bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamical decoration of stabilized-microtubules by Tau-proteins
Authors: Hervy Jordan , Bicout Dominique J. 
Published: August 2019

AbstractTau is a microtubule-associated protein that regulates axonal transport, stabilizes and spatially organizes microtubules in parallel networks. The Tau-microtubule pair is crucial for maintaining the architecture and integrity of axons. Therefore, it is essential to understand how these two entities interact to ensure and modulate the normal axonal functions. Based on evidence from several published experiments, we have developed a two-dimensional model that describes the interaction between a population of Tau proteins and a stabilized microtubule at the scale of the tubulin dimers (binding sites) as an adsorption-desorption dynamical process in which Tau can bind on the microtubule outer surface via two distinct modes: a longitudinal (along a protofilament) and lateral (across adjacent protofilaments) modes. Such a process yields a dynamical distribution of Tau molecules on the microtubule surface referred to as microtubule decoration that we have characterized at the equilibrium using two observables: the total microtubule surface coverage with Tau’s and the distribution of nearest neighbors Tau’s. Using both analytical and numerical approaches, we have derived expressions and computed these observables as a function of key parameters controlling the binding reaction: the stoichiometries of the Taus in the two binding modes, the associated dissociation constants and the ratio of the Tau concentration to that of microtubule tubulin dimers.
The Single-molecule long-read sequencing of Scylla paramamosain
Authors: Wan Haifu , Jia Xiwei , Zou Pengfei , Zhang Ziping , Wang Yilei 
Published: August 2019

AbstractScylla paramamosain is an important aquaculture crab, which has great economical and nutritional value. To the best of our knowledge, few full-length crab transcriptomes are available. In this study, a library composed of 12 different tissues including gill, hepatopancreas, muscle, cerebral ganglion, eyestalk, thoracic ganglia, intestine, heart, testis, ovary, sperm reservoir, and hemocyte was constructed and sequenced using Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology. A total of 284803 full-length non-chimeric reads were obtained, from which 79005 high-quality unique transcripts were obtained after error correction and sequence clustering and redundant. Additionally, a total of 52544 transcripts were annotated against protein database (NCBI nonredundant, Swiss-Prot, KOG, and KEGG database). A total of 23644 long non-coding RNAs (lncRNAs) and 131561 simple sequence repeats (SSRs) were identified. Meanwhile, the isoforms of many genes were also identified in this study. Our study provides a rich set of full-length cDNA sequences for S. paramamosain, which will greatly facilitate S. paramamosain research.
Mid-upper arm circumference and body mass index as different screening tools of nutritional and weight status in Polish schoolchildren across socio-political changes
Authors: Nowak-Szczepanska Natalia , Gomula Aleksandra , Koziel Slawomir 
Published: August 2019

AbstractIntergenerational changes in many biological traits are indicators of environmental conditions. One of such anthropometric measures is the mid-upper arm circumference (MUAC) which estimates nutritional status. Likewise, Body Mass Index (BMI) is widely used as an anthropometric indicator of relative weight. The aim of this study was to reveal secular trends in MUAC and BMI, as biological indicators of changing living conditions, between 1966 and 2012 among Polish children from different socioeconomic groups. Total sample involved 64 393 schoolchildren aged 7–18 years, investigated in 4 Surveys (1966, 1978, 1988, 2012). Overall socioeconomic status (SES) was divided into two categories: lower and higher (including: urbanization, family size, parental education). Results showed that MUAC and BMI differed significantly with respect to the year of survey, sex and SES category. Both measures were higher within higher SES group compared to the lower one until 1988, while in 2012 convergence of these indicators in both SES categories was observed. Both the year of survey, sex, SES category and interactions between them had higher impact on MUAC than BMI (measured by effect size). Our findings revealed that long-term socioeconomic changes affect MUAC more noticeably than BMI. Therefore MUAC may be a more accurate screening tool.
The complex structure of bile salt hydrolase from Lactobacillus salivarius reveals the structural basis of substrate specificity
Authors: Xu Fuzhou , Hu Xiao-Jian , Singh Warispreet , Geng Wenjing , Tikhonova Irina G. , Lin Jun 
Published: August 2019

