bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterisation of AmpC Hyper-Producing Escherichia coli from Humans and Dairy Farms Collected in Parallel in the Same Geographical Region
Authors: Alzayn Maryam , Findlay Jacqueline , Schubert Hannah , Mounsey Oliver , Gould Virginia C. , Heesom Kate J. , Turner Katy M. , Barrett David C. , Reyher Kristen K. , Avison Matthew B. 
Published: October 2019

AbstractObjectivesTo characterise putative AmpC hyper-producing 3rd generation cephalosporin-resistant E. coli from dairy farms and their phylogenetic relationships as well as to identify risk factors for their presence; to assess evidence for their zoonotic transmission into the local human populationMethodsProteomics was used to explain differences in antimicrobial susceptibility. Whole genome sequencing allowed phylogenetic analysis. Multilevel, multivariable logistic regression modelling was used to identify risk factors.ResultsIncreased use of amoxicillin-clavulanate was associated with an increased risk of finding AmpC hyper-producers on farms. Expansion of cephalosporin resistance in AmpC hyper-producers was seen in farm isolates with marR mutations (conferring cefoperazone resistance) or when AmpC was mutated (conferring 4th generation cephalosporin and cefoperazone resistance). Phylogenetic analysis confirmed the dominance of ST88 amongst farm AmpC hyper-producers but there was no evidence for acquisition of farm isolates by members of the local human population.ConclusionsIn this two-year surveillance study of 53 dairy farms, AmpC hyper-production was the cause of cefotaxime resistance in 46.2% of E. coli. There was evidence of recent farm-to-farm transmission and of adaptive mutations to expand resistance. Whilst there was no evidence of isolates entering the local human population, efforts to reduce 3rd generation cephalosporin resistance on dairy farms must address the high prevalence of AmpC hyper-producers. The finding that amoxicillin-clavulanate use was associated with increased risk of finding AmpC hyper-producers is important because this is not currently categorised as a highest-priority critically important antimicrobial and so is not currently targeted for specific usage restrictions in the UK.
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases
Authors: Chen Qingyu , Britto Ramona , Erill Ivan , J. Jeffery Constance , Liberzon Arthur , Magrane Michele , Onami Jun-ichi , Robinson-Rechavi Marc , Sponarova Jana , Zobel Justin , Verspoor Karin 
Published: October 2019

AbstractThe volume of biological database records is growing rapidly, populated by complex records drawn from heterogeneous sources. A specific challenge is duplication, that is, the presence of redundancy (records with high similarity) or inconsistency (dissimilar records that correspond to the same entity). The characteristics (which records are duplicates), impact (why duplicates are significant), and solutions (how to address duplication), are not well understood. Studies on the topic are neither recent nor comprehensive. In addition, other data quality issues, such as inconsistencies and inaccuracies, are also of concern in the context of biological databases. A primary focus of this paper is to present and consolidate the opinions of over 20 experts and practitioners on the topic of duplication in biological sequence databases. The results reveal that survey participants believe that duplicate records are diverse; that the negative impacts of duplicates are severe, while positive impacts depend on correct identification of duplicates; and that duplicate detection methods need to be more precise, scalable, and robust. A secondary focus is to consider other quality issues. We observe that biocuration is the key mechanism used to ensure the quality of this data, and explore the issues through a case study of curation in UniProtKB/Swiss-Prot as well as an interview with an experienced biocurator. While biocuration is a vital solution for handling of data quality issues, a broader community effort is needed to provide adequate support for thorough biocuration in the face of widespread quality concerns.
Physiological synchrony promotes cooperative success in real-life interactions
Authors: Behrens F. , Snijdewint J. A. , Moulder R. G. , Prochazkova E. , Sjak-Shie E. E. , Boker S. M. , Kret M. E. 
Published: October 2019

