bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell type-specific expression profiling sheds light on the development of a peculiar neuron, housing a complex organelle
Authors: Sunagar Kartik , Columbus-Shenkar Yaara , Fridrich Arie , Gutkovich Nadya , Aharoni Reuven , Moran Yehu 
Published: July 2017

AbstractSpecialized neurons called cnidocytes define the phylum Cnidaria. They possess an ‘explosive’ organelle called cnidocyst that is important for prey capture and antipredator defense. An extraordinary morphological and functional complexity of the cnidocysts has inspired numerous studies to investigate their structure and development. However, the transcriptomes of the cells bearing these unique organelles are yet to be characterized, impeding our understanding of the genetic basis of their biogenesis. By generating transgenic lines of the sea anemoneNematostella vectensisusing the CRISPR/Cas9 system, we have characterized cell-type specific transcriptomic profiles of various stages of cnidocyte maturation and show that nematogenesis (the formation of functional cnidocysts) is underpinned by dramatic shifts in the spatiotemporal gene expression. We also highlight the stark fall in transcriptional-levels of toxin and structural protein coding genes within cnidocytes with the maturation of capsule. We further reveal that the majority of upregulated genes and enriched biochemical pathways specific to cnidocytes are yet to be characterized. Finally, we unravel the recruitment of a metazoan stress-related transcription factor complex into nematogenesis and highlight its role in the formation of a structural protein of the cnidocyst wall. Thus, we provide novel insights into the biology, development, and evolution of cnidocytes.
Sleep deprivation negatively impacts reproductive output inDrosophila melanogaster
Authors: Potdar Sheetal , Daniel Danita K. , Thomas Femi A. , Lall Shraddha , Sheeba Vasu 
Published: July 2017

AbstractMost animals sleep or exhibit a sleep-like state, yet the adaptive significance of this phenomenon remains unclear. Although reproductive deficits are associated with lifestyle induced sleep deficiencies, how sleep loss affects reproductive physiology is poorly understood, even in model organisms. We aimed to bridge this mechanistic gap by impairing sleep in female fruit flies and testing its effect on egg output. We find that sleep deprivation by feeding caffeine or by mechanical perturbation results in decreased egg output. Transient activation of wake-promoting dopaminergic neurons decreases egg output in addition to sleep levels, thus demonstrating a direct negative impact of sleep deficit on reproductive output. Similarly, loss-of-function mutation in dopamine transporterfumin(fmn)leads to both significant sleep loss and lowered fecundity. This demonstration of a direct relationship between sleep and reproductive fitness indicates a strong driving force for the evolution of sleep.
Decreased intra-lymphocyte cytokines measurement in septic shock patients: a whole blood proof of concept study
Authors: Letessier Wilfried , Demaret Julie , Gossez Morgane , Allam Camille , Venet Fabienne , Rimmelé Thomas , Monneret Guillaume 
Published: July 2017

ABSTRACTFunctional testing protocols are thought to be the gold standard for the exploration of the immune system. However, in terms of routine analysis, they present numerous drawbacks and consequently their use is mainly limited to research applications. In the clinical context of septic shock, characterized by marked lymphocyte alterations, a new approach for lymphocyte intracellular cytokine measurement in whole blood upon was evaluated in a proof-of-concept study. Following lymphocyte activation, simultaneous intracellular labeling of Interferon-γ (IFN-γ), Tumor Necrosis Factor-α (TNF-α), and Interleukin-2 (IL-2) was performed in CD4+and CD8+T cells (identified by surface marking). The analysis was carried out by flow cytometry (6 colors). Results obtained in septic patients (n = 22) were compared to those of healthy volunteers (n = 8). Independently of lymphopenia, there were significant differences between groups. In particular there was significant decrease in the production of IL-2 and TNF-α in septic patients, while the production of IFN-γ was not significantly altered. Polyfunctional results showed that patients presented with increased percentages of triple negative lymphocytes. In contrast, volunteers had higher proportions of triple positive cells. The approach could be performed in a robust and consistent way, taking 4.5 hours to complete. Moreover, clear differences could be observed between clinical groups with this modified method. These characteristics illustrate the potential of this novel whole blood protocol for clinical applications. However, further research is required to determine the applicability compared to alternative test and to evaluate clinical performances in larger cohorts of patients.
Engineering post-translational proofreading to discriminate non-standard amino acids
Authors: Kunjapur Aditya M. , Stork Devon A. , Kuru Erkin , Vargas-Rodriguez Oscar , Landon Matthieu , Söll Dieter , Church George M. 
Published: July 2017

