bluuebunny/crossref_metadata_2025 huggingface dataset:
Anatomical and behavioral impact of a lentiviral tool tapping onto hippocampal serotonin reuptake in rats
Authors: Zoratto Francesca , Buccheri Clelia , Mura Romina , Altabella Luisa , Vanneste Marion , Villotte Marie , Laviola Giovanni , Dauphin Francois , Paizanis Eleni , Adriani Walter , Canese Rossella
Published: October 2019

We aimed at the further characterization of rats in which SERT gene silencing was achieved by hippocampal injection of a lentiviral vector, carrying three si‐RNA to block SERT mRNA at 66% of normal levels. Improved self‐control and reduced restlessness were already demonstrated in these rats. Present further studies consisted of male adult rats, bilaterally inoculated within the hippocampus; control rats received lentivirus particles inactivated with heat. Both groups were maintained in isolation for 5 months, starting from inoculation. Neurochemical changes were studied by proton magnetic resonance spectroscopy (1H‐MRS): we found increased hippocampal viability and bioenergetic potential; however, rats showed a behaviorally depressive pattern, also characterized by enhanced affiliation. Based on the extent of such effects, the whole lenti‐SERT group was divided into two subgroups, termed intermediate‐ and extreme‐ phenotype profiles. While all rats had a widespread modification within dorsal/ventral striatum, amygdala, and hypothalamus, only the former subgroup showed an involvement of Raphé medialis, while, for the latter subgroup, an increase of SERT within hippocampus was unexpectedly caused. Within the less‐affected “intermediate” rats, hippocampal 5‐HT7 receptors were down‐modulated, and also similarly within substantia nigra, septum, and neocortex. This picture demonstrates that additional rather than fewer neurobiological changes accompany a lower phenotypic expression. Overall, tapping hippocampal SERT affected the balance between habits versus strategies of coping by promoting morphogenetic processes indicative of a serotonergic fiber plasticity. Supplementary studies about serotonergic dynamics and neurogenesis within fronto‐striatal circuits are needed.
Application of a cellulose filter aid in municipal sewage sludge dewatering and drying: Jar, pilot, and factory scale
Authors: Shi Qi , Lu Yufei , Guo Wenjing , Wang Tianrun , Zhu Qinyun , Zhang Yaxian , Wang Hongtao , Li Fengting , Xu Taiming , Li Chunjiang
Published: October 2019

Cellulose filter aid (CFA), a skeleton builder, has been studied for sludge conditioning at laboratory scale because of its function in reducing compressibility of sludge cake. However, there are few practical applications of CFA at the pilot and factory scales. In this study, we combined CFA with an advanced sludge dewatering technology, in practical applications. For jar test, the optimum CFA dose was 3 wt.% dry solid (DS); furthermore, the combination of CFA with polyaluminum chloride (PAC) and polyacrylamide (PAM) resulted in the lowest moisture content (73.92%) and the highest calorific value (13,628 kJ/kg) of the sludge cake. In the pilot test, the 5 wt.% DS of the CFA resulted in the optimal sludge feeding amount. In the factory test, the optimal CFA dose was further increased to 10%, and the amount of sludge feeding in a single batch was 20.5% higher than that without CFA. The optimal dose of CFA in the jar–pilot–factory test increased, which may occur because the CFA more easily penetrated the cake and performed better in building the skeleton when the sludge cake was thin. This study could provide a reference for the application of CFA and other skeleton builders in sludge dewatering and drying.

Practitioner points

An advanced sludge treatment process—low‐temperature vacuum dewatering and drying was tested.

Cellulose filter aid showed good effect in jar test, pilot test, and factory test.

When the scale of the experiment was from jar to factory, the optimal dosage of the cellulose filter aid was magnified.

The amplification phenomenon of optimal dosage was related to the distribution pattern of cellulose filter aid in different thickness mud cakes.
Thoracoscopic Resection of Congenital Lung Malformation: Looking for the Right Preoperative Assessment
Authors: Macchini Francesco , Borzani Irene , Cavalli Silvia , Morandi Anna , D'Angelo Ida Daniela , Zanini Andrea , Ferrari Carlo , Ichino Martina , Leva Ernesto
Published: October 2019

Introduction Consensus on the best postnatal radiological evaluation of congenital lung malformations (CLMs) is still lacking. In recent years, the interest on magnetic resonance imaging (MRI) has grown, but its role is still unknown.

Aim The aim of the study was to identify the best preoperative diagnostic assessment for CLM.