AbstractCooperation is pivotal for society to flourish and prosper. To ease cooperation, humans express and read emotions and intentions via explicit signals or subtle reflections of arousal visible in the face. Evidence is accumulating that humans synchronize these nonverbal expressions, as well as the physiological mechanisms underlying them, potentially promoting cooperative behavior. The current study is designed to verify the existence of this putative linkage between synchrony and cooperation. To that extent, 152 participants played multiple rounds of the Prisoner’s Dilemma game in a naturalistic dyadic interaction setting. During one round of games they could see each other, and during a second round they could not. The results showed that when people’s heart rate and skin conductance level aligned, they cooperated more successfully. Interestingly, for skin conductance level synchrony to boost cooperation, face to face contact was essential. The effect of heart rate synchrony on cooperation was context independent. Skin conductance level, but not heart rate, tended to closely correlate with changes in pupil size and we discuss how the pupil might provide a window to partners’ sympathetic arousal. These findings show how unconscious mechanisms guide social behavior and emphasize the importance of studying social processes between rather than within individuals in real-life interactions.Significance StatementHuman cooperation is remarkable in its scale, complexity, and efficiency. However, whereas people think of themselves as rational agents, they actually partly base their decision to cooperate with someone on gut feelings. These feelings are informed by non-verbal expressions that are picked up implicitly and that synchronize across interaction partners. For the first time, we show that the alignment of people’s arousal over multiple rounds of the Prisoners’ dilemma game predicts cooperative success. Through synchrony, partners converge emotionally, fostering understanding and bonding, which are key ingredients when it comes to successful cooperation. This suggests that successfully cooperating does not depend on individuals, but on the connection between individuals, emphasizing the importance of studying social decision-making processes in real-life settings.
A Solution Method for Predictive Simulations in a Stochastic Environment
Authors: Koelewijn Anne D. , van den Bogert Antonie J. 
Published: October 2019

AbstractThis short communication describes a method to solve predictive simulations of human movements in a stochastic environment using a collocation method. The optimization is performed over multiple noisy episodes of the trajectory, instead of a single episode in a deterministic environment. Each episode used the same control parameters. The method was verified on a torque-driven pendulum swing-up problem. A different optimal trajectory was found in a stochastic environment than in the deterministic environment. Secondly, it was applied to gait to show its application in human movements. We show that nonzero minimum foot clearance during swing is energetically optimal in a stochastic environment. The amount of clearance increased with the noise amplitude.
Evidence of a cellulosic layer in Pandoravirus tegument and the mystery of the genetic support of its biosynthesis
Authors: Brahim Belhaouari Djamal , Baudoin Jean-Pierre , Gnankou Franck , Di Pinto Fabrizio , Colson Philippe , Aherfi Sarah , La Scola Bernard 
Published: October 2019

AbstractPandoraviruses are giant viruses of amoebae with 1 μm-long virions. They have an ovoid morphology and are surrounded by a tegument-like structure lacking any capsid protein nor any gene encoding a capsid protein. In this work, we studied the ultrastructure of the tegument surrounding Pandoravirus massiliensis virions and noticed that this tegument is composed of a peripheral sugar layer, an electron-dense membrane, and a thick electron-dense layer consisting in several tubules arranged in a helicoidal structure resembling that of cellulose. Pandoravirus massiliensis particles were stained by Calcofluor white, a fluorescent dye of cellulose, and the enzymatic treatment of particles by cellulase showed the degradation of the viral tegument. We first hypothesized that the cellulose tegument could be synthesized by enzymes encoded by Pandoravirus. Bioinformatic analyses revealed in Pandoravirus massiliensis, a candidate gene encoding a putative cellulose synthase, with a homology with the BcsA domain, one of the catalytic subunits of the bacterial cellulose synthase, but with a low level of homology. This gene was transcribed during the replicative cycle of Pandoravirus massiliensis, but several arguments run counter to this hypothesis. Indeed, even if this gene is present in other Pandoraviruses, the one of the strain studied is the only one to have this BcsA domain and no other enzymes involved in the synthesis of cellulose could be detected, although we cannot rule out that such genes could have been undetected among the large proportion of Orfans of Pandoraviruses. As an alternative, we investigated whether Pandoravirus could divert the cellulose synthesis machinery of the amoeba to its own account. Indeed, contrary to what is observed in the case of infections with other giant viruses such as mimivirus, it appears that the transcription of the amoeba, at least for the cellulose synthase gene, continues throughout the growth phase of envelopes of Pandoravirus. Finally, we believe that this scenario is more plausible. If confirmed, it could be a unique mechanism in the virosphere.
Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria
Authors: Galbusera Luca , Bellement-Theroue Gwendoline , Urchueguia Arantxa , Julou Thomas , Nimwegen Erik van 
Published: October 2019