AbstractProgress in genetic code expansion requires accurate, selective, and high-throughput detection of non-standard amino acid (NSAA) incorporation into proteins. Here, we discover how the N-end rule pathway of protein degradation applies to commonly used NSAAs. We show that several NSAAs are N-end stabilizing and demonstrate that other NSAAs can be made stabilizing by rationally engineering the N-end rule adaptor protein ClpS. We use these insights to engineer a synthetic quality control method, termed “Post-Translational Proofreading” (PTP). By implementing PTP, false positive proteins resulting from misincorporation of structurally similar standard amino acids or undesired NSAAs rapidly degrade, enabling high-accuracy discrimination of desired NSAA incorporation. We illustrate the utility of PTP during evolution of the biphenylalanine orthogonal translation system used for synthetic biocontainment. Our new OTS is more selective and confers lower escape frequencies and greater fitness in all tested biocontained strains. Our approach presents a new paradigm for molecular recognition of amino acids in target proteins.
Plant‐ants use resistance‐related plant odours to assess host quality before colony founding
Authors: Razo‐Belman Rosario , Molina‐Torres Jorge , Martínez Octavio , Heil Martin 
Published: July 2017

Abstract

Establishing a horizontally transmitted mutualism is a critical step for many organisms, particularly when an individual can engage with only one partner over its lifetime. Ant foundresses shed their wings before they start to lay eggs, which makes host choice particularly critical for plant‐ants that exclusively colonize myrmecophytes.

Volatile organic compounds (VOCs) can indicate the identity and physiological condition of an individual and frequently serve as signals or cues that facilitate partner choice. Thus, we hypothesized that obligate plant‐ants use VOCs to determine the quality of potential host plants.

Indeed, winged females of the plant‐ant, Pseudomyrmex ferrugineus, used plant odours to identify high‐quality acacia hosts among different species and among individuals of the same species. The VOC blend of a branch was related to reward production and, interestingly, the least attractive blend contained the highest number of compounds.

Although only seven different VOCs could be detected in the blend of the high‐reward host species, the low‐reward host emitted 13 different compounds, among which (S)‐(‐)‐limonene and β‐linalool were the dominant ones. Complementing the odour of the high‐reward host with (S)‐(‐)‐limonene, β‐linalool or α‐terpinene reduced its attractiveness. Strikingly, these compounds inhibited bacterial pathogens of the host plant.

Synthesis. Plant‐ants can use host plant odours that contain resistance‐related VOCs to judge on host quality, likely because of negative crosstalk between direct resistance to disease and investment in ant‐mediated defence. VOCs can serve as cues that provide reliable information for partner choice, particularly when their emission results from a physiological process that causally relates to the quality of an individual as a mutualist.
Plant–soil feedbacks mediate shrub expansion in declining forests, but only in the right light
Authors: Pfennigwerth Alix A. , Van Nuland Michael E. , Bailey Joseph K. , Schweitzer Jennifer A. 
Published: July 2017

AbstractContemporary global change, including the widespread mortality of foundation tree species, is altering ecosystems and plant communities at unprecedented rates. Plant–soil interactions drive myriad community dynamics, and we hypothesized that such interactions may be an important driver of succession following the loss of foundation tree species.We examined whether plant–soil biota interactions, in the context of a putatively important light gradient associated with foundation tree decline, mediate the expansion ofRhododendron maximumin southeasternUSforests whereTsuga canadensis(eastern hemlock), a dominant foundation tree species, is in decline. Using an 11‐month, controlled inoculation experiment paired with Illumina sequencing, we tested the following hypotheses: (1) Relative to conspecific (R. maximum‐conditioned) soils,R. maximumseedlings have higher performance in soils conditioned byT. canadensisand lower performance in interspace soils (conditioned by neitherT. canadensisnorR. maximum) due to variation in soil fungal biota, and (2) seedling performance is greater in high‐light vs. low‐light environments (matching environments under infested vs. uninfestedT. canadensiscrowns, respectively).In partial support of the first hypothesis, we found thatR. maximumseedling performance was highest inT. canadensis‐conditioned andR. maximum‐conditioned soils and lowest in interspace soils. Mechanistically, soils conditioned byT. canadensisandR. maximumhad more ericoid and ectomycorrhizal fungi, less saprotrophic fungi, and were less species‐rich than interspace soils, and variation in these community traits predicted substantial variation inR. maximumseedling biomass. However, in support of our second hypothesis, soil effects on plant performance were evident in high light only; in low light, soil inoculation did not affect plant performance and plants performed worse on average.Synthesis. Our findings suggest that interactions with soil biota act synergistically with altered abiotic environments to mediate species responses to widespread foundation tree mortality, providing evidence for a novel mechanism of plant response to large‐scale disturbance. Examining plant–soil interactions in the context of relevant abiotic gradients can, therefore, enhance our understanding, predictions and management of community development processes following forest disturbance.
Effectiveness of intensive practice nurse counselling versus brief general practitioner advice, both combined with varenicline, for smoking cessation: a randomized pragmatic trial in primary care
Authors: van Rossem Carolien , Spigt Mark , Viechtbauer Wolfgang , Lucas Annelies E. M. , van Schayck Onno C. P. , Kotz Daniel 
Published: July 2017