Materials and Methods All patients with a prenatal suspicion of CLM between January 2014 and February 2018 were studied. Asymptomatic newborns underwent MRI, during spontaneous sleep without contrast. Patients with a positive MRI were scheduled for computed tomography (CT) within the fourth month of life. Thoracoscopic resection was performed in cases with a pathological CT. MRI, CT, and surgical findings were compared based on dimension, localization, and features of the CLM using the Cohen's kappa test (K).

Results A total of 20 patients were included (10 males). No difference was found in the diameter and site of the lesions always localized in the same side (K = 1) and in the same pulmonary lobe (K = 1). Infants who underwent thoracoscopic resection included: three congenital pulmonary airway malformations (CPAMs), five extralobar and eight intralobar sequestrations (bronchopulmonary sequestrations [BPSs]), three bronchogenic cysts, and one congenital emphysema. The concordance between MRI and CT and between radiological investigations and pathology was satisfactory for the greatest part of the studied variables. MRI showed sensitivity of 100%, specificity of 82%, positive predictive value of 50% and negative predictive value of 100% for CPAM and 77, 100, 100, and 80% for BPS, respectively.

Conclusion MRI proved to be a reliable diagnostic investigation for CLM with high sensitivity and specificity. Early MRI in spontaneous sleep without contrast and preoperative contrast CT scan is a valuable preoperatory assessment.
Premorbid Hemostasis in Women with a History of Pregnancy Loss
Authors: Peshkova Alina D. , Safiullina Svetlana I. , Evtugina Natalia G. , Baras Yelena S. , Ataullakhanov Fazoil I. , Weisel John W. , Litvinov Rustem I.
Published: October 2019

Background Congenital and acquired hemostatic disorders are among the pathogenic factors of pregnancy loss. Studying mechanistic relations between impaired hemostasis and fetal losses is important for the prognosis and prophylaxis of obstetric complications.

Objective This article aims to establish latent hemostatic disorders in nonpregnant women as an important premorbid risk factor of pregnancy loss.

Methods and Results Hemostasis was characterized using two relatively new in vitro assays, namely thrombodynamics (spatial clot growth) and kinetics of blood clot contraction, which together reflect the hemostatic or thrombotic potential. In addition, platelet functionality was assessed using flow cytometry. Our study included 50 women with a history of pregnancy loss and 30 parous women without previous obstetric complications. In patients with pregnancy loss, hypercoagulability was observed along with significant impairment of blood clot contraction associated with chronic platelet activation and dysfunction. Both hypercoagulability and defective clot contraction were significantly more pronounced in patients with a history of three or more miscarriages compared with patients with a history of one or two miscarriages. In addition, a significant inhibition of clot contraction was found in patients with miscarriage occurring after 10 weeks of gestation compared with those who lost a fetus earlier in pregnancy.

Conclusion These results indicate that chronic hypercoagulability and impaired clot contraction constitute a premorbid status in patients with pregnancy loss. The data confirm a significant pathogenic role of hemostatic disorders in pregnancy loss and suggest the predictive value of thrombodynamics and blood clot contraction assays in evaluating the risk of pregnancy loss.
A simplified model for understanding the performance of two-pot enclosed mud cookstoves
Authors: Parajuli Ayush , Agrawal Saurabh , Tharu Janak Kumar , Kamat Anil Kumar , Jha Ajay Kumar , Darlami Hari Bahadur
Published: October 2019

The objective of this study is to develop a mathematical model for a two-pot enclosed mud cookstove. A new model has been developed combining transient heat transfer, combustion chemistry and fluid flow. The model can be used for variation of the operation and design parameters. The model predicts performance parameters such as efficiency, boiling time, excess air ratio (EAR), transient wall, flame and char temperature. For an input power of 5.1 kW, the estimated overall efficiency, EAR and boiling time were 17.1%, 1.97 and 43 minutes, respectively. The model outcome is compared with experimental results. Further, 10 parameters are varied and their impact on cookstove performance is analysed. The optimum dimension for the door opening, combustion-chamber height and wall thickness are suggested. Therefore, this study can serve as an effective tool for cookstove design.
Forest Road Status Assessment Using Airborne Laser Scanning
Authors: Waga Katalin , Tompalski Piotr , Coops Nicholas C , White Joanne C , Wulder Michael A , Malinen Jukka , Tokola Timo
Published: October 2019