AbstractFluorescence flow cytometry is a highly attractive technology for quantifying single-cell expression distributions in bacteria in high-throughput. However, so far there has been no systematic investigation of the best practices for quantitative analysis of such data, what systematic biases exist, and what accuracy and sensitivity can be obtained. We here investigate these issues by systematically comparing flow cytometry measurements of fluorescent reporters in E. coli with measurements of the same strains in microscopic setups and develop a method for rigorous quantitative analysis of fluorescence flow cytometry data.We find that forward and side scatter cannot be used to reliably estimate cell size in bacteria. Second, we show that cytometry measurements contain a large shot noise component that can be easily mistaken for intrinsic noise in gene expression, and show how calibration measurements can be used to correct for this measurement shot noise.To aid other researchers with quantitative analysis of flow cytometry expression data in bacteria, we distribute E-Flow, an open-source R package that implements our methods for filtering cells based on forward and side scatter, and for estimating true biological expression means and variances from the fluorescence signal. The package is available at https://github.com/vanNimwegenLab/E-Flow.
Epidermal cell surface structure and chitin-protein co-assembly determine fiber architecture in the Locust cuticle
Authors: Sviben Sanja , Spaeker Oliver , Bennet Mathieu , Albéric Marie , Dirks Jan-Henning , Moussian Bernard , Fratzl Peter , Bertinetti Luca , Politi Yael 
Published: October 2019

SummaryThe geometrical similarity of helicoidal fiber arrangement in many biological fibrous extracellular matrices, such as bone, plant cell wall or arthropod cuticle, to that of cholesteric liquid mesophases has led to the hypothesis that they may form passively through a mesophase precursor rather than by direct cellular control. In search of direct evidence to support or refute this hypothesis, here, we studied the process of cuticle formation in the tibia of the migratory locust, Locusta migratoria, where daily growth layers arise by the deposition of fiber arrangements alternating between unidirectional and helicoidal structures. Using FIB/SEM volume imaging and scanning X-ray scattering, we show that the epidermal cells determine an initial fiber orientation from which the final architecture emerges by the self-organized co-assembly of chitin and proteins. Fiber orientation in the locust cuticle is therefore determined by both active and passive processes.
Lytic infection with murine gammaherpesvirus 68 activates host and viral RNA polymerase III promoters and enhances non-coding RNA expression
Authors: Knox Ashley N. , Mueller Alice , Medina Eva M. , Clambey Eric T. , van Dyk Linda F. 
Published: October 2019

ABSTRACTRNA polymerase III (pol III) transcribes multiple non-coding (nc) RNAs that are essential for cellular function. Pol III-dependent transcription is also engaged during certain viral infections, including the gammaherpesviruses (γHVs), where pol III-dependent viral ncRNAs promote pathogenesis. Additionally, several host ncRNAs are upregulated during γHV infection and play integral roles in pathogenesis by facilitating viral establishment and gene expression. Here, we sought to investigate how pol III promoters and transcripts are regulated during gammaherpesvirus infection using the murine gammaherpesvirus 68 (γHV68) system. To compare the transcription of host and viral pol III-dependent ncRNAs, we analyzed a series of pol III promoters for host and viral ncRNAs using a luciferase reporter optimized to measure pol III activity. We measured promoter activity from the reporter gene at the translation level via luciferase activity and at the transcription level via RT-qPCR. We further measured endogenous ncRNA expression at single cell-resolution by flow cytometry. These studies demonstrated that lytic infection with γHV68 increased the transcription from multiple host and viral pol III promoters, and further identified the ability of accessory sequences to influence both baseline and inducible promoter activity after infection. RNA flow cytometry revealed the induction of endogenous pol III-derived ncRNAs that tightly correlated with viral gene expression. These studies highlight how lytic gammaherpesvirus infection alters the transcriptional landscape of host cells to increase pol III-derived RNAs, a process that may further modify cellular function and enhance viral gene expression and pathogenesis.IMPORTANCEGammaherpesviruses are a prime example of how viruses can alter the host transcriptional landscape to establish infection. Despite major insights into how these viruses modify RNA polymerase II-dependent generation of messenger RNAs, how these viruses influence the activity of host RNA polymerase III remains much less clear. Small non-coding RNAs produced by RNA polymerase III are increasingly recognized to play critical regulatory roles in cell biology and virus infection. Studies of RNA polymerase III dependent transcription are complicated by multiple promoter types and diverse RNAs with variable stability and processing requirements. Here, we characterized a reporter system to directly study RNA polymerase III-dependent responses during gammaherpesvirus infection and utilized single-cell flow cytometry-based methods to reveal that gammaherpesvirus lytic replication broadly induces pol III activity to enhance host and viral non-coding RNA expression within the infected cell.
Prevalence of atopy and staphylococcal superantigen‐specific immunoglobulin E (IgE) antibodies and total serum IgE in primary cutaneous T‐ and B‐cell lymphoma
Authors: Vonderheid Eric C. , Hamilton Robert G. , Kadin Marshall E. 
Published: October 2019

