bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the impact of competing intra- and intermolecular triplet-state quenching on photobleaching and photoswitching kinetics of organic fluorophores
Authors: Smit Jochem H. , van der Velde Jasper H. M. , Huang Jingyi , Trauschke Vanessa , Henrikus Sarah S. , Chen Si , Eleftheriadis Nikolaos , Warszawik Eliza M. , Herrmann Andreas , Cordes Thorben 
Published: July 2018

AbstractWhile buffer cocktails remain the gold-standard for photostabilization and photoswitching of fluorescent markers, intramolecular triplet-state quenchers emerge as an alternative strategy to impart fluorophores with ‘self-healing’ or even functional properties such as photoswitching. In this contribution, we evaluated various combinations of both approaches and show that inter- and intramolecular triplet-state quenching processes compete with each other rather than being additive or even synergistic. Often intramolecular processes dominate the photophysical situation for combinations of covalently-linked and solution-based photostabilizers and photoswitching agents. In this context we identified a new function of intramolecular photostabilizers, i.e., protection of fluorophores from reversible off-switching events caused by solution-additives, which were previously misinterpreted as photobleaching. Our studies also provide practical guidance for usage of photostabilizer-dye conjugates for STORM-type super-resolution microscopy permitting the exploitation of their improved photophysics for increased spatio-temporal resolution. Finally, we provide evidence that the biochemical environment, e.g., proximity of aromatic amino-acids such as tryptophan, reduces the photostabilization efficiency of commonly used buffer cocktails. Not only have our results important implications for a deeper mechanistic understanding of self-healing dyes, but they will provide a general framework to select label positions for optimal and reproducible photostability or photoswitching kinetics.
Alternative splicing and translation play important roles in parallel with transcriptional regulation during rice hypoxic germination
Authors: Chen Mo-Xian , Zhu Fu-Yuan , Wang Feng-Zhu , Ye Neng-Hui , Gao Bei , Chen Xi , Zhao Shan-Shan , Fan Tao , Cao Yun-Ying , Liu Tie-Yuan , Su Ze-Zhuo , Xie Li-Juan , Hu Qi-Juan , Wu Hui-Jie , Xiao Shi , Zhang Jianhua , Liu Ying-Gao 
Published: July 2018

AbstractPost-transcriptional mechanisms, including alternative splicing (AS) and alternative translation initiation (ATI), have been used to explain the protein diversity involved in plant developmental processes and stress responses. Rice germination under hypoxia conditions is a classical model system for the study of low oxygen stress. It is known that there is transcriptional regulation during rice hypoxic germination, but the potential roles of AS and ATI in this process are not well understood. In this study, a proteogenomic approach was used to integrate the data from RNA sequencing, qualitative and quantitative proteomics to discover new players or pathways in the response to hypoxia stress. The improved analytical pipeline of proteogenomics led to the identification of 10,253 intron-containing genes, 1,729 of which were not present in the current annotation. Approximately 1,741 differentially expressed AS (DAS) events from 811 genes were identified in hypoxia-treated seeds in comparison to controls. Over 95% of these were not present in the list of differentially expressed genes (DEG). In particular, regulatory pathways such as spliceosome, ribosome, ER protein processing and export, proteasome, phagosome, oxidative phosphorylation and mRNA surveillance showed substantial AS changes under hypoxia, suggesting that AS responses are largely independent of traditional transcriptional regulation. Massive AS changes were identified, including the preference usage of certain non-conventional splice sites and enrichment of splicing factors in the DAS datasets. In addition, using self-constructed protein libraries by 6-frame translation, thousands of novel proteins/peptides contributed by ATI were identified. In summary, these results provide deeper insights towards understanding the underlying mechanisms of AS and ATI during rice hypoxic germination.
Comprehensive functional screening of taste sensation in vivo
Authors: Han Jisoo , Choi Myunghwan 
Published: July 2018