Forest roads allow access for silvicultural operations, harvesting, recreational activities, wildlife management, and fire suppression. In British Columbia, Canada, roads that are no longer required must be deactivated (temporarily, semipermanently, or permanently) in order to minimize the impact on the overall forested ecosystem. However, the remoteness and size of the road network present challenges for monitoring. Our aim was to examine the utility of airborne laser scanning data to assess the status and quality of forest roads across 52,000 hectares of coastal forest in British Columbia. Within the forest estate, roads can be active or deactivated, or have an unknown status. We classified road segments based on the vegetation growth on the road surface, and edges, by classifying the height distribution of airborne laser scanning returns within each road segment into four groups: no vegetation, minor vegetation, dense understory vegetation, and dense overstory vegetation. Validation indicated that 73 percent of roads were classified correctly when compared to independent field observations. The majority were classified as active roads with no vegetation or deactivated with dense vegetation. The approach presented herein can aid forest managers in verifying the status of the roads in their management area, especially in remote areas where field assessments are costly and time-consuming.
Effiiency of the Essential Oil of Porophyllum linaria (Asteraceae) a Mexican Endemic Plant Against Sitophilus zeamais (Coleoptera: Curculionidae)
Authors: Hernández-Cruz Julián , Luna-Cruz Alfonso , Loera-Alvarado Esperanza , Villanueva-Sánchez Evert , Landero-Valenzuela Nadia , Zárate-Nicolás Baldomero Hortencio , Diego-Nava Fidel , Granados-Echegoyen Carlos A
Published: October 2019

The insecticidal and repellent effect of essential oil isolated from fresh leaves of Porophyllum linaria on maize weevil was evaluated, as well as the effect on the grain germination after treated. In total, 28 constituents were identified by gas chromatography coupled with mass spectrometry accounting for 99.86% of whole essential oil. The main majority compounds were β-myrcene (41.94%), D-limonene (20.29%), and estragole (20.03%). Contact toxicity significantly increased with dose and time after treatment. With the 800 ppm (highest concentration), the mortality (%) obtained for the tenth and fifteenth day was 43 and 82%, respectively, whereas with 50 ppm (lowest concentration) 30% mortality was obtained at the end of the experiment (fifteenth day). At 15 d (end of the experiment), the LC50 y LC90 were obtained with values of 329.01 ± 44.35 y 1058.86 ± 117.76 ppm, respectively. For a concentration of 800 ppm, a selection index of zero was obtained, indicating the preference of the pest to the untreated maize (control). The maize grains germination test showed a significant reduction both in the length of hypocotyl and radicle of maize grain. So, in the highest dose, the hypocotyl and radicle length was 1.40 ± 0.34 and 9.14 ± 0.55 cm, respectively, whereas the control group registered 3.28 ± 0.39 and 13.02 ± 0.97 cm, respectively. This finding is promising since as it could result in the identification of botanical substances capable of suppressing maize weevil, Sitophilus zeamais development.
Composition Primer: An Educator’s Guide to Teaching Foundational Composition Skills for Music Therapy
Authors: Winter Patricia , Haines James
Published: October 2019

The purpose of this article is to outline foundational techniques and strategies that music therapy educators can use to teach students to compose music for clinical practice. The overarching goals are to highlight the importance of therapeutic design and rational, and the intentional use of musical form and function to address clinical goals and objectives. The techniques described can be implemented in the classroom, with the goal of supporting students to transfer these skills to fieldwork and internship experiences.
Normative and isolated rapid eye movement sleep without atonia in adults without REM sleep behavior disorder
Authors: Feemster John C , Jung Youngsin , Timm Paul C , Westerland Sarah M , Gossard Thomas R , Teigen Luke N , Buchal Lauren A , Cattaneo Elena F D , Imlach Charlotte A , Mccarter Stuart J , Smith Kevin L , Boeve Bradley F , Silber Michael H , St Louis Erik K
Published: October 2019

Study Objectives

Values for normative REM sleep without atonia (RSWA) remain unclear. Older age and male sex are associated with greater RSWA, and isolated elevated RSWA has been reported. We aimed to describe normative RSWA and characterize isolated RSWA frequency in adults without REM sleep behavior disorder (RBD).

Methods

We visually quantified phasic, “any,” and tonic RSWA in the submentalis (SM) and anterior tibialis (AT) muscles, and the automated Ferri REM Atonia Index during polysomnography in adults without RBD aged 21–88. We calculated RSWA percentiles across age and sex deciles and compared RSWA in older (≥ 65) versus younger (<65) men and women. Isolated RSWA (exceeding diagnostic RBD cutoffs, or >95th percentile) frequency was also determined.

Results

Overall, 95th percentile RSWA percentages were SM phasic, any, tonic = 8.6%, 9.1%, 0.99%; AT phasic and “any” = 17.0%; combined SM/AT phasic, “any” = 22.3%, 25.5%; and RAI = 0.85. Most phasic RSWA burst durations were ≤1.0 s (85th percentiles: SM = 1.07, AT = 0.86 seconds). Older men had significantly higher AT RSWA than older women and younger patients (all p < 0.04). Twenty-nine (25%, 18 men) had RSWA exceeding the cohort 95th percentile, while 17 (14%, 12 men) fulfilled diagnostic cutoffs for phasic or automated RBD RSWA thresholds.

