bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isophorone derivatives as a new structural motif of aggregation pheromones in Curculionidae
Authors: Vidal Diogo Montes , Moreira Marcos Antonio Barbosa , Coracini Miryan Denise Araujo , Zarbin Paulo Henrique Gorgatti 
Published: January 2019

AbstractThe beetle Homalinotus depressus (Coleoptera: Curculionidae) is a major pest of coconuts in the Northern region of Brazil, for which environmentally friendly methods of control are desired. Behavioral responses of H. depressus to airborne volatile extracts from conspecifics suggested the presence of a male-produced aggregation pheromone. GC analyses of these extracts showed the presence of four male-specific compounds. Analytical data in combination with the synthesis of standards led to the identification of the male-released semiochemicals as epoxyisophorone (1), isophorone (2), homalinol (3), and 2-hydroxyisophorone (4), of which (3) was the major constituent. The configuration of homalinol was determined to be cis on the basis of retention times of synthetic cis and trans synthetic standards. Enantiomers of cis-homalinol were obtained in high enantiomeric excess by using biocatalysis. Their separation on a GC enantioselective column (β-Dex325®), allowed us to unambiguously determine that the absolute configuration of natural homalinol was (1R,2R,6S). Field bioassays demonstrated that both the synthetic major compound per se and mixtures of all four male-specific compounds were attractive to H. depressus.
Modeling Oral Multispecies Biofilm Recovery After Antibacterial Treatment
Authors: Jing Xiaobo , Huang Xiangya , Haapasalo Markus , Shen Ya , Wang Qi 
Published: January 2019

AbstractRecovery of multispecies oral biofilms is investigated following treatment by chlorhexidine gluconate (CHX), iodine-potassium iodide (IPI) and Sodium hypochlorite (NaOCl) both experimentally and theoretically. Experimentally, biofilms taken from two donors were exposed to the three antibacterial solutions (irrigants), respectively, for 10 minutes. We observe that (a) live bacterial cell ratios decline for a week after the exposure and the trend then reverses beyond the week; after fifteen weeks, live bacterial cell ratios in biofilms fully return to their pretreatment levels; (b) NaOCl is shown as the strongest antibacterial agent for the oral biofilms; (c) multispecies oral biofilms from different donors showed no difference in their susceptibility to all the bacterial solutions. Guided by the experiment, a mathematical model for biofilm dynamics is developed, accounting for multiple bacterial phenotypes, quorum sensing, and growth factor proteins, to describe the nonlinear time evolutionary behavior of the biofilms. The model captures time evolutionary dynamics of biofilms before and after antibacterial treatment very well. It reveals the important role played by quorum sensing molecules and growth factors in biofilm recovery and verifies that the source of biofilms has a minimal effect to their recovery. The model is also applied to describe the state of biofilms of various ages treated respectively by CHX, IPI and NaOCl, taken from different donors. Good agreement with experimental data predicted by the model is obtained as well, confirming its applicability to modeling biofilm dynamics in general.
Directed evolution of super-secreted variants from phage-displayed human Interleukin-2
Authors: Rojas Gertrudis , Carmenate Tania , Santo-Tomás Julio Felipe , Valiente Pedro A. , Becker Marlies , Pérez-Riverón Annia , Tundidor Yaima , Ortiz Yaquelín , Fernandez de Cossio-Diaz Jorge , Graça Luis , Dübel Stefan , León Kalet 
Published: January 2019

AbstractSelection from a phage display library derived from human Interleukin-2 (IL-2) yielded mutated variants with greatly enhanced display levels of the functional cytokine on filamentous phages. Introduction of a single amino acid replacement selected that way (K35E) increased the secretion levels of IL-2-containing fusion proteins from human transfected host cells up to 20-fold. Super-secreted (K35E) IL-2/Fc is biologically activein vitroandin vivo, has anti-tumor activity and exhibits a remarkable reduction in its aggregation propensity- the major manufacturability issue limiting IL-2 usefulness up to now. Improvement of secretion was also shown for a panel of IL-2-engineered variants with altered receptor binding properties, including a selective agonist and a super agonist that kept their unique properties. Our findings will improve developability of the growing family of IL-2-derived immunotherapeutic agents and could have a broader impact on the engineering of structurally related four-alpha-helix bundle cytokines.
HRGPred: Prediction of herbicide resistant genes with k-mer nucleotide compositional features and support vector machine
Authors: Meher Prabina Kumar , Sahu Tanmaya Kumar , Raghunandan K. , Gahoi Shachi , Choudhury Nalini Kanta , Rao Atmakuri Ramakrishna 
Published: January 2019