ABSTRACTThe initial event in taste sensation is mediated by taste cells on the tongue that translate ingested chemicals into cellular signals. Current understanding on this cellular level taste encoding process has relied on ex vivo model systems that cannot fully recapitulate natural cellular microenvironment in vivo. To resolve this methodological limitation, we invented a microfluidics-on-a-tongue imaging chamber that has integrated multichannel microfluidics for auto-controlled tastant delivery. Using this system, we screened over 100 fungiform taste cells to the five basic taste qualities, and obtained comprehensive functional maps. We revealed that taste cells are composed of 70% of single-tuned and 30% of dual-tuned cells, and also discovered a novel population of dual-tuned taste cells encoding a positive valence. We believe that our novel screening platform will pave a way for the deeper understanding of taste coding logic.
Characterization of the role of glycine lipids inBacteroides thetaiotaomicron
Authors: Lynch Alli , Tammireddy Seshu R. , Doherty Mary K. , Whitfield Phillip D. , Clarke David J. 
Published: July 2018

AbstractAcylated amino acids function as important components of the cellular membrane in some bacteria. Biosynthesis is initiated by the N-acylation of the amino acid and this is followed by subsequent O-acylation of the acylated molecule resulting in the production of the mature diacylated amino acid lipid. In this study we use both genetics and liquid chromatography-mass spectrometry (LC-MS) to characterize the biosynthesis and function of novel diacylated glycine lipid (GL) species inBacteroides thetaiotaomicron. We, and others, have previously reported the identification of a gene, namedglsBin this study, that encodes a N-acyltransferase activity responsible for the production of a monoacylated glycine called N-acyl-3-hydroxy-palmitoyl glycine (or commendamide). In all of theBacteroidalesgenomes so far sequenced theglsBgene is located immediately downstream from a gene, namedglsA, also predicted to encode a protein with acyltransferase activity. We use LC-MS to show that co-expression ofglsBandglsAresults in the production of GL inEscherichia coli. We constructed a deletion mutant of theglsBgene inB. thetaiotaomicronand we confirm thatglsBis required for the production of GL inB. thetaiotaomicron. Moreover, we show thatglsBis important for the ability ofB. thetaiotaomicronto adapt to stress and colonize the mammalian gut. Therefore, this report is the first to describe the genetic requirements for the biosynthesis of GL, a novel diacylated amino acids species that contributes to fitness in the human gut bacterium,B. thetaiotaomicron.
Apigenin relaxes rat intrarenal arteries: involvement of Cl− channels and K+ channels
Authors: Jing Yixin , Dong Miaomiao , Liu Yu , Hou Xiaomin , Guo Pengmei , Li Weiping , Zhang Mingsheng , Lv Jiyuan 
Published: July 2018

AbstractThe vasodilator effect of apigenin (API) was demonstrated in a number of vascular beds. We aimed to characterize the vasospasmolytic and electrophysiological effects of apigenin (API) in intrarenal arteries (IRAs). The vascular tone of male rat isolated IRAs was recorded with a myograph. Transmembrane Cl− currents through Ca2+-activated Cl− channels (CaCCs), K+ currents through voltage-gated K+ (Kv) channels and inwardly rectifier K+ (Kir) channels were recorded with patch clamp in the freshly isolated arterial smooth muscle cells (ASMCs). Preincubation with API (10-100 μM) concentration-dependently depressed the contractions induced by KCl, 9,11-dideoxy-9α,11α-methanoepoxy prostaglandin F2α (U46619), phenylephrine and vasopressin without significant preference and the IC50 values were 13.27-26.26 μM. Acute application of API elicited instant relaxations in the IRAs precontracted with these vasoconstrictors and the RC50 values were 5.80-24.33 μM. API relaxation was attenuated by chloride deprivation, CaCC blockers, Kv blocker and nitric oxide synthase inhibitor, but not by Kir blocker and cyclooxygenase inhibitor. At 10-100 μM, API depressed CaCC currents and Kir currents while enhanced Kv currents of IRA ASMCs. The present results demonstrate that API counteracts various vasoconstrictors noncompetitively and nonspecifically and suggest that modulation of CaCCs, Kv and Kir channels of IRA ASMCs is involved in its vasospasmolytic effects.
Exploring the unmapped DNA and RNA reads in a songbird genome
Authors: Laine Veronika N. , Gossmann Toni I. , van Oers Kees , Visser Marcel E. , Groenen Martien A.M. 
Published: July 2018