Conclusions

RSWA levels are highest in older men, mirroring the demographic characteristics of RBD, suggesting that older men frequently have altered REM sleep atonia control. These data establish normative adult RSWA values and thresholds for determination of isolated RSWA elevation, potentially aiding RBD diagnosis and discussions concerning incidental RSWA in clinical sleep medicine practice.
Predictors of long-term adherence to continuous positive airway pressure in patients with obstructive sleep apnea and cardiovascular disease
Authors: Van Ryswyk Emer , Anderson Craig S , Antic Nicholas A , Barbe Ferran , Bittencourt Lia , Freed Ruth , Heeley Emma , Liu Zhihong , Loffler Kelly A , Lorenzi-Filho Geraldo , Luo Yuanming , Margalef Maria J Masdeu , McEvoy R Doug , Mediano Olga , Mukherjee Sutapa , Ou Qiong , Woodman Richard , Zhang Xilong , Chai-Coetzer Ching Li
Published: October 2019

Study Objectives

Poor adherence to continuous positive airway pressure (CPAP) commonly affects therapeutic response in obstructive sleep apnea (OSA). We aimed to determine predictors of adherence to CPAP among participants of the Sleep Apnea and cardioVascular Endpoints (SAVE) trial.

Methods

SAVE was an international, randomized, open trial of CPAP plus usual care versus usual care (UC) alone in participants (45–75 years) with co-occurring moderate-to-severe OSA (≥12 episodes/h of ≥4% oxygen desaturation) and established cardiovascular (CV) disease. Baseline sociodemographic, health and lifestyle factors, OSA symptoms, and 1-month change in daytime sleepiness, as well as CPAP side effects and adherence (during sham screening, titration week, and in the first month), were entered in univariate linear regression analyses to identify predictors of CPAP adherence at 24 months. Variables with p <0.2 were assessed for inclusion in a multivariate linear mixed model with country, age, and sex included a priori and site as a random effect.

Results

Significant univariate predictors of adherence at 24 months in 1,121 participants included: early adherence measures, improvement in daytime sleepiness at 1 month, fixed CPAP pressure, some measures of OSA severity, cardiovascular disease history, breathing pauses, and very loud snoring. While observed adherence varied between countries, adherence during sham screening, initial titration, and the first month of treatment retained independent predictive value in the multivariate model along with fixed CPAP pressure and very loud snoring.

Conclusions

Early CPAP adherence had the greatest predictive value for identifying those at highest risk of non-adherence to long-term CPAP therapy.

Clinical Trial Registration

SAVE is registered with clinicaltrials.gov (NCT00738179).
Posttraumatic stress disorder increases the odds of REM sleep behavior disorder and other parasomnias in Veterans with and without comorbid traumatic brain injury
Authors: Elliott Jonathan E , Opel Ryan A , Pleshakov Dennis , Rachakonda Tara , Chau Alexander Q , Weymann Kristianna B , Lim Miranda M
Published: October 2019

Study Objectives

To describe the crude prevalence of rapid eye movement (REM) sleep behavior disorder (RBD) following traumatic brain injury (TBI) and posttraumatic stress disorder (PTSD) in Veterans, given potential relationships between TBI, PTSD, RBD, and neurodegeneration.

Methods

Veterans (n = 394; 94% male; 54.4 ± 15.5 years of age) were prospectively/cross-sectionally recruited from the VA Portland Health Care System and completed in-lab video-polysomnography and questionnaires. TBI and PTSD were assessed via diagnostic screening and medical record review. Subjects were categorized into four groups after assessment of REM sleep without atonia (RSWA) and self-reported dream enactment: (1) “Normal,” neither RSWA nor dream enactment, (2) “Other Parasomnia,” dream enactment without RSWA, (3) “RSWA,” isolated-RSWA without dream enactment, and (4) “RBD,” RSWA with dream enactment. Crude prevalence, prevalence odds ratio, and prevalence rate for parasomnias across subjects with TBI and/or PTSD were assessed.

Results

Overall prevalence rates were 31%, 7%, and 9% for Other Parasomnia, RSWA, and RBD, respectively. The prevalence rate of RBD increased to 15% in PTSD subjects [age adjusted POR: 2.81 (1.17–4.66)] and to 21% in TBI + PTSD subjects [age adjusted POR: 3.43 (1.20–9.35)]. No subjects met all diagnostic criteria for trauma-associated sleep disorder (TASD), and no overt dream enactment was captured on video.