AbstractAimsTo study the effectiveness of intensive counselling by a practice nurse (PN) versus brief advice by a general practitioner (GP), each combined with pharmacotherapy, for 6 months’ tobacco abstinence (primary outcome). Secondary outcomes included 12‐month abstinence, medication adherence and incremental costs per life‐year gained.DesignA multi‐site (n = 10), two‐group, parallel, pragmatic randomized controlled trial.SettingA network of primary health‐care centres in the Netherlands.ParticipantsA total of 295 adult daily smokers (mean age = 48 years; mean cigarettes/day = 19).Intervention and comparatorPatients were randomized to receive individual counselling by a practice nurse (PN) (n = 149) or brief advice by a general practitioner (GP) (146). All patients received 12 weeks of open‐label varenicline.MeasurementsThe primary outcome was prolonged biochemically validated abstinence from weeks 9 to 26 after treatment initiation. Secondary outcomes included abstinence from weeks 9 to 52, good dosing adherence (> 80% days taken) and incremental costs per life‐year gained.FindingsAbstinence rates in the PN versus GP groups were 32.2% (n = 48) versus 39.0% [n = 57; odds ratio (OR) = 0.71; 95% confidence interval (CI) = 0.44–1.16] from weeks 9 to 26 and 25.5% (n = 38) versus 28.8% (n = 42; OR = 0.84, 95% CI = 0.50–1.43) from weeks 9 to 52, respectively. Values of the Bayes factor indicated that the PN and GP were equally effective. Good dosing adherence was significantly lower in the PN (45.5%, n = 56/123) than in the GP group (62.0%, n = 75/121; OR = 0.45, 95% CI = 0.26–0.77), and the incremental costs per life‐year gained were –€416.10.ConclusionsAmong people seeking help to stop smoking from their general practice, one‐off brief advice from a general practitioner appears to be as effective as several sessions of behavioural support from a practice nurse when smoking cessation medication is provided.
Is cystic artery lymph node excision during laparoscopic cholecystectomy a marker of technique?
Authors: Wysocki Arkadiusz P. , Murphy Skyle , Ware Robert S. 
Published: July 2017

BackgroundIn order to minimize bile duct injury, experts suggest that dissection during laparoscopic cholecystectomy (LC) should be performed lateral to the lymph node (LN). This study aims to determine whether the frequency of excision of the LN is related to patient factors, disease severity or surgical difficulty.MethodsAll LCs performed or supervised by one surgeon were identified from a prospective database. The presence of LN was retrospectively determined by reviewing the gallbladder histology report.ResultsThe LN was identified in 10.4% of 1332 cholecystectomies. The American Society of Anesthesiologists class 3 was associated with a lower rate of LN excision compared with class 1 (odds ratio: 0.36; P = 0.049) as was the presence of a senior surgical trainee (odds ratio: 0.18; P < 0.001). Rate of LN excision was independent of patient demographic and clinical characteristics, including indication for cholecystectomy, conversion to open, gallbladder perforation, cholangiography, bile duct exploration and overall surgical difficulty.ConclusionsThe frequency with which the LN is excised during LC by the one surgeon is independent of the majority of clinical and surgical factors and may represent a surrogate marker of surgical technique. Whether this is related to the rate of bile duct injury remains to be determined.
A one‐step immune‐chromatographic Helicobacter pylori stool antigen test for children was quick, consistent, reliable and specific
Authors: Kalach Nicolas , Gosset Pierre , Dehecq Eric , Decoster Anne , Georgel Anne‐France , Spyckerelle Claire , Papadopoulos Stephanos , Dupont Christophe , Raymond Josette 
Published: July 2017

