bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targets of olivocochlear collaterals in cochlear nucleus of rat and guinea pig
Authors: Baashar Ahmaed , Robertson Donald , Yates Nathanael James , Mulders Wilhelmina Henrica Antonia Maria 
Published: March 2019

AbstractDescending auditory pathways can modify afferent auditory input en route to cortex. One component of these pathways is the olivocochlear system which originates in brainstem and terminates in cochlea. Medial olivocochlear (MOC) neurons also project collaterals to cochlear nucleus and make synaptic contacts with dendrites of multipolar neurons. Two broadly distinct populations of multipolar cells exist: T‐stellate and D‐stellate neurons, thought to project to inferior colliculus and contralateral cochlear nucleus, respectively. It is unclear which of these neurons receive direct MOC collateral input due to conflicting results between in vivo and in vitro studies. This study used anatomical techniques to identify which multipolar cell population receives synaptic innervation from MOC collaterals. The retrograde tracer Fluorogold was injected into inferior colliculus or cochlear nucleus to label T‐stellate and D‐stellate neurons, respectively. Axonal branches of MOC neurons were labeled by biocytin injections at the floor of the fourth ventricle. Fluorogold injections resulted in labeled cochlear nucleus multipolar neurons. Biocytin abundantly labeled MOC collaterals which entered cochlear nucleus. Microscopic analysis revealed that MOC collaterals made some putative synaptic contacts with the retrogradely labeled neurons but many more putative contacts were observed on unidentified neural targets. This suggest that both T‐ and D‐stellate neurons receive synaptic innervation from the MOC collaterals on their somata and proximal dendrites. The prevalence of these contacts cannot be stated with certainty because of technical limitations, but the possibility exists that the collaterals may also make contacts with neurons not projecting to inferior colliculus or the contralateral cochlear nucleus.
A Randomized, Double‐Blind, Placebo‐Controlled, First‐Time‐in‐Human Study to Assess the Safety, Tolerability, and Pharmacokinetics of Single and Multiple Ascending Doses of GSK3389404 in Healthy Subjects
Authors: Han Kelong , Cremer Jennifer , Elston Robert , Oliver Stuart , Baptiste‐Brown Sharon , Chen Shuguang , Gardiner David , Davies Matt , Saunders Joanne , Hamatake Robert , Losos Jan , Leivers Martin , Hood Steve , van der Berg Frans , Paff Melanie , Ritter James M. , Theodore Dickens 
Published: March 2019

AbstractGSK3389404 is a liver‐targeted antisense oligonucleotide that inhibits synthesis of hepatitis B surface antigen and all other hepatitis B virus proteins. This first‐in‐human, randomized, double‐blind, phase 1 study assessed the safety and pharmacokinetics of GSK3389404 administered subcutaneously (SC) in healthy subjects. Four single ascending‐dose cohorts (10 mg, 30 mg, 60 mg, and 120 mg) and 3 multiple ascending‐dose cohorts (30 mg, 60 mg, and 120 mg once weekly for 4 weeks) each comprised 6 subjects randomized to GSK3389404 and 2 subjects randomized to placebo. There were no serious adverse events (AEs) or withdrawals due to AEs. The safety profile did not worsen with repeated dosing. The most frequent treatment‐related AEs were injection site reactions (19.0% [n = 8/42], frequency unrelated to dose levels); all were mild (Grade 1) and resolved without dose modification or discontinuation. GSK3389404 administered subcutaneously was readily absorbed with a time to maximum plasma concentration (Tmax) of 1–4 hours and an elimination half‐life of 3–6 hours in plasma. Plasma area under the concentration‐time curve (AUC) and maximum observed concentration (Cmax) were dose‐proportional. Dose‐normalized plasma AUC from time 0 to infinity averaged 69.9 ng·h/(mL·mg dose) across cohorts, and Cmax 9.5 ng/(mL·mg dose). Pharmacokinetic profiles and parameters were comparable between single and multiple dosing. No accumulation was observed with once‐weekly dosing. The metabolite was undetectable in urine and plasma. In the pooled urine, GSK3389404 was estimated to account for <0.1% of the total dose. In summary, GSK3389404 dosing has been tested up to 120 mg for 4 weeks with an acceptable safety and pharmacokinetic profile, supporting further clinical investigation in patients with chronic hepatitis B.
Agrobacterium‐Mediated Transformation of Brachypodium distachyon
Authors: Chen Fengjuan , Liu Qi , P. Vogel John , Wu Jiajie 
Published: March 2019

