bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineering a Polyspecific Pyrrolysyl-tRNA Synthetase by a High Throughput FACS Screen
Authors: Hohl Adrian , Karan Ram , Akal Anastassja , Renn Dominik , Liu Xuechao , Ghorpade Seema , Groll Michael , Rueping Magnus , Eppinger Jörg 
Published: August 2019

AbstractThe Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNAPyl are extensively used to add non-canonical amino acids (ncAAs) to the genetic code of bacterial and eukaryotic cells. However, new ncAAs often require a cumbersome de novo engineering process to generate an appropriate PylRS/tRNAPyl pair. We here report a strategy to predict a PylRS variant with novel properties. The designed polyspecific PylRS variant HpRS catalyzes the aminoacylation of 31 structurally diverse ncAAs bearing clickable, fluorinated, fluorescent, and for the first time biotinylated entities. Moreover, we demonstrated a site-specific and copper-free conjugation strategy of a nanobody by the incorporation of biotin. The design of polyspecific PylRS variants offers an attractive alternative to existing screening approaches and provides insights into the complex PylRS-substrate interactions.
The genetic relationship between female reproductive traits and six psychiatric disorders
Authors: Ni Guiyan , Amare Azmeraw T. , Zhou Xuan , Mills Natalie , Gratten Jacob , Lee S. Hong 
Published: August 2019

AbstractFemale reproductive behaviours have important implications for evolutionary fitness and health of offspring. Here we used the second release of UK Biobank data (N = 220,685) to evaluate the association between five female reproductive traits and polygenic risk scores (PRS) projected from genome-wide association study summary statistics of six psychiatric disorders (N = 429,178). We found that the PRS of attention-deficit/hyperactivity disorder (ADHD) were strongly associated with age at first birth (AFB) (genetic correlation of −0.68 ± 0.03), age at first sexual intercourse (AFS) (−0.56 ± 0.03), number of live births (NLB) (0.36 ± 0.04) and age at menopause (−0.27 ± 0.04). There were also robustly significant associations between the PRS of eating disorder (ED) and AFB (0.35 ± 0.06), ED and AFS (0.19 ± 0.06), major depressive disorder (MDD) and AFB (−0.27 ± 0.07), MDD and AFS (−0.27 ± 0.03) and schizophrenia and AFS (−0.10 ± 0.03). These associations were mostly explained by pleiotropic effects and there was little evidence of causal relationships. Our findings can potentially help improve reproductive health in women, hence better child outcomes. Our findings also lend partial support to the evolutionary hypothesis that causal mutations underlying psychiatric disorders have positive effects on reproductive success.
Intercomparing varied erosion, deposition and transport process representations for simulating sediment yield
Authors: Zi Tan , Kumar Mukesh , Albertson John 
Published: August 2019

AbstractOver the past several decades there has been an enormous proliferation of sediment models, ranging from empirical to physically-based. Most of these models aim to capture the impacts of three primary sediment processes viz. erosion, deposition, and transport. As a range of process representations exist for simulating these three processes, it is natural to wonder about their influence on estimates of suspended sediment yield from a watershed. While several studies have focused on intercomparison of sediment models, their scopes have generally been restricted to comparing the individual model performances, rather than understanding the role of process representations on sediment model output. Here, six model configurations, which span the different permutations of erosion, deposition and transport process representations being used in extant models, are considered to evaluate the role of process representations on sediment yield estimates. The numerical experiments are designed to evaluate the extent to which the sediment dynamics as modeled by a physically-based model with coupled surface-subsurface hydrologic interactions are captured by simpler models. The presented work delineates the applicability and limitations of widely used representations of sediment processes, and could help users identify the pros and cons of using a sediment model at a given temporal scale.
Ocean acidification effects on in situ coral reef metabolism
Authors: Doo Steve S. , Edmunds Peter J. , Carpenter Robert C. 
Published: August 2019