AbstractAimThis French study assessed a quick, noninvasive, immuno‐chromatographic, Helicobacter pylori (H. pylori) stool antigen test for detecting infections in children.MethodsWe enrolled 158 children, with a median age of 8.5 years (range eight months to 17 years), with digestive symptoms suggesting upper gastrointestinal tract disease. Upper digestive endoscopy was performed with gastric biopsy specimens for histology, a rapid urease test, culture test and quantitative real‐time polymerase chain reaction. The H. pylori stool antigen test was performed twice for each child and the results were compared to the reference method.ResultsThe reference methods showed that 23 (14.6%) of the 158 children tested were H. pylori positive. The H. pylori stool antigen test showed 91.3% sensitivity, with a 95% confidence interval (95% CI) of 86.9–95.6 and 97% specificity (95% CI 94.3–99.6), 30.84 positive likelihood ratio and 0.09 negative likelihood ratio. The test accuracy was 96.2% (95% CI 93.2–99.1). The two blinded independent observers produced identical H. pylori stool antigen test results and the Kappa coefficient for the H. pylori stool antigen test was one.ConclusionThe H. pylori stool antigen test was found to be a consistent, reliable, quick and specific test for detecting the H. pylori infection in children.
Informal sector taxes and equity: Evidence from presumptive taxation in Zimbabwe
Authors: Dube Godwin , Casale Daniela 
Published: July 2017

AbstractUsing a mixed‐methods approach, this article evaluates the equity implications of Zimbabwe's presumptive tax system, introduced in 2005 to raise revenue from the country's growing informal sector. The representative taxpayer method, which compares the hypothetical tax burdens of formal and informal sector taxpayers at varying income levels, shows that the presumptive tax regime undermines both vertical and horizontal equity. In addition, interviews with key informants from the tax authorities, other relevant organizations and informal sector operators were conducted to probe issues around collection, compliance and perceptions of fairness. The qualitative data suggest that weak enforcement, with more visible informal activities bearing the brunt of the tax burden, and selective (and sometimes politically motivated) application of the legislation, compromise equity further.
Coronal advanced flap in combination with a connective tissue graft. Is the thickness of the flap a predictor for root coverage? A prospective clinical study
Authors: Garces‐McIntyre Teresa , Carbonell Josep Maria , Vallcorba Lluís , Santos Antonio , Valles Cristina , Nart José 
Published: July 2017

AbstractAimEvaluate if there is any relationship between the flap thickness (FT) and the presence of complete root coverage (CRC) when performing coronally advanced flaps in combination with a connective tissue graft (CTG).Materials and methodsProspective clinical study, in which multiple Miller class I and II recessions were treated with a coronally advanced flap and a CTG standardized at 1 mm of thickness. Individual stents permitted repeated measurements of conventional periodontal parameters at the same point. The primary outcome variable was CRC. Secondary outcomes were recession reduction, gingival thickness and width of keratinized tissue (KT) achieved at 6 months post‐surgery.ResultsForty‐five recessions (2.4 ± 0.75 mm) were treated in 20 patients. Mean root coverage was 93.4 ± 10.98%; 65% achieved CRC. The mean FT was 1.01 mm ± 0.64 mm and 1.01 ± 0.61 mm at 2 and 5 mm from the gingival margin, respectively. No relationship could be found between FT and CRC (p > .05). Statistical significant changes (p < .05) were observed for recession depth, clinical attachment level, KT and soft tissue thickness at the end of the study.ConclusionsFlap thickness seems not to be a predictor for CRC when performing a coronally advanced flap plus a CTG. This technique may be of choice when treating thin biotypes.
Differential growth costs and nitrogen fixation in Cytisus multiflorus (L′Hér.) Sweet and Cytisus scoparius (L.) Link are mediated by sources of inorganic N
Authors: Pérez‐Fernández M. A. , Calvo‐Magro E. , Rodríguez‐Sánchez J. , Valentine A. 
Published: July 2017

Abstract

Shrubby legumes in Mediterranean‐type ecosystems face strong nutrient limitations that worsen in summer, when water is absent. Nitrogen‐fixing legumes are likely to be able to switch between soil N and atmospheric N (N2) sources to adjust the C costs of N acquisition in different seasons.