AbstractBrachypodium distachyon is an excellent model system for the grasses and has been adopted as a research organism by many laboratories around the world. It has all of the biological traits required for a model system, including small stature, short life cycle, small genome, simple growth requirements, and a close relationship to major crop plants (cereals). In addition, numerous resources have been developed for working with this species, including genome sequences for many lines, sequenced mutant collections, and a large, freely available germplasm collection. Fortunately, among grasses B. distachyon is one of the most easily transformed species, an absolute necessity for a model system. Agrobacterium‐mediated transformation is the preferred method to transform plants because it usually results in simple insertions of target DNA. In this article, we describe a method for Agrobacterium‐mediated transformation of the inbred B. distachyon lines Bd21 and Bd21‐3. Embryogenic callus induced from immature embryos is co‐cultivated with Agrobacterium tumefaciens strain AGL1 or Agrobacterium rhizogenes strain 18r12v. Hygromycin and paromomycin are used as selective agents, with comparable transformation efficiencies (defined as the percentage of co‐cultivated callus that produce transgenic plants) of 40% to 70%. It takes 20 to 30 weeks to obtain T1 seeds starting from the initial step of dissecting out immature embryos. This protocol has been shown to be efficient and facile in several studies that resulted in the creation of over 22,000 T‐DNA mutants. © 2019 by John Wiley & Sons, Inc.
Universal Methods for Transgene Induction Using the Dexamethasone‐Inducible Transcription Activation System pOp6/LhGR in Arabidopsis and Other Plant Species
Authors: Samalova Marketa , Kirchhelle Charlotte , Moore Ian 
Published: March 2019

AbstractUse of chemically inducible systems for transgene expression is a crucial requirement for modern plant biology research, as it allows (1) expression of transgenes that compromise plant viability or fertility when constitutively expressed and (2) spatiotemporal control of transgene expression levels. We describe the stringently regulated and highly responsive dexamethasone‐inducible gene expression system pOp6/LhGR, which comprises the chimeric transcription activator LhGR and the corresponding pOp6 promoter. Upon induction, the LhGR activator binds to the pOp6 promoter and induces expression of the target gene of interest. We provide detailed protocols for inducing transgene expression at different developmental stages and in different plant species and discuss dexamethasone stability and use of its analogs. We also introduce new, versatile, GATEWAY‐compatible binary vectors that are now available for the pOp6/LhGR system. © 2019 by John Wiley & Sons, Inc.
Pharmacokinetic Parameters of Infliximab Influence the Rate of Relapse After De‐Escalation in Adults With Inflammatory Bowel Diseases
Authors: Petitcollin Antoine , Brochard Charlène , Siproudhis Laurent , Tron Camille , Verdier Marie‐Clémence , Lemaitre Florian , Lucidarme Camille , Bouguen Guillaume , Bellissant Éric 
Published: March 2019

This study aimed at exploring the link among individual concentrations, pharmacokinetic parameters, and the probability of relapse after de‐escalation in a real‐world prospective cohort of patients with inflammatory bowel disease (IBD) who underwent infliximab treatment de‐escalation. Ninety‐one patients were included. A time‐varying compartment model was used to estimate individual pharmacokinetic parameters and trough concentrations. A Cox model was implemented to explore the parameters influencing the probability of relapse after de‐escalation. Volume, clearance, and trough before and after de‐escalation were linked to the relapse risk at the univariate step. Independent predictors of relapse were tobacco use and/or ulcerative colitis (P = 0.0093), a higher C‐reactive protein (CRP; P = 0.00064), and an infliximab trough < 2.4 μg/mL after de‐escalation (P = 0.0001). Patients with trough > 5.7 μg/mL are eligible to de‐escalation, but infliximab pharmacokinetics is highly variable in time. Therefore, drug monitoring is mandatory after de‐escalation to maintain trough > 2.4 μg/mL. Clearance monitoring seems an appealing approach for patient selection and relapse prediction.
Query optimization mechanisms in the cloud environments: A systematic study
Authors: Azhir Elham , Navimipour Nima Jafari , Hosseinzadeh Mehdi , Sharifi Arash , Darwesh Aso 
Published: March 2019