AbstractThe Anthropocene climate has largely been defined by a rapid increase in atmospheric CO2,causing global climate change (warming) and ocean acidification (OA, a reduction in oceanic pH). OA is of particular concern for coral reefs, as the associated reduction in carbonate ion availability impairs biogenic calcification and promotes dissolution of carbonate substrata. While these trends ultimately affect ecosystem calcification, scaling experimental analyses of the response of organisms to OA to consider the response of ecosystems to OA has proved difficult. The benchmark of ecosystem-level experiments to study the effects of OA is provided through Free Ocean CO2Enrichment (FOCE), which we use in the present analyses for a 21-d experiment on the back reef of Mo’orea, French Polynesia. Two natural coral reef communities were incubatedin situ, with one exposed to ambient pCO2(393 µatm), and one to high pCO2(949 µatm). Our results show a decrease in 24-h net community calcification (NCC) under high pCO2, and a reduction in nighttime NCC that attenuated and eventually reversed over 21-d. This effect was not observed in daytime NCC, and it occurred without any effect of high pCO2on net community production (NCP). These results contribute to previous studies on ecosystem-level responses of coral reefs to the OA conditions projected for the end of the century, and they highlight potential attenuation of high pCO2effects on nighttime net community calcification.
Lyso-Gb3 modulates the gut microbiota and decreases butyrate production
Authors: Aguilera-Correa John-Jairo , Madrazo-Clemente Patricia , Martínez-Cuesta María del Carmen , Peláez Carmen , Ortiz Alberto , Sánchez-Niño María Dolores , Esteban Jaime , Requena Teresa 
Published: August 2019

AbstractFabry disease is a rare X-linked lysosomal storage disorder resulting from deficient activity of α-galactosidase A, leading to the accumulation of glycosphingolipids such as globotriaosylsphingosine (lyso-Gb3). The gastrointestinal symptoms of this disease may be disabling, and the life expectancy of affected patients is shortened by kidney and heart disease. Our hypothesis was that lyso-Gb3 may modify the gut microbiota. The impact of a clinically relevant concentration of lyso-Gb3 on mono- or multispecies bacterial biofilms were evaluated. A complex bacterial community from the simulated transverse colon microbiota was studied using quantitative PCR to estimate different bacterial group concentrations and a HPLC was used to estimate short-chain fatty acids concentrations. We found that lyso-Gb3 increased the biofilm-forming capacity of several individual bacteria, including Bacteroides fragilis and significantly increased the growth of B. fragilis in a multispecies biofilm. Lyso-Gb3 also modified the bacterial composition of the human colon microbiota suspension, increasing bacterial counts of B. fragilis, among others. Finally, lyso-Gb3 modified the formation of short-chain fatty acids, leading to a striking decrease in butyrate concentration. Lyso-Gb3 modifies the biology of gut bacteria, favoring the production of biofilms and altering the composition and short-chain fatty-acid profile of the gut microbiota.
Rodent mothers increase vigilance behaviour when facing infanticide risk
Authors: Breedveld Merel C. , Folkertsma Remco , Eccard Jana A. 
Published: August 2019

AbstractInfanticide, the killing of unrelated young, is widespread and frequently driven by sexual conflict. Especially in mammals with exclusive maternal care, infanticide by males is common and females suffer fitness costs. Recognizing infanticide risk and adjusting offspring protection accordingly should therefore be adaptive in female mammals. Using a small mammal (Myodes glareolus) in outdoor enclosures, we investigated whether lactating mothers adjust offspring protection, and potential mate search behaviour, in response to different infanticide risk levels. We presented the scent of the litter’s sire or of a stranger male near the female’s nest, and observed female nest presence and movement by radiotracking. While both scents simulated a mating opportunity, they represented lower (sire) and higher (stranger) infanticide risk. Compared to the sire treatment, females in the stranger treatment left their nest more often, showed increased activity and stayed closer to the nest, suggesting offspring protection from outside the nest through elevated alertness and vigilance. Females with larger litters spent more time investigating scents and used more space in the sire but not in the stranger treatment. Thus, current investment size affected odour inspection and resource acquisition under higher risk. Adjusting nest protection and resource acquisition to infanticide risk could allow mothers to elicit appropriate (fitness-saving) counterstrategies, and thus, may be widespread.
Quantitative modeling of transcription and translation of an all-E. coli cell-free system
Authors: Marshall Ryan , Noireaux Vincent 
Published: August 2019