AbstractThe prevalence of atopy was investigated in 20 patients with Sézary syndrome (SS), 20 patients with plaque phase mycosis fungoides (MF), 9 patients with primary cutaneous marginal zone lymphoma (pcMZL) and 8 patients with primary cutaneous follicle center lymphoma (pcFCL) with the Phadiatop multi‐allergen test. The relationship among serologic atopy, IgE reactivity against Staphyloccocal enterotoxin superantigens, and serum total IgE (IgE‐t) levels and their prognostic implications in SS was investigated. Phadiatop test was positive in 45%, 15%, 33% and 0% of samples of SS, MF, pcMZL and pcFCL, respectively. IgE‐t levels were also increased in SS, pcMZL and marginally MF. No correlation was found with patients’ history of atopic disorders. Staphylococcal superantigen‐specific IgE ≥ 0.35 kUa/L, most often against toxic shock syndrome toxin‐1, was detected in 40% of Sézary samples followed by MF (20%). In the absence of serologic atopy (negative Phadiatop test), IgE‐t levels for patients with SS and MF were not significantly higher than controls whereas the levels for pcMZL remained high. Furthermore, even with a negative Phadiatop test, IgE‐t values were higher in sera of patients with SSAg‐IgE ≥ 0.35 kUa/L vis‐à‐vis < 0.35 kUa/L across all diagnostic categories including controls albeit the difference was statistically significant only for SS. The presence of specific IgE antibodies ≥ 0.35 kUa/L, IgE‐t > 122 kU/L or eosinophils > 500/µL had no impact on survival of patients with SS. These results indicate that a pathogenic link may exist between an atopic diathesis and development of SS and possibly pcMZL
Better continuity of the facial nerve demonstrated in the temporal bone on three‐dimensional T1‐weighted imaging with volume isotropic turbo spin echo acquisition than that with fast field echo at 3.0 tesla MRI
Authors: Haneda Jun , Ishikawa Kazuhiro , Okamoto Kouichirou 
Published: October 2019

AbstractIntroductionThree‐dimensional (3D) T1‐weighted imaging (T1WI) is used for evaluation of the facial nerve. The signal intensity of normal and pathological facial nerves has been well evaluated at both 1.5T and 3.0T MRI after gadolinium (Gd)‐enhancement with various pulse sequences. However, the continuity of the facial nerve has not been evaluated on 3D‐T1WI. This study aims to compare the continuity of the normal facial nerve in the temporal bone demonstrated on T1‐weighted volume isotropic turbo spin echo acquisition (T1‐VISTA), which is a spin‐echo sequence, to that on T1‐weighted fast field echo (T1‐FFE), which is a gradient‐echo sequence, at 3.0T MRI.MethodsForty‐four normal facial nerves in 22 healthy volunteers were imaged with both sequences using 3.0T MRI without Gd‐enhancement. The facial nerves were evaluated visually by two neuroradiologists in four anatomical segments with a 3‐point grading system of continuity. The continuity was assessed by summing the grades of the four segments as a total score. The grades at each segment and the total scores were compared statistically between the T1‐VISTA and T1‐FFE.ResultsThe grades in all segments and the total score were significantly higher with T1‐VISTA than those with T1‐FFE.ConclusionsT1‐VISTA was superior to demonstrate the facial nerve as a continuous anatomical structure in the temporal bone at 3.0T MRI.
Determining the conversion ratios for oral versus sublingual administration of tacrolimus in solid organ transplant recipients
Authors: Al Sagheer Tiba , Enderby Cher Y. 
Published: October 2019