SummaryThe goal of a query optimizer is to provide an optimal Query Execution Plan (QEP) by comparing alternative query plans. In a distributed database system over cloud environment, the relations required by a query plan may be stored at multiple sites. This leads to an exponential increase in the number of possible equivalent plan alternatives to find an optimal QEP. Although it is not computationally reasonable to explore exhaustively all possible plans in such large search space. Although query optimization mechanisms are important in the cloud environments, to the best of our knowledge, there exists no complete and systematic review on investigating these issues. Therefore, in this paper, four categories to study these mechanisms are considered which are search‐based, machine learning‐based, schema‐based, and security‐based mechanisms. Also, this paper represents the advantages and disadvantages of the selected query optimization techniques and investigates the metrics of their techniques. Finally, the important challenges of these techniques are reviewed to develop more efficient query optimization techniques in the future.
A slippery slope for Cryogenian diamictites?
Authors: Le Heron Daniel Paul , Vandyk Thomas M. 
Published: March 2019

AbstractThe Death Valley region has previously been claimed to preserve the sedimentary records of both the Sturtian and Marinoan snowball Earth events within the Kingston Peak Formation, which outcrops in a number of disconnected mountain ranges. In this context, new sedimentary logs are presented together with detailed clast textural analyses which allow diamictites of the Alexander Hills and the Saddle Peak Hills to be compared in detail for the first time, and to be contrasted with rocks of well‐established glaciogenic origin from the Kingston Range. Notably, in the Saddle Peak Hills, clasts identical in composition and facies to that of the Noonday Dolomite—a unit previously interpreted as the post‐Marinoan cap carbonate—are incorporated into diamictites at the top of the Kingston Peak Formation. Combined with the carbonate‐rich composition of rocks at the top of the formation, these observations suggest that the uppermost diamictites of the Saddle Peak Hills and Alexander Hills are genetically related to the Noonday Dolomite and are unrelated to glacial processes. We propose that they formed through local slope foundering and basinward collapse of the adjacent carbonate platform, substantiating recent interpretations of Noonday carbonate platform dynamics, and demonstrating that they are genetically unrelated to Cryogenian glaciation. Thus, clast textural analyses play a valuable role in establishing whether contested ‘snowball Earth’ outcrops are truly glaciogenic or simply the product of local slope collapse.
Protein intake is not associated with progression of diabetic kidney disease in patients without macroalbuminuria
Authors: Kaji Ayumi , Hashimoto Yoshitaka , Kobayashi Yukiko , Wada Sayori , Kuwahata Masashi , Yamazaki Masahiro , Fukui Michiaki 
Published: March 2019

AbstractBackgroundDiabetic kidney disease is an important problem in individuals with diabetes. The effect of dietary protein intake on the renal function of patients with diabetes is controversial. Here, we sought to clarify the association between dietary protein intake and changes in the urinary albumin excretion (UAE) or estimated glomerular filtration rate (eGFR) in patients with type 2 diabetes.MethodsIn this retrospective cohort study, we included 144 patients (70 men, mean ± standard deviation of age 64 ± 10 years, and median (interquartile range) of UAE 15.0 (7.0‐38.9) mg/gCr) without an eGFR less than 30 mL/min/1.73 m2 and/or UAE greater than or equal to 300 mg/gCr. Changes in the UAE or eGFR were defined as (logarithms [UAE+1] or eGFR at follow‐up minus logarithms [UAE+1] or eGFR at baseline examination)/follow‐up duration (years). Habitual protein intake was estimated by a self‐administered diet history questionnaire.ResultsThe median follow‐up duration was 5 years. Protein intake (g/kg ideal body weight/day) was not associated with the change in the UAE (r = −0.130, p = 0.120) or change in the eGFR (r = −0.074, p = 0.381). Multiple linear regression analyses showed that after adjusting for covariates, the patients' protein intake was not associated with change in their UAE (standardized regression coefficient: 0.044, p = 0.732) or change in their eGFR (standardized regression coefficient: 0.250, p = 0.085).ConclusionsDietary protein intake does not influence changes in the UAE or eGFR among patients with type 2 diabetes without macroalbuminuria.
Proposals for optimizing sea lamprey passage through a vertical‐slot fishway
Authors: Pereira E. , Cardoso G.R. , Quintella B.R. , Mateus C.S. , Alexandre C.M. , Oliveira R.L. , Belo A.F. , Telhado A. , Quadrado M.F. , Batista C.M. , Almeida P.R. 
Published: March 2019