AbstractHerbicide resistance (HR) is a major concern for the agricultural producers as well as environmentalists. Resistance to commonly used herbicides are conferred due to mutation(s) in the genes encoding herbicide target sites/proteins (GETS). Identification of these genes through wet-lab experiments is time consuming and expensive. Thus, a supervised learning-based computational model has been proposed in this study, which is first of its kind for the prediction of seven classes of GETS. The cDNA sequences of the genes were initially transformed into numeric features based on the k-mer compositions and then supplied as input to the support vector machine. In the proposed SVM-based model, the prediction occurs in two stages, where a binary classifier in the first stage discriminates the genes involved in conferring the resistance to herbicides from other genes, followed by a multi-class classifier in the second stage that categorizes the predicted herbicide resistant genes in the first stage into any one of the seven resistant classes. Overall classification accuracies were observed to be ~89% and >97% for binary and multi-class classifications respectively. The proposed model confirmed higher accuracy than the homology-based algorithms viz., BLAST and Hidden Markov Model. Besides, the developed computational model achieved ~87% accuracy, while tested with an independent dataset. An online prediction server HRGPred (http://cabgrid.res.in:8080/hrgpred) has also been established to facilitate the prediction of GETS by the scientific community.
mmSTORM: Multimodal localization based super-resolution microscopy
Authors: Gajdos Tamás , Cserteg Zsófia , Szikora Szilárd , Novák Tibor , H. Kovács Bálint Barna , Szabó Gábor , Mihály József , Erdélyi Miklós 
Published: January 2019

AbstractSuper-resolution localization microscopy provides a powerful tool to study biochemical mechanisms at single molecule level. Although the lateral position of the fluorescent dye molecules can be determined routinely with high precision, measurement of other modalities such as 3D and multicolor without the degradation of the original super-resolved image is still in the focus. In this paper a dual-objective multimodal single molecule localization microscopy (SMLM) technique has been developed, optimized and tested. The proposed optical arrangement can be implemented onto a conventional inverted microscope without serious system modification. The performance of the method was tested using fluorescence beads, F-actin filaments and sarcomere structures. It was shown that the proposed imaging method does not degrade the image quality of the original SMLM 2D image but could provide information on the axial position or emission spectra of the dye molecules.
Overcoming NADPH product inhibition improves D-sorbitol conversion to L-sorbose
Authors: Kim Tae-Su , Gao Hui , Li Jinglin , Kalia Vipin C. , Muthusamy Karthikeyan , Sohng Jae Kyung , Kim In-Won , Lee Jung-Kul 
Published: January 2019

AbstractGluconobacter oxydans sorbitol dehydrogenase (GoSLDH) exhibits a higher catalytic efficiency than other l-sorbose producing enzymes. During the reaction catalysed by GoSLDH, NADP+ is reduced to NADPH and d-sorbitol is oxidized to l-sorbose. However, GoSLDH activity is inhibited by the NADPH (Ki = 100 μM) formed during the enzymatic reaction. Therefore, Escherichia coligosldh-lrenox producing both GoSLDH for d-sorbitol oxidation and LreNOX (NAD(P)H oxidase from Lactobacillus reuteri) for NADP+ regeneration was generated and used for l-sorbose production. Whole cell biocatalysts with the LreNOX cofactor recycling system showed a high conversion rate (92%) of d-sorbitol to l-sorbose in the presence of low concentration of NADP+ (0.5 mM). By alleviating NADPH accumulation during the catalytic reactions, E. coligosldh-lrenox exhibited 23-fold higher conversion rate of d-sorbitol than E. coligosldh. l-Sorbose production by E. coligosldh-lrenox reached 4.1 g/L after 40 min, which was 20.5-fold higher than that of E. coligosldh. We also constructed G. oxydansgosldh and G. oxydansgosldh-lrenox strains, and they exhibited 1.2- and 2.9-fold higher conversion rates than the wild-type G. oxydans KCTC 1091. The results indicate that overcoming NADPH product inhibition using LreNOX improves chemical production in NADP+-dependent enzymatic reactions.
A Comparative Analysis of the Status Anxiety Hypothesis of Socio-economic Inequalities in Health Based on 18,349 individuals in Four Countries and Five Cohort Studies
Authors: Layte Richard , McCrory Cathal , Cheallaigh Cliona Ni , Bourke Nollaig , Kivimaki Mika , Ribeiro Ana Isabel , Stringhini Silvia , Vineis Paolo 
Published: January 2019