AbstractCell-free transcription-translation (TXTL) is expanding as a polyvalent experimental platform to engineer biological systems outside living organisms. As the number of TXTL applications and users is rapidly growing, some aspects of this technology could be better characterized to provide a broader description of its basic working mechanisms. In particular, developing simple quantitative biophysical models that grasp the different regimes of in vitro gene expression, using relevant kinetic constants and concentrations of molecular components, remains insufficiently examined. In this work, we present an ODE (Ordinary Differential Equation)-based model of the expression of a reporter gene in an all E. coli TXTL that we apply to a set of regulatory elements spanning several orders of magnitude in strengths, far beyond the T7 standard system used in most of the TXTL platforms. Several key biochemical constants are experimentally determined through fluorescence assays. The robustness of the model is tested against the experimental parameters, and limitations of TXTL resources are described. We establish quantitative references between the performance of E. coli and synthetic promoters and ribosome binding sites. The model and the data should be useful for the TXTL community interested either in gene network engineering or in biomanufacturing beyond the conventional platforms relying on phage transcription.
Regular exercise improves asthma control in adults: A randomized controlled trial
Authors: Jaakkola Jouni J. K. , Aalto Sirpa A. M. , Hernberg Samu , Kiihamäki Simo-Pekka , Jaakkola Maritta S. 
Published: August 2019

AbstractWe conducted a randomized controlled trial to test the hypothesis that a 24-week exercise intervention improves asthma control in adults. Adults with mild or moderate asthma were randomly assigned to either the exercise intervention group (IG) or the reference group (RG). Participants in IG received an individualized exercising program, including aerobic exercise at least three times a week for ≥30 minutes, muscle training, and stretching. The primary outcome was asthma control, measured by Asthma Control Test (ACT), asthma-related symptoms, and peak expiratory flow (PEF) variability. We estimated the risk (i.e. probability) of improvement in asthma control and the risk difference (RD) between IG and RG. Of 131 subjects (67 IG/64 RG) entered, 105 subjects (51/54) completed the trial (80%), and 89 (44/45) were analysed (68%). The ACT became better among 26 (62%) participants in IG and among 17 (39%) participants in RG. The effect of intervention on improving asthma control was 23% (RD = 0.23, 95% CI 0.027–0.438; P = 0.0320). The intervention also reduced shortness of breath by 30.1% (RD = 0.301, 95% CI 0.109–0.492; P = 0.003). The change in PEF variability was similar in both groups. Regular exercise improves asthma control measured by the ACT, while has little effect on PEF variability.
Efficacy of TIMOLOL nasal spray as a treatment for epistaxis in hereditary hemorrhagic telangiectasia. A double-blind, randomized, placebo-controlled trial
Authors: Dupuis-Girod Sophie , Pitiot Vincent , Bergerot Cyrille , Fargeton Anne-Emmanuelle , Beaudoin Marjolaine , Decullier Evelyne , Bréant Valentine , Colombet Bettina , Philouze Pierre , Faure Frédéric , Letievant Jean-Charles 
Published: August 2019

AbstractHereditary hemorrhagic telangiectasia is a rare vascular genetic disease. Epistaxis is the most frequent and disabling manifestation, and timolol appears to be a new therapeutic option as non-selective beta-blockers have in vitro and in vivo anti-angiogenic properties. Our main objective was to evaluate the efficacy of TIMOLOL nasal spray as a treatment for epistaxis in hereditary hemorrhagic telangiectasia. This study is a single-center, randomized, phase 2, double-blind placebo-controlled study with an allocation ratio of 1:1. It was proposed to patients with hereditary hemorrhagic telangiectasia monitored at the French Reference Center, and we included patients aged over 18 years, diagnosed with hereditary hemorrhagic telangiectasia and epistaxis. The treatment was self-administered by the patient with a posology of one spray (50 µL) of timolol 0.5% or placebo in each nostril twice a day for 28 consecutive days. The primary efficacy endpoint was mean monthly epistaxis duration, assessed by monitoring epistaxis grids. A total of 58 patients were randomized and treated. The baseline characteristics were similar in the 2 groups. Mean monthly epistaxis duration measured at 3 months was not significantly different in the 26 patients receiving the drug in comparison with the placebo group (p = 0.54). Toxicity was low and no severe adverse events were reported. One limitation is that we included all HHT patients with nosebleeds and did not take into account history of nasal surgery or nasal crusts. Timolol, administered by nasal spray at a dose of 0.25 mg in each nostril twice a day for 28 consecutive days, did not improve epistaxis in patients with hereditary hemorrhagic telangiectasia at 4 months after the beginning of the treatment.
Role of S2− ions on the microstructure change and the pitting behaviour of aluminum in saline solution
Authors: EL-Deeb Mohamed M. 
Published: August 2019