AbstractBackgroundA widely used approach in next-generation sequencing projects is the alignment of reads to a reference genome. A significant percentage of reads, however, frequently remain unmapped despite improvements in the methods and hardware, which have enhanced the efficiency and accuracy of alignments. Usually unmapped reads are discarded from the analysis process, but significant biological information and insights can be uncovered from this data. We explored the unmapped DNA (normal and bisulfite treated) and RNA sequence reads of the great tit (Parus major) reference genome individual. From the unmapped reads we generatedde novoassemblies. The generated sequence contigs were then aligned to the NCBI non-redundant nucleotide database using BLAST, identifying the closest known matching sequence.ResultsMany of the aligned contigs showed sequence similarity to sequences from different bird species and genes that were absent in the great tit reference assembly. Furthermore, there were also contigs that represented knownP. majorpathogenic species. Most interesting were several species of blood parasites such asPlasmodiumandTrypanosoma.ConclusionsOur analyses revealed that meaningful biological information can be found when further exploring unmapped reads. It is possible to discover sequences that are either absent or misassembled in the reference genome and sequences that indicate infection or sample contamination. In this study we also propose strategies to aid the capture and interpretation of this information from unmapped reads.
Efficient propagation of misfolded tau between individual neurons occurs in absence of degeneration
Authors: Hallinan Grace I , Vargas-Caballero Mariana , West Jonathan , Deinhardt Katrin 
Published: July 2018

AbstractIn Alzheimer’s disease, misfolded tau protein propagates through the brain in a prion-like manner along connected circuits. Tauopathy correlates with significant neuronal death, but the links between tau aggregation, propagation, neuronal dysfunction and death remain poorly understood, and the direct functional consequences for the neuron containing the tau aggregates are unclear. Here, by monitoring individual neurons within a minimal circuit, we demonstrate that misfolded tau efficiently spreads from presynaptic to postsynaptic neurons. Within postsynaptic cells, tau aggregates initially in distal axons, while proximal axons remain free of tau pathology. In the presence of tau aggregates neurons display axonal transport deficits, but remain viable and electrically competent. This shows that misfolded tau species are not immediately toxic to neurons, and suggests that propagation of misfolded tau is an early event in disease, occurring prior to neuronal dysfunction and cell death.
Conserved and divergent development of brainstem vestibuloacoustic nuclei
Authors: Lipovsek Marcela , Wingate Richard JT 
Published: July 2018

ABSTRACTVestibular function was established early in vertebrates and has remained, for the most part, unchanged. In contrast, tetrapods underwent independent evolutionary processes to solve the problem of hearing on land. Thus, the vestibuloacoustic nuclei of the hindbrain provide an ideal framework on which to address the participation of developmental processes to the evolution of neuronal circuits.We employed an electroporation strategy to unravel the contribution of dorsoventral and axial lineages to the development of the chick hindbrain vestibular and auditory nuclei. We compare the chick developmental map with recently stablished genetic fate-maps of the mouse hindbrain. Overall, we find considerable conservation of developmental origin for the vestibular nuclei. In contrast, auditory hindbrain development echoes the complex evolutionary history of the auditory system. In particular, we find that the developmental origin of a chick sound localisation circuit supports its emergence from an ancient vestibular network, unrelated to the analogous mammalian counterpart.
Modeling and simulation of drag force for coated PET fabric with silica nano particles
Authors: Nazemi Siamak , Khajavi Ramin , Rabie Far Hamidreza , Yazdanshenas Mohammad Esmail , Raad Manouchehr 
Published: July 2018

Purpose
This paper is based on the simulation of wind tunnel experiment for better understanding and predicting the behavior of PET fabric in the wind tunnel. This software calculates the drag force of fabric, illustrates pressure in the surrounding of airfoil and velocity of wind in the tunnel during different angles of attack (0°, 45° and 90°). The paper aims to discuss these issues.

Design/methodology/approach
The sol-gel method was applied for the synthesis of silica nano particles. So, PET fabric was coated with precursor (Tetra ethyl ortho silicate) solution first and the process continued on PET fabric. The morphology of obtained hydrophobic fabric samples and their surface roughness was observed and determined by atomic microscopes (AFM and SEM). Experimental data were used for simulation and modeling, and then results were interpreted.

Findings
It was concluded that the surface roughness and its amount can play a significant role in the drag reduction of PET fabric, and surface roughness can change the boundary layer from laminar to turbulent.