AbstractThe status anxiety hypothesis proposes that systematic inflammation as a consequence of chronic psycho-social stress is a possible pathway linking socio-economic position (SEP) to premature ageing and is a possible explanation for cross-national variation in patterns of health and well-being. Harmonised data from the LIFEPATH consortium on 18,349 individuals aged 50 to 75 and 30,632 observations are used to measure variation in the association between inflammation measured as C-reactive protein and SEP across four countries (Britain, Ireland, Portugal and Switzerland) and five studies (ELSA, Whitehall II, TILDA, EPIPorto and SKIPOGH). Adjusting for population composition, mean concentrations of CRP are highest in Portugal, the country with the highest income inequality and lowest in Switzerland, a lower income inequality country. Across all of the studies, lower SEP groups have higher mean concentrations of CRP and, as predicted by the theory, absolute differentials between SEP groups reflect the pattern of societal income inequality. Adjustment for lifestyle indicators reduces SEP differentials by between 45% and 52% but cannot account for country variation in mean inflammation.
Identification of microbiota in peri-implantitis pockets by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
Authors: Yeh Hwey-Chin , Lu Jang-Jih , Chang Shih-Cheng , Ge Mao-Cheng 
Published: January 2019

AbstractThe purpose of this study was to identify the microbial communities that colonize peri-implantitis pockets using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Subjects having at least one implant with peri-implantitis, no diabetes, and not taking antibiotics in the previous 3 months were selected. Peri-implantitis was defined when surrounding bone loss ≥0.5 mm and bleeding on probing was found. Microbial samples were collected from peri-implantitis pockets using paper points. After incubation and isolation, the colonies were analyzed by MALDI-TOF MS. A total of 126 isolates were cultivated and identified from 12 samples, in identification rates of 82.5% at the species level and 12.72% at the genus level. Although the compositions were highly variable, major habitants in different peri-implant pockets could be identified. Among them the most distinguished were Neisseria flavescens (87%), Streptococcus constellatus (56%), Slackia exigua (46%), Streptococcus intermedius (45%), Fusobacterium nucleatum (45%) and Gemella morbillorum (43%). This preliminary study provides comprehensive and reliable data for future study designs involving MALDI-TOF MS and peri-implantitis in a more specific, easy, rapid and economical way. MALDI-TOF MS could be a new clinical method to evaluate and monitor oral microbiota associated with the disease.
Population dynamics of multiple triplet excitons revealed from time-dependent fluorescence quenching of single conjugated polymer chains
Authors: Datko Benjamin D. , Grey John K. 
Published: January 2019

AbstractThe advent of multiple exciton harvesting schemes and prolonging exciton lifetimes to improve performance attributes of solar cells based on conjugated organic materials presents some interesting challenges that must be overcome in order to realize the full potential of these strategies. This is especially important for applications involving multi-chromophoric conjugated polymers where interactions between multiple spin-forbidden triplet excitons can be significant and are mediated by chain conformation. We use single molecule spectroscopic techniques to investigate interactions between multiple triplet excitons and emissive singlets by monitoring time-dependent fluorescence quenching on time scales commensurate with the triplet lifetime. Structurally related conjugated polymers differing by heteroatom substitution were targeted and we use a stochastic photodynamic model to numerically simulate the evolution of multi-exciton populations following photoexcitation. Single chains of poly(3-hexylthiophene) (P3HT) exhibit longer-lived triplet dynamics and larger steady-state triplet occupancies compared to those of poly(3-hexylselenophene) (P3HS), which has a larger reported triplet yield. Triplet populations evolve and relax much faster in P3HS which only becomes evident when considering all kinetic factors governing exciton population dynamics. Overall, we uncover new guidelines for effectively managing multi-exciton populations and interactions in conjugated polymers and improving their light harvesting efficiency.
Detecting sequences of system states in temporal networks
Authors: Masuda Naoki , Holme Petter 
Published: January 2019