AbstractThe gut bacterial bile salt hydrolase (BSH) plays a critical role in host lipid metabolism and energy harvest. Therefore, BSH is a promising microbiome target to develop new therapies to regulate obesity in humans and novel non-antibiotic growth promoters for food animals. We previously reported the 1.90 Å apo crystal structure of BSH from Lactobacillus salivarius (lsBSH). In this study, we soaked the lsBSH crystal with glycocholic acid (GCA), a substrate, and obtained a 2.10 Å structure containing complex of lsBSH bound to GCA and cholic acid (CA), a product. The substrate/product sits in the water-exposed cavity molded by Loops 2 and 3. While the glycine moiety of GCA is exposed into a highly polar pocket, the sterane core of GCA is stabilized by aromatic and hydrophobic interactions. Comparison of product binding with BSH from Clostridium perfringenes reveals a distinct orientation of the sterane core in the binding site. The stability of the substrate-lsBSH complex and the putative catalytic mechanism were explored with molecular dynamics simulations. Site-directed mutagenesis of lsBSH demonstrated that Cys2 and Asn171 are critical for enzymatic activity, while Tyr24, Phe65 and Gln257 contribute to the substrate specificity. Together, this study provides structural insights into BSH-substrate interaction, the mechanism of catalysis and substrate specificity, which facilitate rational design of BSH inhibitors.
Acute Physical Exercise Can Influence the Accuracy of Metacognitive Judgments
Authors: Palmer Matthew A. , Stefanidis Kayla , Turner Ashlee , Tranent Peter J. , Breen Rachel , Kucina Talira , Brumby Laura , Holt Glenys A. , Fell James W. , Sauer James D. 
Published: August 2019

AbstractAcute exercise generally benefits memory but little research has examined how exercise affects metacognition (knowledge of memory performance). We show that a single bout of exercise can influence metacognition in paired-associate learning. Participants completed 30-min of moderate-intensity exercise before or after studying a series of word pairs (cloud-ivory), and completed cued-recall (cloud-?; Experiments 1 & 2) and recognition memory tests (cloud-?spoon; ivory;drill;choir; Experiment 2). Participants made judgments of learning prior to cued-recall tests (JOLs; predicted likelihood of recalling the second word of each pair when shown the first) and feeling-of-knowing judgments prior to recognition tests (FOK; predicted likelihood of recognizing the second word from four alternatives). Compared to no-exercise control conditions, exercise before encoding enhanced cued-recall in Experiment 1 but not Experiment 2 and did not affect recognition. Exercise after encoding did not influence memory. In conditions where exercise did not benefit memory, it increased JOLs and FOK judgments relative to accuracy (Experiments 1 & 2) and impaired the relative accuracy of JOLs (ability to distinguish remembered from non-remembered items; Experiment 2). Acute exercise seems to signal likely remembering; this has implications for understanding the effects of exercise on metacognition, and for incorporating exercise into study routines.
The generalized Vogel-Fulcher-Tamman equation for describing the dynamics of relaxor ferroelectrics
Authors: Levit Rafael , Martinez-Garcia Julio C. , Ochoa Diego A. , García José E. 
Published: August 2019

AbstractRelaxor ferroelectrics (RF) are outstanding materials owing to their extraordinary dielectric, electromechanical, and electro-optical properties. Although their massive applications, they remain to be one of the most puzzling solid-state materials because understanding their structural local order and relaxation dynamics is being a long-term challenge in materials science. The so-called Vogel-Fulcher-Tamman (VFT) relation has been extensively used to parameterize the relaxation dynamics in RF, although no microscopic description has been firmly established for such empirical relation. Here, we show that VFT equation is not always a proper approach for describing the dielectric relaxation in RF. Based on the Adam-Gibbs model and the Grüneisen temperature index, a more general equation to disentangle the relaxation kinetic is proposed. This approach allows to a new formulation for the configurational entropy leading to a local structural heterogeneity related order parameter for RF. A new pathway to disentangle relaxation phenomena in other relaxor ferroics could have opened.
Antibody response against koala retrovirus (KoRV) in koalas harboring KoRV-A in the presence or absence of KoRV-B
Authors: Olagoke O. , Quigley B. L. , Eiden M. V. , Timms P. 
Published: August 2019