We investigated the utilisation of different inorganic N sources by two indigenous shrubby legumes (Cytisus multiflorus and Cytisus scoparius). Plant performance in terms of photosynthesis and biomass production was also analysed. Plants were cultivated in sterile river sand supplied with Hoagland nutrient solution, grown in N‐free nutrient solution and inoculated with effective rhizobial strains from nodules of adult plants of the same species. A second treatment consisted of plants given 500 μm NH4NO3 added into the nutrient solution. In a third treatment, plants were watered with another source of N (500 μm NH4NO3) as well as being inoculated with effective rhizobial strains.

The application of NH4NO3 to the legumes resulted in a larger increase in plant dry matter. Carbon construction costs were higher in plants supplied with mineral and symbiotic N sources and always higher in the endemic C. multiflorus. Differences in photosynthesis rates were only observed between species, regardless of the N source. Non‐fertilised inoculated plants had more effective root nodules and a clear dependence on N2 fixation.

We propose that the ability of C. scoparius to change N source makes it a plastic species, which would account for its broader distribution in nature.
Utilizing the Ensemble Kalman Filter and Ensemble Kalman Smoother for Combined State and Parameter Estimation of a Three-Dimensional Towed Underwater Cable Model
Authors: Vidar Grindheim Jan , Revhaug Inge , Pedersen Egil 
Published: July 2017

Abstract
A finite difference method (FDM) solving the coupled partial differential equations governing three-dimensional (3D) motions of a towed underwater cable has been implemented in a combined ensemble Kalman filter (EnKF) and ensemble Kalman smoother (EnKS), as a new approach to combined state and parameter estimation for towed underwater cables. A simulation study of the method applied to a seismic streamer has been performed. Cable state variables as well as model parameters are estimated. Parameters estimated are crossline ocean current varying with time as well as cable tangential drag coefficient. The presented results indicate that the method is able to estimate state as well as parameters for seismic streamers.
CgMED3
Changes Membrane Sterol Composition To Help Candida glabrata Tolerate Low-pH Stress
Authors: Lin Xiaobao , Qi Yanli , Yan Dongni , Liu Hui , Chen Xiulai , Liu Liming 
Published: July 2017

ABSTRACT

Candida glabrata
is a promising microorganism for organic acid production. The present study aimed to investigate the role of
C. glabrata
Mediator complex subunit 3 (
Cg
Med3p) in protecting
C. glabrata
under low-pH conditions. To this end, genes
CgMED3A
and
CgMED3B
were deleted, resulting in the double-deletion
Cgmed3AB
Δ strain. The final biomass and cell viability levels of
Cgmed3AB
Δ decreased by 64.5% and 35.8%, respectively, compared to the wild-type strain results at pH 2.0. In addition, lack of
Cg
Med3ABp resulted in selective repression of a subset of genes in the lipid biosynthesis and metabolism pathways. Furthermore, C18:1, lanosterol, zymosterol, fecosterol, and ergosterol were 13.2%, 80.4%, 40.4%, 78.1%, and 70.4% less abundant, respectively, in the
Cgmed3AB
Δ strain. In contrast, the concentration of squalene increased by about 44.6-fold. As a result, membrane integrity, rigidity, and H
+
-ATPase activity in the
Cgmed3AB
Δ strain were reduced by 62.7%, 13.0%, and 50.3%, respectively. In contrast, overexpression of
CgMED3AB
increased the levels of C18:0, C18:1, and ergosterol by 113.2%, 5.9%, and 26.4%, respectively. Moreover, compared to the wild-type results, dry cell weight and pyruvate production increased, irrespective of pH buffering. These results suggest that
CgMED3AB
regulates membrane composition, which in turn enables cells to tolerate low-pH stress. We propose that regulation of
Cg
Med3ABp may provide a novel strategy for enhancing low-pH tolerance and increasing organic acid production by
C. glabrata
.

IMPORTANCE
The objective of this study was to investigate the role of
Candida glabrata
Mediator complex subunit 3 (
Cg
Med3ABp) and its regulation of gene expression at low pH in
C. glabrata
. We found that
Cg
Med3ABp was critical for cellular survival and pyruvate production during low-pH stress. Measures of the levels of plasma membrane fatty acids and sterol composition indicated that
Cg
Med3ABp could play an important role in regulating homeostasis in
C. glabrata
. We propose that controlling membrane lipid composition may enhance the robustness of
C. glabrata
for the production of organic acids.