Originality/value
At 45 degrees angle of attack, larger boundary layer separation results in a large increase in the drag force. This model is useful for predicting flow behavior in the experimental wind tunnel.
Factors associated with professional identity, job satisfaction and burnout for occupational therapists working in eating disorders: A mixed methods study
Authors: Devery Helen , Scanlan Justin Newton , Ross Jessica 
Published: July 2018

BackgroundOccupational therapists employed within eating disorder services provide unique and valuable interventions. However, existing literature suggests that occupational therapists in this area may be at substantial risk of experiencing poor work‐related wellbeing (e.g., high levels of burnout and low levels of job satisfaction). Despite these risks, no previous studies have explored the work‐related experiences of occupational therapists in this specialist area of practice.ObjectivesTo explore challenges faced by occupational therapists working in eating disorders, their sense of professional identity, burnout and job satisfaction.MethodA mixed methods sequential design was adopted. Australian occupational therapists working in eating disorder services were invited to complete a survey exploring job challenges, burnout, professional identity and job satisfaction. Follow‐up interviews were conducted and analysed using Braun and Clarke's method of thematic analysis.ResultsTen occupational therapists (representing approximately 50% of the workforce in this specialist area in Australia) participated. There were strong correlations between challenges from the client group and exhaustion (a component of burnout), and moderate correlations between stronger professional identity, pressure to adopt generalist approaches and exhaustion. Qualitative analysis suggested job challenges arose from structural, personal and client‐related sources, especially underutilisation of occupational therapy and pressure to adopt non‐occupation‐based practices. Participants reported using strategies such as maintaining an occupation focus, supervision, professional interactions and maintaining work–life balance to mitigate job stress.ConclusionOccupational therapists working in eating disorders do face challenges. These are particularly related to the lack of evidence base for occupational therapy in this area. Future research should focus on developing further evidence for occupational therapy in eating disorders and designing outcome measures that capture improvements in daily functioning. These efforts would strengthen the role of occupational therapy and may reduce the risk of burnout and improve job satisfaction and sense of professional identity.
Mifepristone in the treatment of the ectopic adrenocorticotropic hormone syndrome
Authors: Wannachalee Taweesak , Turcu Adina F. , Auchus Richard J. 
Published: July 2018

SummaryObjectivesMifepristone, a glucocorticoid receptor antagonist, can be used to manage hypercortisolism in patients with ectopic adrenocorticotropic hormone syndrome (EAS) when surgical cure is not feasible. Outcomes of EAS patients treated with mifepristone have been limited to reports of isolated cases. We aimed to determine the efficacy and limitations of mifepristone in the treatment of EAS and to compare outcomes with those of patients who underwent bilateral adrenalectomy.MethodA retrospective cohort study of EAS patients from the University of Michigan between 1997 and 2017 was conducted.ResultsOf the 55 patients with EAS, 16 were treated with mifepristone: eight neuroendocrine tumours, two carcinomas and six occult tumours. Treatment with mifepristone was most commonly prompted by psychosis, uncontrolled glucose and/or hypertension. The median maintenance dose was 600 mg/d. Amelioration of psychosis was observed within 48 hours in 3/3 patients, and the glycaemic control was improved in 14/16 patients. The median duration of treatment was 9 months, and three patients were treated for more than 24 months. The overall survival at 24 months was equivalent between patients with EAS treated with mifepristone vs bilateral adrenalectomy (N = 12) (P = 0.6).ConclusionsMifepristone is effective in treating EAS for over 2 years, and survival was not different from that of patients treated with bilateral adrenalectomy. Aggressive concomitant therapy for hypokalaemia and hypertension is necessary.
Fine‐needle aspiration in all thyroid incidentalomas at 18F‐FDG PET/CT: Can EU‐TIRADS revise the dogma?
Authors: Trimboli Pierpaolo , Paone Gaetano , Treglia Giorgio , Virili Camilla , Ruberto Teresa , Ceriani Luca , Piccardo Arnoldo , Giovanella Luca 
Published: July 2018