AbstractKoala retrovirus (KoRV) is in the process of endogenization into the koala (Phascolarctos cinereus) genome and is currently spreading through the Australian koala population. Understanding how the koala’s immune system responds to KoRV infection is critical for developing an efficacious vaccine to protect koalas. To this end, we analyzed the antibody response of 235 wild koalas, sampled longitudinally over a four-year period, that harbored KoRV-A, and with or without KoRV-B. We found that the majority of the sampled koalas were able to make anti-KoRV antibodies, and that there was a linear increase in anti-KoRV IgG levels in koalas up to approximately seven years of age and then a gradual decrease thereafter. Koalas infected with both KoRV-A and KoRV-B were found to have slightly higher anti-KoRV IgG titers than koalas with KoRV-A alone and there was an inverse relationship between anti-KoRV IgG levels and circulating KoRV viral load. Finally, we identified distinct epitopes on the KoRV envelope protein that were recognized by antibodies. Together, these findings provide insight into the koala’s immune response to KoRV and may be useful in the development of a therapeutic KoRV vaccine.
Proteasome subunit α1 overexpression preferentially drives canonical proteasome biogenesis and enhances stress tolerance in yeast
Authors: Howell Lauren A. , Peterson Anna K. , Tomko Robert J. 
Published: August 2019

AbstractThe 26S proteasome conducts the majority of regulated protein catabolism in eukaryotes. At the heart of the proteasome is the barrel-shaped 20S core particle (CP), which contains two β-rings sandwiched between two α-rings. Whereas canonical CPs contain α-rings with seven subunits arranged α1-α7, a non-canonical CP in which a second copy of the α4 subunit replaces the α3 subunit occurs in both yeast and humans. The mechanisms that control canonical versus non-canonical CP biogenesis remain poorly understood. Here, we have repurposed a split-protein reporter to identify genes that can enhance canonical proteasome assembly in mutant yeast producing non-canonical α4-α4 CPs. We identified the proteasome subunit α1 as an enhancer of α3 incorporation, and find that elevating α1 protein levels preferentially drives canonical CP assembly under conditions that normally favor α4-α4 CP formation. Further, we demonstrate that α1 is stoichiometrically limiting for α-ring assembly, and that enhancing α1 levels is sufficient to increase proteasome abundance and enhance stress tolerance in yeast. Together, our data indicate that the abundance of α1 exerts multiple impacts on proteasome assembly and composition, and we propose that the limited α1 levels observed in yeast may prime cells for alternative proteasome assembly following environmental stimuli.
A label-free optical whole-cell Escherichia coli biosensor for the detection of pyrethroid insecticide exposure
Authors: Riangrungroj Pinpunya , Bever Candace Spier , Hammock Bruce D. , Polizzi Karen M. 
Published: August 2019

AbstractThere is a growing need for low-cost, portable technologies for the detection of threats to the environment and human health. Here we propose a label-free, optical whole-cell Escherichia coli biosensor for the detection of 3-phenoxybenzoic acid (3-PBA), a biomarker for monitoring human exposure to synthetic pyrethroid insecticides. The biosensor functions like a competitive ELISA but uses whole-cells surface displaying an anti-3-PBA VHH as the detection element. When the engineered cells are mixed with 3-PBA-protein conjugate crosslinking that can be visually detected occurs. Free 3-PBA in samples competes with these crosslinks, leading to a detectable change in the output. The assay performance was improved by coloring the cells via expression of the purple-blue amilCP chromoprotein and the VHH expression level was reduced to obtain a limit of detection of 3 ng/mL. The optimized biosensor exhibited robust function in complex sample backgrounds such as synthetic urine and plasma. Furthermore, lyophilization enabled storage of biosensor cells for at least 90 days without loss of functionality. Our whole-cell biosensor is simple and low-cost and therefore has potential to be further developed as a screening tool for monitoring exposure to pyrethroids in low-resource environments.
Glaucoma incidence risk in a cohort of Mayak PA workers occupationally exposed to ionizing radiation
Authors: Bragin Evgeny V. , Azizova Tamara V. , Bannikova Maria V. , Grigoryeva Evgeniya S. , Hamada Nobuyuki 
Published: August 2019