AbstractThe electrochemical behaviour and the passive film microstructure of aluminum during its exposure to 3.5 wt% NaCl solution in the absence and presence of S2−ions are investigated using potentiodynamic polarization curves, electrochemical impedance spectroscopy measurements, XRD, XRF, SEM and AFM. Electrochemical measurements show that the presence of S2−ions enhances the uniform corrosion of aluminum in NaCl solution, but delay its susceptibility to the pitting corrosion. In addition, EIS analysis illustrate that the formation of more compact and protective passive layer in the presence of S2−ions compared to its rough surface in the absence of S2−ions as evidenced by the lower value of constant phase element (CPE) and higher value of phase shift (N). Cracks, non- homogenous and open large pits with high degree of roughness are clearly observed on the aluminum surface in the absence of S2−ions, compared to oriented grooves, elongated ridges with the accumulation of the corrosion products inside the pits in the presence of S2−ions. The inhibitory effect of S2−ions for the pitting corrosion of aluminum is interpreted on the basis of the change in its microstructure of the passive film in the absence and presence of S2−ions.
Evaluation of the effects of humic acids on maize root architecture by label-free proteomics analysis
Authors: Nunes Rosane Oliveira , Domiciano Giselli Abrahão , Alves Wilber Sousa , Melo Ana Claudia Amaral , Nogueira Fábio Cesar Sousa , Canellas Luciano Pasqualoto , Olivares Fábio Lopes , Zingali Russolina Benedeta , Soares Márcia Regina 
Published: August 2019

AbstractHumic substances have been widely used as plant growth promoters to improve the yield of agricultural crops. However, the mechanisms underlying this effect remain unclear. Root soluble protein profiles in plants 11 days after planting and cultivated with and without humic acids (HA, 50 mg CL−1), were analyzed using the label-free quantitative proteomic approach. Cultivation of maize with HA resulted in higher fresh weight of roots than in untreated plants (control). Plants treated with HA showed increased number, diameter and length of roots. In the proteomics analysis, differences were detected in the following categories: energy metabolism, cytoskeleton, cellular transport, conformation and degradation of proteins, and DNA replication. Thirty-four proteins were significantly more abundant in the seedlings treated with HA, whereas only nine proteins were abundant in the control. The effects on root architecture, such as the induction of lateral roots and biomass increase were accompanied by changes in the energy metabolism-associated proteins. The results show that the main effect of HA is protective, mainly associated with increased expression of the 2-cys peroxidase, putative VHS/GAT, and glutathione proteins. Indeed, these proteins had the highest fold-difference. Overall, these results improve our understanding of the molecular mechanisms of HA-promoted plant growth.
Physiological responses of Goji berry (Lycium barbarum L.) to saline-alkaline soil from Qinghai region, China
Authors: Zhang Zhenzhong , He Kangning , Zhang Tan , Tang Da , Li Runjie , Jia Shaofeng 
Published: August 2019

AbstractRecently, Goji berry (Lycium barbarum L.) has been extensively cultivated to improve the fragile ecological environment and increase the income of residents in Qinghai Province, northwestern China. However, few studies have focused on the physiological responses of Goji berry under salt stress and alkali stress. Gas exchange, photosynthetic pigments, and chlorophyll fluorescence were evaluated in response to neutral (NaCl) and alkali (NaHCO3) salt stresses. Nine irrigation treatments were applied over 30 days and included 0(Control group), 50, 100, 200, and 300 mM NaCl and NaHCO3. The results showed that salt and alkali stress reduced all the indicators and that alkali stress was more harmful to Goji berry than salt stress under the same solution concentrations. The salt tolerance and alkali resistance thresholds were identified when the index value exceeded the 50% standard of the control group, and threshold values of 246.3 ± 2.9 mM and 108.4.7 ± 2.1 mM, respectively, were determined by regression analysis. These results were used to identify the optimal water content for Goji berry. The minimum soil water content to cultivate Goji berry should be 16.22% and 23.37% under mild and moderate salt stress soils, respectively, and 29.10% and 42.68% under mild and moderate alkali stress soil, respectively.
Ephrin-A5 potentiates netrin-1 axon guidance by enhancing Neogenin availability
Authors: Croteau L.-P. , Kao T.-J. , Kania A. 
Published: August 2019