Conclusions

The prevalence of RBD and related parasomnias is significantly higher in Veterans compared with the general population and is associated with PTSD and TBI + PTSD. Considering the association between idiopathic-RBD and synucleinopathy, it remains unclear whether RBD (and potentially TASD) associated with PTSD or TBI + PTSD similarly increases risk for long-term neurologic sequelae.
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

Objectives

To 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 population

Methods

Proteomics 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.

Results

Increased 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.

Conclusions

In 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

The 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

Cooperation 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 Statement

Human 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

This 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

Pandoraviruses 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

Fluorescence 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

The 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.
The human sperm beats anisotropically and asymmetrically in 3D
Authors: Gadêlha Hermes , Hernández-Herrera Paul , Montoya Fernando , Darszon Alberto , Corkidi Gabriel
Published: October 2019

The canonical beating of the human sperm flagellum is postulated to be symmetric. This is despite the reported asymmetries inherent to the flagellar axonemal structure, from distribution and activation of molecular motors to, even, the localisation of regulatory ion channels. This raises a fundamental question: how symmetric beating is possible within such intrinsically asymmetric flagellar complex? Here, we employ high-speed 3D imaging with mathematical analysis capable of resolving the flagellar movement in 4D (3D+time). This reveals that the human sperm beating is both anisotropic and asymmetric, and composed by a superposition of two transversal waves: an asymmetric travelling wave and a symmetric standing wave. This novel anisotropic travelling-pulsation mechanism induces sperm rolling self-organisation and causes a flagellar kinematic illusion, so that the beat appears to be symmetric if observed with 2D microscopy. The 3D beating anisotropy thus regularises the intrinsic flagellar asymmetry to achieve symmetric side-to-side movement and straight-line swimming.
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

RNA 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.

IMPORTANCE

Gammaherpesviruses 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

The 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

Introduction

Three‐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.

Methods

Forty‐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.

Results

The grades in all segments and the total score were significantly higher with T1‐VISTA than those with T1‐FFE.

Conclusions

T1‐VISTA was superior to demonstrate the facial nerve as a continuous anatomical structure in the temporal bone at 3.0T MRI.
A new conception of visual aesthetic sensitivity
Authors: Corradi Guido , Chuquichambi Erick G. , Barrada Juan Ramón , Clemente Ana , Nadal Marcos
Published: October 2019

Aesthetic sensitivity has been defined as the ability to recognize and appreciate beauty and compositional excellence, and to judge artistic merit according to standards of aesthetic value. The Visual Aesthetic Sensitivity Test (VAST) has often been used to assess this ability, but recent research has revealed it has several psychometric problems. Such problems are not easily remedied, because they reflect flawed assumptions inherent to the concept of aesthetic sensitivity as traditionally understood, and to the VAST itself. We introduce a new conception of aesthetic sensitivity defined as the extent to which someone's aesthetic valuation is influenced by a given feature. Experiment 1 aimed to characterize aesthetic sensitivity to four prominent features in visual aesthetics: complexity, symmetry, contour, and balance. Experiment 2 aimed to replicate the findings of Experiment 1 and to assess the test–retest reliability of an instrument designed to measure aesthetic sensitivity to these features using an abridged set of stimuli. Our results reveal that people differ remarkably in the extent to which visual features influence their liking, highlighting the crucial role of individual variation when modelling aesthetic preferences. We did not find clear relations between the four measures of aesthetic sensitivity and personality, intelligence, and art interest and knowledge. Finally, our measurement instrument exhibited an adequate‐to‐good test–retest reliability.
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

Tacrolimus 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

End‐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

Sources 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.
How structural mitigation shapes risk perception and affects decision‐making
Authors: Starominski‐Uehara Marvin
Published: October 2019

This paper reviews the relationships between risk perception and structural measures in an Australian context in three respects: (i) opinions about authorities’ ability to mitigate flood risks; (ii) the role of flood experience in shaping views on risk; and (iii) perspectives on the ways in which structural measures shape decision‐making pertaining to protective action. The main finding of this analysis is that the study participants do not suffer from the ‘levee paradox'. Most take precautionary steps to guard against residual flood risk. Such actions, however, do not mean that there is a lack of trust in structural measures to reduce significant flood risk. The majority of the respondents agreed about the necessity of engineering structures to mitigate inherent flood risk. This support, though, does not extend to their management. Losses during major flooding in southeast Queensland, Australia, in 2010–11 were attributed primarily by residents to operational decisions concerning dam water releases.