AbstractGlaucoma is a major cause of visual impairment, and secondary glaucoma manifested as neovascular glaucoma has long been known to occur following high-dose fractionated radiation therapy. In contrast, little is known as to whether ionizing radiation exposure causes primary glaucoma, except that a single study in Japanese atomic bomb survivors has reported a significantly increase risk. Therefore, the effect of lower dose and lower dose rate remains unclear. Here we report that in Russian Mayak Production Association workers occupationally exposed to chronic radiation for prolonged periods, incidence of total primary glaucoma and primary open-angle glaucoma is significantly associated with various non-radiation factors (sex, attained age, and cataract diagnosed prior to glaucoma), but neither with cumulative dose from external γ-rays nor with cumulative neutron dose nor with the unweighted sum of cumulative γ and neutron doses. The present results suggest for the first time that chronic radiation exposure does not cause primary glaucoma, although the analyses need to be made in other cohorts exposed at various dose and dose rate.
On the unusual amber coloration of nanoporous sol-gel processed Al-doped silica glass: An experimental study
Authors: Chang Alvin , He Yujuan , Arango Maria A. Torres , Wang Maoyu , Ren Yang , Feng Zhenxing , Chang Chih-Hung , Sierros Konstantinos A. 
Published: August 2019

AbstractSilica is the most abundant component on the earth’s surface. It plays an important role in many natural processes. Silica is also a critical material for a wide range of technical applications such as in optics and electronics. In this work, we discuss our recent experimental observation of the unusual amber coloration of aluminum doped sol-gel glass that has not been reported in the past. We characterized Al-doped sol-gel glasses, prepared at different sintering temperature, using a plethora of techniques to investigate the origin of this unusual coloration and to understand their structural and chemical properties. We used these experimental results to test a number of possible coloring mechanisms. The results suggested this coloring is likely caused by temperature-dependent aluminum-associated defect centers associated with different amorphous-to-crystalline ratios of the annealed sol-gel silica glass structures.
Post-training TMS abolishes performance improvement and releases future learning from interference
Authors: Bang Ji Won , Milton Diana , Sasaki Yuka , Watanabe Takeo , Rahnev Dobromir 
Published: August 2019

AbstractThe period immediately after the offset of visual training is thought to be critical for memory consolidation. Nevertheless, we still lack direct evidence for the causal role of this period to perceptual learning of either previously or subsequently trained material. To address these issues, we had human subjects complete two consecutive trainings with different tasks (detecting different Gabor orientations). We applied continuous theta burst stimulation (cTBS) to either the visual cortex or a control site (vertex) immediately after the offset of the first training. In the vertex cTBS condition, subjects showed improvement on the first task but not on the second task, suggesting the presence of anterograde interference. Critically, cTBS to the visual cortex abolished the performance improvement on the first task and released the second training from the anterograde interference. These results provide causal evidence for a role of the immediate post-training period in the consolidation of perceptual learning.
Metallophores associated with Trichodesmium erythraeum colonies from the Gulf of Aqaba
Authors: Gledhill Martha , Basu Subhajit , Shaked Yeala 
Published: August 2019

Abstract
Trichodesmium is a globally important marine nitrogen fixing cyanobacteria which forms colonies and utilizes atmospherically derived dust as a source for the limiting micro-nutrient iron. Here we report the identification of metallophores isolated from incubations of natural Trichodesmium colonies collected from the Gulf of Aqaba in the Red Sea. Three of our compounds were identified as the ferrioxamine siderophores B, E, and G. The remaining fifteen metallophores had mass to charge ratios that, to our knowledge, are not common to known siderophores. Putative sum formulas suggest most of these compounds were not structurally related to each other. We also found that the novel metallophores readily formed complexes with aluminium and were less specific for iron than the ferrioxamines. In our incubations of Trichodesmium colonies, the abundance of ten of the novel metallophores positively correlated with Trichodesmium biomass, but not with bacterial biomass, whilst ferrioxamine siderophores were more strongly associated with bacterial biomass. We identified ferrioxamines and our novel metallophores in filtered surface seawater samples from the Gulf of Aqaba. However, our novel metallophores were only observed in the surface seawater sample collected at the time of highest Trichodesmium abundance, while ferrioxamines were observed even when Trichodesmium was not present. We hypothesize that the novel metallophores were specifically associated with Trichodesmium colonies. Together with the bacterially produced ferrioxamines they likely contribute to a distinctive “ligandosphere” surrounding the Trichodesmium colonies, with potential implications for metal homeostasis within the colony environment.
Threshold Estimation Using “Chained Stimuli” for Cortical Auditory Evoked Potentials in Individuals With Normal Hearing and Hearing Impairment
Authors: Kalaiah Mohan Kumar , Poovaiah Sanjana , Shastri Usha 
Published: August 2019