AbstractMany time-evolving systems in nature, society and technology leave traces of the interactions within them. These interactions form temporal networks that reflect the states of the systems. In this work, we pursue a coarse-grained description of these systems by proposing a method to assign discrete states to the systems and inferring the sequence of such states from the data. Such states could, for example, correspond to a mental state (as inferred from neuroimaging data) or the operational state of an organization (as inferred by interpersonal communication). Our method combines a graph distance measure and hierarchical clustering. Using several empirical data sets of social temporal networks, we show that our method is capable of inferring the system’s states such as distinct activities in a school and a weekday state as opposed to a weekend state. We expect the methods to be equally useful in other settings such as temporally varying protein interactions, ecological interspecific interactions, functional connectivity in the brain and adaptive social networks.
Plasma coenzyme Q10 status is impaired in selected genetic conditions
Authors: Montero Raquel , Yubero Delia , Salgado Maria C. , González María Julieta , Campistol Jaume , O’Callaghan Maria del Mar , Pineda Mercè , Delgadillo Verónica , Maynou Joan , Fernandez Guerau , Montoya Julio , Ruiz-Pesini Eduardo , Meavilla Silvia , Neergheen Viruna , García-Cazorla Angels , Navas Placido , Hargreaves Iain , Artuch Rafael 
Published: January 2019

AbstractIdentifying diseases displaying chronic low plasma Coenzyme Q10 (CoQ) values may be important to prevent possible cardiovascular dysfunction. The aim of this study was to retrospectively evaluate plasma CoQ concentrations in a large cohort of pediatric and young adult patients. We evaluated plasma CoQ values in 597 individuals (age range 1 month to 43 years, average 11 years), studied during the period 2005–2016. Patients were classified into 6 different groups: control group of healthy participants, phenylketonuric patients (PKU), patients with mucopolysaccharidoses (MPS), patients with other inborn errors of metabolism (IEM), patients with neurogenetic diseases, and individuals with neurological diseases with no genetic diagnosis. Plasma total CoQ was measured by reverse-phase high-performance liquid chromatography with electrochemical detection and ultraviolet detection at 275 nm. ANOVA with Bonferroni correction showed that plasma CoQ values were significantly lower in the PKU and MPS groups than in controls and neurological patients. The IEM group showed intermediate values that were not significantly different from those of the controls. In PKU patients, the Chi-Square test showed a significant association between having low plasma CoQ values and being classic PKU patients. The percentage of neurogenetic and other neurological patients with low CoQ values was low (below 8%). In conclusión, plasma CoQ monitoring in selected groups of patients with different IEM (especially in PKU and MPS patients, but also in IEM under protein-restricted diets) seems advisable to prevent the possibility of a chronic blood CoQ suboptimal status in such groups of patients.
Data-Driven Subtyping of Parkinson’s Disease Using Longitudinal Clinical Records: A Cohort Study
Authors: Zhang Xi , Chou Jingyuan , Liang Jian , Xiao Cao , Zhao Yize , Sarva Harini , Henchcliffe Claire , Wang Fei 
Published: January 2019

AbstractParkinson’s disease (PD) is associated with diverse clinical manifestations including motor and non-motor signs and symptoms, and emerging biomarkers. We aimed to reveal the heterogeneity of PD to define subtypes and their progression rates using an automated deep learning algorithm on the top of longitudinal clinical records. This study utilizes the data collected from the Parkinson’s Progression Markers Initiative (PPMI), which is a longitudinal cohort study of patients with newly diagnosed Parkinson’s disease. Clinical information including motor and non-motor assessments, biospecimen examinations, and neuroimaging results were used for identification of PD subtypes. A deep learning algorithm, Long-Short Term Memory (LSTM), was used to represent each patient as a multi-dimensional time series for subtype identification. Both visualization and statistical analysis were performed for analyzing the obtained PD subtypes. As a result, 466 patients with idiopathic PD were investigated and three subtypes were identified. Subtype I (Mild Baseline, Moderate Motor Progression) is comprised of 43.1% of the participants, with average age 58.79 ± 9.53 years, and was characterized by moderate functional decay in motor ability but stable cognitive ability. Subtype II (Moderate Baseline, Mild Progression) is comprised of 22.9% of the participants, with average age 61.93 ± 6.56 years, and was characterized by mild functional decay in both motor and non-motor symptoms. Subtype III (Severe Baseline, Rapid Progression) is comprised 33.9% of the patients, with average age 65.32 ± 8.86 years, and was characterized by rapid progression of both motor and non-motor symptoms. These subtypes suggest that when comprehensive clinical and biomarker data are incorporated into a deep learning algorithm, the disease progression rates do not necessarily associate with baseline severities, and the progression rate of non-motor symptoms is not necessarily correlated with the progression rate of motor symptoms.
Historical contingency and productivity effects on food-chain length
Authors: Doi Hideyuki , Hillebrand Helmut 
Published: January 2019