AbstractAxonal growth cones are guided by molecular cues in the extracellular environment. The mechanisms of combinatorial integration of guidance signals at the growth cone cell membrane are still being unravelled. Limb-innervating axons of vertebrate spinal lateral motor column (LMC) neurons are attracted to netrin-1 via its receptor, Neogenin, and are repelled from ephrin-A5 through its receptor EphA4. The presence of both cues elicits synergistic guidance of LMC axons, but the mechanism of this effect remains unknown. Using fluorescence immunohistochemistry, we show that ephrin-A5 increases LMC growth cone Neogenin protein levels and netrin-1 binding. This effect is enhanced by overexpressing EphA4 and is inhibited by blocking ephrin-A5-EphA4 binding. These effects have a functional consequence on LMC growth cone responses since bath addition of ephrin-A5 increases the responsiveness of LMC axons to netrin-1. Surprisingly, the overexpression of EphA4 lacking its cytoplasmic tail, also enhances Neogenin levels at the growth cone and potentiates LMC axon preference for growth on netrin-1. Since netrins and ephrins participate in a wide variety of biological processes, the enhancement of netrin-1 signalling by ephrins may have broad implications.
Comparison of the effects of an ERAS program and a single-port laparoscopic surgery on postoperative outcomes of colon cancer patients
Authors: Kim Min Ki , Kim Jun-Gi , Lee Gyeora , Won Daeyoun David , Lee Yoon Suk , Kye Bong-Hyeon , Kim Jihoon , Lee In Kyu 
Published: August 2019

AbstractAdvancement of the surgical modality and perioperative care are the two main dimensions for the modern improvement of surgical outcome. The purpose of this study was to compare the effectiveness of the two by using the data from the single-port laparoscopic surgery and the early recovery after surgery (ERAS) program. Patients who underwent elective surgery for primary adenocarcinoma of the colon were divided into three groups and compared: ERAS (multi-port laparoscopic surgery with ERAS perioperative care), Conventional-SILS (single-port surgery with conventional perioperative care), or Conventional-Multi (multi-port laparoscopic surgery with conventional perioperative care). Ninety-one, 83, and 96 patients were registered, respectively. There were no differences among the three groups in baseline characteristics except pathological stage and operation site in colon. Although the ERAS group started a soft diet earlier and had earlier discharge, there were no differences in intra- and post-operative morbidity rate, readmission rate, or reoperation rate. The ERAS perioperative care was a significant factor for reducing length of hospital stay in the multivariate analysis, while single-port surgery was not. In modern laparoscopic colon cancer treatment, a systemic approach such as the ERAS program appears to be more effective than a technical approach for significantly improving short-term surgical outcomes.
Evaluation of antigenic differences between wild and Sabin vaccine strains of poliovirus using the pseudovirus neutralization test
Authors: Arita Minetaro , Iwai-Itamochi Masae 
Published: August 2019

AbstractIn the endgame of global polio eradication, serosurveillance is essential to monitor each country’s vulnerability to poliomyelitis outbreaks. Previously, we developed pseudovirus poliovirus (PV) neutralization test (pPNT) with type 1, 2, and 3 PV pseudovirus (PVpv), which possess a luciferase-encoding PV replicon in the capsids of wild-type strains (PVpv[WT]), showing that pPNT with type 2 and 3 PVpv(WT) but not type 1 shows high correlation with the conventional PV neutralization test (cPNT) performed with vaccine strains. Here, we analyse the antigenicity of PVpv(WT) and PVpv with capsid proteins of Sabin vaccine strains (PVpv[Sabin]) in human serum. Type 2 and 3 PVpv(WT) and PVpv(Sabin) show similar antigenicity in the analysed set of human sera in contrast to type 1 PVpv. The levels of PVpv(Sabin) infection (%), including about 70% of PVpv infection (%) measured in the presence of human serum diluted to the cPNT titre, serve as the optimal threshold values for pPNT (5% for type 1 and 2, 10% for type 3) to show high correlation with cPNT results. Our results suggest that pPNT with PVpv(Sabin) could serve as an alternative to cPNT and provide a rationale for pPNT threshold values.