Purpose
We investigated the utility of chained stimuli for threshold estimation using cortical auditory evoked potentials (CAEPs) in individuals with normal hearing sensitivity and hearing loss. The effect of the order of frequency in chained stimuli on CAEPs was also studied.

Method
Seventeen individuals with normal hearing and 17 individuals with mild to severe sensorineural hearing loss participated in the study. In individuals with normal hearing, CAEPs were recorded at 80 dB nHL for 4 chained stimuli with different orders of frequencies within them (Chained Stimuli 1 [CS1]: 500, 1000, 2000, 4000 Hz; Chained Stimuli 2: 4000, 2000, 1000, 500 Hz; Chained Stimuli 3: 500, 2000, 1000, 4000 Hz; Chained Stimuli 4: 4000, 1000, 2000, 500 Hz). CAEP threshold estimation was carried out using CS1 in both groups and was compared with behavioral pure-tone thresholds.

Results
CS1 elicited the largest amplitude responses at low and mid frequencies, whereas all 4 stimuli elicited similar amplitude responses at high frequencies. CAEP thresholds were generally within 10–20 dB above the participants' behavioral threshold in both groups. The difference between CAEP threshold and behavioral threshold was less for individuals with hearing loss compared to individuals with normal hearing. There was a significant positive correlation between CAEP threshold and behavioral threshold at all the frequencies.

Conclusions
CS1 could be used to elicit CAEPs for threshold estimation in adult participants with normal hearing and hearing loss of varied degrees with theoretically reduced testing time. The actual time reduction using chained stimuli and the correction factor to be applied to estimate behavioral threshold can be studied in future investigations.
The physical and chemical structure of Sagittarius B2
Authors: Meng F. , Sánchez-Monge Á. , Schilke P. , Padovani M. , Marcowith A. , Ginsburg A. , Schmiedeke A. , Schwörer A. , DePree C. , Veena V. S. , Möller Th. 
Published: August 2019

Context. The giant molecular cloud Sagittarius B2 (hereafter Sgr B2) is the most massive region with ongoing high-mass star formation in the Galaxy. In the southern region of the 40-pc large envelope of Sgr B2, we encounter the Sgr B2(DS) region, which hosts more than 60 high-mass protostellar cores distributed in an arc shape around an extended H II region. Hints of non-thermal emission have been found in the H II region associated with Sgr B2(DS).
Aims. We seek to characterize the spatial structure and the spectral energy distribution of the radio continuum emission in Sgr B2(DS). We aim to disentangle the contribution from the thermal and non-thermal radiation, as well as to study the origin of the non-thermal radiation.
Methods. We used the Very Large Array in its CnB and D configurations, and in the frequency bands C (4–8 GHz) and X (8–12 GHz) to observe the whole Sgr B2 complex. Continuum and radio recombination line maps are obtained.
Results. We detect radio continuum emission in Sgr B2(DS) in a bubble-shaped structure. From 4 to 12 GHz, we derive a spectral index between − 1.2 and − 0.4, indicating the presence of non-thermal emission. We decomposed the contribution from thermal and non-thermal emission, and find that the thermal component is clumpy and more concentrated, while the non-thermal component is more extended and diffuse. The radio recombination lines in the region are found to be not in local thermodynamic equilibrium but stimulated by the non-thermal emission.
Conclusions. Sgr B2(DS) shows a mixture of thermal and non-thermal emission at radio wavelengths. The thermal free–free emission is likely tracing an H II region ionized by an O 7 star, while the non-thermal emission can be generated by relativistic electrons created through first-order Fermi acceleration. We have developed a simple model of the Sgr B2(DS) region and found that first-order Fermi acceleration can reproduce the observed flux density and spectral index.