AbstractFood-chain length (FCL) is a fundamental ecosystem attribute, integrating information on both food web composition and ecosystem processes. It remains untested whether FCL also reflects the history of community assembly known to affect community composition and ecosystem functioning. Here, we performed microcosm experiments with a copepod (top predator), two ciliate species (intermediate consumers), and bacteria (producers), and modified the sequence of species introduction into the microcosm at four productivity levels to jointly test the effects of historical contingency and productivity on FCL. FCL increased when the top predator was introduced last; thus, the trophic position of the copepod reflected assembly history. A shorter FCL occurred at the highest productivity level, probably because the predator switched to feeding at the lower trophic levels because of the abundant basal resource. Thus, we present empirical evidence that FCL was determined by historical contingency, likely caused by priority effects, and by productivity.
A visual illusion that influences perception and action through the dorsal pathway
Authors: de la Malla Cristina , Brenner Eli , de Haan Edward H. F. , Smeets Jeroen B. J. 
Published: January 2019

AbstractThere are two main anatomically and physiologically defined visual pathways connecting the primary visual cortex with higher visual areas: the ventral and the dorsal pathway. The influential two-visual-systems hypothesis postulates that visual attributes are analyzed differently for different functions: in the dorsal pathway visual information is analyzed to guide actions, whereas in the ventral pathway visual information is analyzed for perceptual judgments. We here show that a person who cannot identify objects due to an extensive bilateral ventral brain lesion is able to judge the velocity at which an object moves. Moreover, both his velocity judgements and his interceptive actions are as susceptible to a motion illusion as those of people without brain lesions. These findings speak in favor of the idea that dorsal structures process information about attributes such as velocity, irrespective of whether such information is used for perceptual judgments or to guide actions.
The metabolite repair enzyme Nit1 is a dual-targeted amidase that disposes of damaged glutathione in Arabidopsis
Authors: Niehaus Thomas D. , Patterson Jenelle A. , Alexander Danny C. , Folz Jakob S. , Pyc Michal , MacTavish Brian S. , Bruner Steven D. , Mullen Robert T. , Fiehn Oliver , Hanson Andrew D. 
Published: January 2019

Abstract
The tripeptide glutathione (GSH) is implicated in various crucial physiological processes including redox buffering and protection against heavy metal toxicity. GSH is abundant in plants, with reported intracellular concentrations typically in the 1–10 mM range. Various aminotransferases can inadvertently transaminate the amino group of the γ-glutamyl moiety of GSH to produce deaminated glutathione (dGSH), a metabolite damage product. It was recently reported that an amidase known as Nit1 participates in dGSH breakdown in mammals and yeast. Plants have a hitherto uncharacterized homolog of the Nit1 amidase. We show that recombinant Arabidopsis Nit1 (At4g08790) has high and specific amidase activity towards dGSH. Ablating the Arabidopsis Nit1 gene causes a massive accumulation of dGSH and other marked changes to the metabolome. All plant Nit1 sequences examined had predicted plastidial targeting peptides with a potential second start codon whose use would eliminate the targeting peptide. In vitro transcription/translation assays show that both potential translation start codons in Arabidopsis Nit1 were used and confocal microscopy of Nit1–GFP fusions in plant cells confirmed both cytoplasmic and plastidial localization. Furthermore, we show that Arabidopsis enzymes present in leaf extracts convert GSH to dGSH at a rate of 2.8 pmol min−1 mg−1 in the presence of glyoxalate as an amino acceptor. Our data demonstrate that plants have a dGSH repair system that is directed to at least two cellular compartments via the use of alternative translation start sites.