AbstractMovement of sea lamprey through a vertical‐slot fishway (built at the Coimbra dam, in central Portugal) was continuously monitored between 2013 and 2016 by a video recording system. Visual count data were used to quantify the overall successful movements and identify seasonal and circadian patterns of fishway use. Explicative models (Boosted Regression Trees) were used to study the relationship between frequency of successful movements during the species migration peak and environmental variables. The aim of the study was to identify predictors that may be related with successful sea lamprey upstream migration through the fishway. Collected information was used to support further management recommendations for optimizing the fishway performance. During the 4‐year study, near 50,000 lampreys successfully negotiated the Coimbra dam fishway reaching the upper stretch of river Mondego. Migratory peak occurred between April and May with an increase in passages during the night period (between 11 p.m. and 6 a.m.). It was observed an increase in use frequency that was related with the combined effect of flow and temperature. Higher passages were achieved when Coimbra dam discharge flows are lower than 100 m3/s and temperature between 15 and 19°C. Flow discharges higher than 150 m3/s seemed to inhibit successful sea lamprey passage. In dry years, when flows are almost constantly lower than 50 m3/s, temperature was the most important factor influencing fishway use.
Mistletoe generates non‐trophic and trait‐mediated indirect interactions through a shared host of herbivore consumers
Authors: Lázaro‐González Alba , Hódar José A. , Zamora Regino 
Published: March 2019

AbstractIndirect interactions emerge among a wide range of herbivores sharing the same plant resource. Consumers usually belong to different trophic guilds, from folivores and sapsuckers to parasitic plants. We propose that mistletoes parasitizing pines could play a key role acting as herbivores on host pines and coming indirectly into competition with other herbivores feeding on the same host. Changes caused by mistletoes on its host have been well studied, but its effects running across trophic webs remain unrevealed. In this study, we investigate the effect of European mistletoe (Viscum albumsubsp.austriacum) on the host‐feeding herbivores via trait‐mediated indirect interactions (TMIIs) across their shared pine host (Pinus nigrasubsp.salzmannii). We performed field and laboratory experiments, and analyzed the net effect of different mistletoe parasite loads on three host‐phytophagous species: the sapsuckerCinara pini(Aphididae), the winter folivoreThaumetopoea pityocampa(Thaumetopoeidae), and the summer folivoreBrachyderessp. (Curculionidae), all being members of different functional feeding groups (FFGs). We summarize the mistletoe–host–herbivore interactions by means of a TMII, where mistletoe parasitism causes non‐trophic links and detrimental indirect interactions on pine‐feeding herbivores across its shared host, suggesting a worsening of host quality as food. These indirect interactions vary according to three parameters. First, the intensity has a non‐proportional relation with parasite load, showing an impact threshold on highly parasitized pines. Second, the movement capacity of insect herbivores determines their response, by decreasing the abundance of herbivores with low movement ability (aphids and pine processionary caterpillars) while altering the behavior (plant selection) of more mobile herbivores (pine weevils). Finally, FFG determines the intensity of mistletoe parasitism effects, folivores being more responsive than sapsuckers. Overall, mistletoe generates non‐trophic interaction linkages in the forest able to modify community structure by becoming a nexus of the entire herbivore community of the pine canopy.
Fungal colonization of plant roots is resistant to nitrogen addition and resilient to dominant species losses
Authors: Henning Jeremiah A. , Read Quentin D. , Sanders Nathan J. , Classen Aimee T. 
Published: March 2019

AbstractGlobal change drivers, such as nitrogen (N) deposition and non‐random species extinctions, may shift interactions among aboveground and belowground communities. However, tightly coupled interactions between aboveground and belowground organisms may buffer ecosystems to global change. Here, we test how four years of organic and inorganic N addition and removal of a dominant plant species, Festuca thurberi, independently and interactively influences fungal colonization patterns and performance in a co‐dominant plant species, Helianthella quinquenervis. Surprisingly, we found N addition and Festuca removal had no measurable effects on the colonization of arbuscular mycorrhizal fungi (AMF) and dark septate endophyte (DSE) or the performance of Helianthella seedlings grown with field‐collected inoculum in a companion greenhouse experiment. However, the proximity of Helianthella to Festuca predicted fungal colonization: DSE colonization decreased by 1% for each cm of distance Helianthella was from Festuca, although the differences in fungal inoculum potential had no effect on Helianthella seedling survival or biomass. Our results suggest that plant–fungal interactions can be resistant to N addition and resilient to the loss of dominant plant species. Additionally, our results suggest that soil legacies, mediated through surviving symbiont communities or changes in soil properties, can shape ecosystem resistance and resilience to disturbance and perturbations.
Summer comes to the Southern Ocean: how phytoplankton shape bacterioplankton communities far into the deep dark sea
Authors: Richert Inga , Yager Patricia L. , Dinasquet Julie , Logares Ramiro , Riemann Lasse , Wendeberg Annelie , Bertilsson Stefan , Scofield Douglas G. 
Published: March 2019

