Ali , Sharifi Ali Mohammad , Oryan Ahmad 
Published: April 2016

SummarySimvastatin is a lipid lowering drug whose beneficial role on bone metabolism was discovered in 1999. Severalin vivostudies evaluated its role on osteoporosis and fracture healing, however, controversial results are seen in the literature. For this reason, Simvastatin has not been the focus of any clinical trials as yet. This systematic review clears the mechanisms of action of Simvastatin on bone metabolism and focuses onin vivoinvestigations that have evaluated its role on osteoporosis and fracture repair to find out (i) whether Simvastatin is effective on treatment of osteoporosis and fracture repair, and (ii) which of the many available protocols may have the ability to be translated in the clinical setting. Simvastatin induces osteoinduction by increasing osteoblast activity and differentiation and inhibiting their apoptosis. It also reduces osteoclastogenesis by decreasing both the number and activity of osteoclasts and their differentiation. Controversial results between thein vivostudies are mostly due to the differences in the route of administration, dose, dosage and carrier type. Local delivery of Simvastatin through controlled drug delivery systems with much lower doses and dosages than the systemic route seems to be the most valuable option in fracture healing. However, systemic delivery of Simvastatin with much higher doses and dosages than the clinical ones seems to be effective in managing osteoporosis. Simvastatin, in a particular range of doses and dosages, may be beneficial in managing osteoporosis and fracture injuries. This review showed that Simvastatin is effective in the treatment of osteoporosis and fracture healing.
Dynamic, mechanistic, molecular‐level modelling of cyanobacteria: Anabaena and nitrogen interaction
Authors: Hellweger Ferdi L. , Fredrick Neil D. , McCarthy Mark J. , Gardner Wayne S. , Wilhelm Steven W. , Paerl Hans W. 
Published: April 2016

SummaryPhytoplankton (eutrophication, biogeochemical) models are important tools for ecosystem research and management, but they generally have not been updated to include modern biology. Here, we present a dynamic, mechanistic, molecular‐level (i.e. gene, transcript, protein, metabolite) model of Anabaena – nitrogen interaction. The model was developed using the pattern‐oriented approach to model definition and parameterization of complex agent‐based models. It simulates individual filaments, each with individual cells, each with genes that are expressed to yield transcripts and proteins. Cells metabolize various forms of N, grow and divide, and differentiate heterocysts when fixed N is depleted. The model is informed by observations from 269 laboratory experiments from 55 papers published from 1942 to 2014. Within this database, we identified 331 emerging patterns, and, excluding inconsistencies in observations, the model reproduces 94% of them. To explore a practical application, we used the model to simulate nutrient reduction scenarios for a hypothetical lake. For a 50% N only loading reduction, the model predicts that N fixation increases, but this fixed N does not compensate for the loading reduction, and the chlorophyll a concentration decreases substantially (by 33%). When N is reduced along with P, the model predicts an additional 8% reduction (compared to P only).
Response of bacterial communities from California coastal waters to alginate particles and an alginolytic Alteromonas macleodii strain
Authors: Mitulla Maximilian , Dinasquet Julie , Guillemette Ryan , Simon Meinhard , Azam Farooq , Wietz Matthias 
Published: April 2016

SummaryAlginate is a major cell wall polysaccharide from marine macroalgae and nutrient source for heterotrophic bacteria. Alginate can form gel particles in contact with divalent cations as found in seawater. Here, we tested the hypothesis that alginate gel particles serve as carbon source and microhabitat for marine bacteria by adding sterile alginate particles to microcosms with seawater from coastal California, a habitat rich in alginate‐containing macroalgae. Alginate particles were rapidly colonized and degraded, with three‐ to eightfold higher bacterial abundances and production among alginate particle‐associated (PA) bacteria. 16S rRNA gene amplicon sequencing showed that alginate PA bacteria were enriched in OTUs related to Cryomorphaceae, Saprospiraceae (Bacteroidetes) and Phaeobacter (Alphaproteobacteria) towards the end of the experiment. In microcosms amended with alginate particles and the proficient alginolytic bacterium Alteromonas macleodii strain 83‐1, this strain dominated the community and outcompeted Cryomorphaceae, Saprospiraceae and Phaeobacter, and PA hydrolytic activities were over 50% higher. Thus, alginolytic activity by strain 83‐1 did not benefit non‐alginolytic strains by cross‐feeding on alginate hydrolysis or other metabolic products. Considering the global distribution and extensive biomass of alginate‐containing macroalgae, the observed bacterial dynamics associated with the utilization and remineralization of alginate microhabitats promote the understanding of carbon cycling in macroalgae‐rich waters worldwide.
Talking About Versus Talking With: an experiential self of the therapist exercise for family therapy training
Authors: Sude Michael E. , Gambrel Laura Eubanks 
Published: April 2016

This article describes an experiential self of the therapist exercise for use in family therapy training. It provides guidelines for instructors to integrate the activity into their courses including step‐by‐step directions, examples of processing questions, and potential readings to accompany the activity. The Talking About Versus Talking With exercise was designed to help family therapy students have a felt sense of some of the differences between individual and relational therapy. It provides trainers with a way to teach therapists in training about clients’ experiences in relational therapy where they talk about relational difficulties directly with someone, as opposed to talking about those same difficulties in individual therapy. The exercise also offers an opportunity for students to do self of the therapist work with a strained relationship in their personal lives, and students report that it is both rewarding and emotionally intense.Practitioner points

Differences between individual and relational therapy may not be easily understood by family therapy students
Self of the therapist work, including working with difficult personal relationships, is a vital component of family therapy training
The experiential nature of the exercise provides students with a felt sense of some differences between individual and relational therapy