SummaryObjectiveFocal thyroid incidentalomas (TIs) are observed in 2% of 18F‐FDG PET/CT representing malignancy in one‐third of cases. Currently, due to the lack of evidence on their optimal management, guidelines suggest fine‐needle aspiration cytology (FNAC). The study aim was to evaluate the role of ultrasound evaluation according to EU‐TIRADS to assess the risk of TIs and inform FNAC prescriptions.DesignWe retrospectively reviewed 18F‐FDG PET/CT TIs recorded during the period 2014‐2017. Enrolled were TIs with histological outcome and autonomous nodules. Cases with uncertain matching between 18F‐FDG PET/CT, ultrasound and histology were excluded.ResultsAccording to the selection criteria, 75 TIs, being 13 (17.3%) malignant and 62 (82.7%) benign, were included. Cancers had significantly higher SUVmax and SUVmax ratio (Mann‐Whitney P < 0.01) than benign, and the most accurate cut‐offs were >7.1 and >3.65, respectively. At ultrasound, the cancer rate was 0% in EU‐TIRADS 2, 2.9% in EU‐TIRADS 3, 4.2% in EU‐TIRADS 4% and 78.6% in EU‐TIRADS 5 (chi‐squared P < 0.001). Sensitivity, specificity, PPV, NPV and accuracy for malignancy were 92%, 64%, 35%, 98% and 69% for SUVmax; 85%, 68%, 36%, 96% and 71% for SUVmax ratio; and 85%, 95%, 79%, 97% and 93% for EU‐TIRADS, respectively. The absence of all these three features reached a specificity of 97.1%.ConclusionsEU‐TIRADS, within a clinical careful approach, can discriminate with significant accuracy lesions at high risk of malignancy from those at low risk among TIs at 18F‐FDG PET/CT. Additionally, a centre‐based threshold for SUV parameters should be useful for the initial assessment of these lesions during PET/CT reading and reporting.
Intra‐ and inter‐examiner agreement when assessing radiographic implant bone levels: Differences related to brightness, accuracy, participant demographics and implant characteristics
Authors: Walton Terry R. , Layton Danielle M. 
Published: July 2018

AbstractObjectivesEvaluate intra‐ and inter‐examiner agreement of radiographic marginal bone level (MBL) assessment around Brånemark single implants; and whether agreement related to radiograph brightness, discrimination level (accuracy), participant demographics or implant characteristics.Materials and MethodsSeventy‐four participants assessed MBLs of 100 digital radiographs twice with normal brightness, and twice with increased brightness. Intra‐examiner agreement with and without increased brightness to the same thread, and within one thread; and inter‐examiner agreement as compared with the group (defined by the mode) for the first assessments with and without increased brightness, to the same thread, and within one thread were calculated with Cohen's Kappa. Relationships between agreement, thread discrimination level (accuracy), brightness, participant and implant characteristics were explored.ResultsWhen assessing 100 “Normal” radiographs twice, a participant on average assessed 24% differently to themselves (poor intra‐examiner agreement, median Kappa 0.58, range 0.21–0.82); and 28% differently to other participants (poor inter‐examiner agreement, median Kappa 0.53, range 0.05–0.80). Agreement within examiners improved when radiographs were “Bright” (median Kappa 0.58 vs. 0.62, p < 0.001, accuracy to same thread; median Kappa 0.94 vs. 0.96, p < 0.001, accuracy within one thread). Agreement between examiners was neither better nor worse when radiographs were “Bright” (median Kappa 0.53 vs. 0.55, p = 0.64, accuracy to same thread; median Kappa 0.93 vs. 0.93, p = 0.23, accuracy within one thread). Intra‐ and inter‐examiner agreements were lower when accuracy to the same thread was required (p < 0.001, p < 0.001). Neither intra‐ nor inter‐examiner agreement related to age, time since graduation, specialty, viewing device, implant experience, external hex familiarity, periimplantitis treatment experience, implant location or width (p‐values 0.05–0.999). Intra‐examiner agreement increased across dental assistants (n = 11), general dentists (n = 16) and specialists (n = 47) (“Bright” assessments, p = 0.045, median Kappa's 0.55, 0.60, 0.65 respectively); and for females (n = 8, males = 58) (“Normal” assessments, p = 0.019, median 0.68 vs. 0.55), but female numbers were low.ConclusionsAgreement within and between examiners when assessing MBLs was poor. Disagreement occurred around 25% of the time, potentially affecting consistent disease assessments. No participant or implant characteristic clearly affected agreement. Brighter radiographs improved intra‐examiner agreement. Overall, perceived MBL changes below 1 mm are likely due to human, not biological variation.