AbstractDuring austral spring and summer, the coastal Antarctic experiences a sharp increase in primary production and a steepening of biotic and abiotic gradients that result from increased solar radiation and retreating sea ice. In one of the largest seasonally ice‐free regions, the Amundsen Sea Polynya, pelagic samples were collected from 15 sites during a massive Phaeocystis antarctica bloom in 2010/2011. Along with a suite of other biotic and abiotic measurements, bacterioplankton were collected and analyzed for community structure by pyrosequencing of the 16S rRNA gene. The aims were to identify patterns in diversity and composition of heterotrophic bacterioplankton and to test mechanistic hypotheses for explaining these differences along variations in depth, water mass, phytoplankton biomass, and organic and inorganic nutrients. The overall goal was to clarify the relationship between primary producers and bacterioplankton community structure in the Southern Ocean. Results suggested that both epipelagic and mesopelagic bacterioplankton communities were structured by phytoplankton blooming in the euphotic zone. As chlorophyll a (chl‐a) increased in surface waters, the abundance of surface bacterioplankton increased, but their diversity decreased. Similarity in bacterioplankton community composition between surface‐water sites increased as the bloom progressed, suggesting that algal blooms may homogenize surface‐water bacterioplankton communities at larger spatial scales. Below the euphotic zone, the opposite relationship was found. Mesopelagic bacterioplankton diversity increased with increasing chl‐a in the overlying surface waters. This shift may be promoted by several factors including local increase in organic and inorganic nutrients from particles sinking out of the euphotic zone, an increase in niche differentiation associated with the particle flux, interactions with deep‐dwelling macrozooplankton, and release from competition with primary producers. Additional multivariate analyses of bacterioplankton community structure and nutrient concentrations revealed distinct depth horizons, with bacterioplankton communities having maximum alpha and beta diversity just below the euphotic zone, while nutrient composition gradually homogenized with increasing depth. Our results provide evidence for bloom‐driven (bottom‐up) control of bacterioplankton community diversity in the coastal Southern Ocean and suggest mechanisms whereby surface processes can shape the diversity of bacterioplankton communities at great depth.
Greenhouse gas emissions from urban ponds are driven by nutrient status and hydrology
Authors: Peacock Mike , Audet Joachim , Jordan Sabine , Smeds Jacob , Wallin Marcus B. 
Published: March 2019

AbstractInland waters emit significant quantities of greenhouse gases (GHGs) such as methane (CH4) and carbon dioxide (CO2) to the atmosphere. On a global scale, these emissions are large enough that their contribution to climate change is now recognized by the Intergovernmental Panel on Climate Change. Much of the past focus on GHG emissions from inland waters has focused on lakes, reservoirs, and rivers, and the role of small, artificial waterbodies such as ponds has been overlooked. To investigate the spatial variation in GHG fluxes from artificial ponds, we conducted a synoptic survey of forty urban ponds in a Swedish city. We measured dissolved concentrations of CH4 and CO2, and made complementary measurements of water chemistry. We found that CH4 concentrations were greatest in high‐nutrient ponds (measured as total phosphorus and total organic carbon). For CO2, higher concentrations were associated with silicon and calcium, suggesting that groundwater inputs lead to elevated CO2. When converted to diffusive GHG fluxes, mean emissions were 30.3 mg CH4·m−2·d−1 and 752 mg CO2·m−2·d−1. Although these fluxes are moderately high on an areal basis, upscaling them to all Swedish urban ponds gives an emission of 8336 t CO2eq/yr (±1689) equivalent to 0.1% of Swedish agricultural GHG emissions. Artificial ponds could be important GHG sources in countries with larger proportions of urban land.