AbstractTacrolimus is utilized as maintenance immunosuppression in solid organ transplant (SOT). Current literature has reported conflicting conversion ratios when transitioning between oral and sublingual tacrolimus, and the exact conversion ratio has not been fully established in SOT. The purpose of this study was to determine the conversion ratios between oral and sublingual tacrolimus needed to achieve equivalent whole blood concentrations in heart, kidney, liver, and lung transplant recipients. A retrospective, single‐center analysis was conducted at Mayo Clinic in Florida. One hundred and eighteen hospitalized SOT recipients who received oral and sublingual tacrolimus during the same inpatient admission from June 1, 2012, through June 1, 2017, were reviewed. The median conversion ratio of sublingual to oral tacrolimus was 1.34 (IQR: 1.03‐1.93) in all SOT, 1.25 (IQR: 1.08‐1.64) in heart transplant, 1.23 (IQR: 1.1‐2.06) in kidney transplant, 1.64 (IQR: 1.27‐2.29) in liver transplant, and 1.34 (IQR: 0.94‐1.93) in lung transplant. A slightly higher dose of oral tacrolimus is needed in the majority of solid organ recipients in our population when converting between sublingual to oral tacrolimus administration.
Real‐world data on healthcare resource consumption and costs before and after kidney transplantation
Authors: Roggeri Daniela Paola , Roggeri Alessandro , Zocchetti Carlo , Cozzolino Mario , Rossi Carlotta , Conte Ferruccio 
Published: October 2019

AbstractEnd‐stage renal disease (ESRD) is increasing worldwide as a consequence of population aging and increasing chronic illness. Treatment consists mostly of dialysis and kidney transplantation (KTx), and KTx offers advantages for life expectancy and long‐term cost reductions compared with dialysis. This study uses the administrative database of the Lombardy Region to analyze the costs of a cohort of patients with ESRD receiving KTx, covering a time period of 24 months before transplant to 12 months after. During 2011, 276 patients underwent kidney transplantation (8.7% preemptive and 91.3% non‐preemptive). In the period before transplantation, the main cost driver was dialysis (66.6% for the period from −24 to −12 months and 73.8% for the period from −12 to 0 months), while in the 12 months after KTx, the most relevant cost was surgery. The total cost −24 to −12 months pre‐KTx was 35 049.2€; the cost −12 to 0 months was 36 745.9€; and the cost 12 months after KTx was 43 805.8€. Non‐preemptive patients showed much higher costs both pre‐ and post‐KTx than preemptive patients. This study highlights how KTx modifies the resource consumption and costs composition of patients with ESRD vs those undergoing dialysis treatment and how KTx may be economically beneficial, especially preemptive intervention.
Racing dragons and remembering aliens: Benefits of playing number and working memory games on kindergartners' numerical knowledge
Authors: Ramani Geetha B. , Daubert Emily N. , Lin Grace C. , Kamarsu Snigdha , Wodzinski Alaina , Jaeggi Susanne M. 
Published: October 2019

AbstractSources that contribute to variation in mathematical achievement include both numerical knowledge and general underlying cognitive processing abilities. The current study tested the benefits of tablet‐based training games that targeted each of these areas for improving the mathematical knowledge of kindergarten‐age children. We hypothesized that playing a number‐based game targeting numerical magnitude knowledge would improve children's broader numerical skills. We also hypothesized that the benefits of playing a working memory (WM) game would transfer to children's numerical knowledge given its important underlying role in mathematics achievement. Kindergarteners from diverse backgrounds (n = 148; 52% girls; Mage = 71.87 months) were randomly assigned to either play a number‐based game, a WM game, or a control game on a tablet for 10 sessions. Structural equation modeling was used to model children's learning gains in mathematics and WM across time. Overall, our results suggest that playing the number game improved kindergarten children's numerical knowledge at the latent level, and these improvements remained stable as assessed 1 month later. However, children in the WM group did not improve their numerical knowledge compared to children in the control condition. Playing both the number game and WM game improved children's WM at the latent level. Importantly, the WM group continued to improve their WM for at least a month after playing the games. The results demonstrate that computerized games that target both domain‐specific and domain‐general skills can benefit a broad range of kindergarten‐aged children.