bluuebunny/crossref_metadata_2025 huggingface dataset:
Can Pediatric Endoscopists Accurately Assess Their Clinical Competency? A Comparison Across Skill Levels
Authors: Scaffidi Michael A. , Khan Rishad , Carnahan Heather , Ling Simon C. , Lightdale Jenifer R. , Mamula Petar , Yu Jeffrey J. , Grover Samir C. , Walsh Catharine M.
Published: November 2018

Background:

Assessment is critical to support pediatric endoscopy training. Although trainee engagement in assessment is encouraged, the use of self‐assessment and its accuracy among pediatric endoscopists is not well described. We aimed to determine the self‐assessment accuracy of novice, intermediate, and experienced pediatric endoscopists.

Methods:

Novice (performed <50 previous colonoscopies), intermediate (50–500), and experienced (>1000) pediatric endoscopists from 3 North American academic teaching hospitals each performed a clinical colonoscopy. Endoscopists were assessed in real‐time by 2 experienced endoscopists using the Gastrointestinal Endoscopy Competency Assessment Tool for Pediatric Colonoscopy (GiECATKIDS). In addition, participants self‐assessed their performance using the same instrument. Self‐assessment accuracy between the externally assessed and self‐assessed scores was evaluated using absolute difference scores, intraclass correlation coefficients, and Bland‐Altman analyses.

Results:

Forty‐seven endoscopists participated (21 novices, 16 intermediates, and 10 experienced). Overall, there was moderate agreement of externally assessed and self‐assessed GiECATKIDS total scores with an intraclass correlation coefficient of 0.72 (95% confidence interval, 0.55–0.83). The absolute difference scores among the 3 groups were significantly different (P = 0.005), with experienced endoscopists demonstrating a more accurate self‐assessment compared to novices (P = 0.003). Bland‐Altman plots revealed that novice endoscopists’ self‐assessed scores tended to be higher than their externally assessed scores, indicating they overestimated their performance.

Conclusions:

We found that endoscopic experience was positively associated with self‐assessment accuracy among pediatric endoscopists. Novices were inaccurate in assessing their endoscopic competence and were prone to overestimation of their performances. Our findings suggest novices may benefit from targeted interventions aimed at improving their insight and self‐awareness.
Esophageal Compliance Quantifies Epithelial Remodeling in Pediatric Patients With Eosinophilic Esophagitis
Authors: Hassan Maheen , Aceves Seema , Dohil Ranjan , Gharibans Armen , Newbury Robert , Proudfoot James , Mousa Hayat
Published: November 2018

Background:

The management of eosinophilic esophagitis (EoE) relies on the severity of esophageal eosinophilia, yet there is poor evidence of its prediction of esophageal fibrotic remodeling and subsequent complications such as dysphagia, food impactions, or strictures. Functional luminal imaging planimetry (FLIP) has had limited use in pediatric patients to evaluate esophageal tissue mechanics. We aimed to standardize the FLIP technique and to measure esophageal compliance in children with EoE in comparison to controls.

Methods:

Subjects were enrolled into a prospective observational study and had FLIP performed at the time of endoscopy. We calculated esophageal distensibility and compliance for the total and segmental esophagus independently (ie, proximal, middle, and distal esophageal segments). We evaluated esophageal biopsies for eosinophilia and epithelial remodeling, calculated endoscopy scores, and documented patient symptoms.

Results:

We enrolled 11 EoE and 12 controls subjects, aged 5 to 18 years old. While EoE subjects had lower esophageal compliance (P = 0.004) than controls, the difference in distensibility did not reach significance (P = 0.151). Epithelial remodeling severity was more strongly correlated with compliance than with distensibility. Epithelial remodeling scores ≥2 had a significant association with lower compliance both segmentally and in the entire esophagus (P = 0.029), but not with distensibility. Compliance measures were more sensitive in detecting subjects with remodeling score ≥2 than distensibility (79% vs 64%).

Conclusions:

Compliance is a more sensitive measure of esophageal epithelial remodeling in children compared to distensibility, and a more appropriate measure of esophageal tissue mechanics. Standardized placement of the FLIP catheter is important to accurately assess esophageal compliance.
Bacteriophage Therapy Testing Against Shigella flexneri in a Novel Human Intestinal Organoid‐Derived Infection Model
Authors: Llanos‐Chea Alejandro , Citorik Robert J. , Nickerson Kourtney P. , Ingano Laura , Serena Gloria , Senger Stefania , Lu Timothy K. , Fasano Alessio , Faherty Christina S.
Published: November 2018

Objective:

Enteric bacterial pathogens cause diarrheal disease and mortality at significant rates throughout the world, particularly in children younger than 5 years. Our ability to combat bacterial pathogens has been hindered by antibiotic resistance, a lack of effective vaccines, and accurate models of infection. With the renewed interest in bacteriophage therapy, we sought to use a novel human intestinal model to investigate the efficacy of a newly isolated bacteriophage against Shigella flexneri.

Methods:

An S. flexneri 2457T‐specific bacteriophage was isolated and assessed through kill curve experiments and infection assays with colorectal adenocarcinoma HT‐29 cells and a novel human intestinal organoid‐derived epithelial monolayer model. In our treatment protocol, organoids were generated from intestinal crypt stem cells, expanded in culture, and seeded onto transwells to establish 2‐dimensional monolayers that differentiate into intestinal cells.

Results:

The isolated bacteriophage efficiently killed S. flexneri 2457T, other S. flexneri strains, and a strain of 2457T harboring an antibiotic resistance cassette. Analyses with laboratory and commensal Escherichia coli strains demonstrated that the bacteriophage was specific to S. flexneri, as observed under co‐culture conditions. Importantly, the bacteriophage prevented both S. flexneri 2457T epithelial cell adherence and invasion in both infection models.

Conclusions:

Bacteriophages offer feasible alternatives to antibiotics for eliminating enteric pathogens, confirmed here by the bacteriophage‐targeted killing of S. flexneri. Furthermore, application of the organoid model has provided important insight into Shigella pathogenesis and bacteriophage‐dependent intervention strategies. The screening platform described herein provides proof‐of‐concept analysis for the development of novel bacteriophage therapies to target antibiotic‐resistant pathogens.
High Interest in Doxycycline for Sexually Transmitted Infection Postexposure Prophylaxis in a Multicity Survey of Men Who Have Sex With Men Using a Social Networking Application
Authors: Spinelli Matthew A. , Scott Hyman M. , Vittinghoff Eric , Liu Albert Y. , Coleman Kenneth , Buchbinder Susan P.
Published: November 2018

Current strategies to prevent sexually transmitted infections (STIs) are not controlling the epidemic. The efficacy of doxycycline STI postexposure prophylaxis shows promise in pilot studies, but wider acceptability is unknown. A majority (84%) of diverse individuals using a gay social networking application were interested in doxycycline STI postexposure prophylaxis. Doxycycline STI postexposure prophylaxis should be examined in larger trials.
Tracheal Intubation Practice and Safety Across International PICUs: A Report From National Emergency Airway Registry for Children*
Authors: Lee Jan Hau , Nuthall Gabrielle , Ikeyama Takanari , Saito Osamu , Mok Yee Hui , Shepherd Michael , Jung Philipp , Shetty Rakshay , Thyagarajan Sujatha , Nett Sholeen , Napolitano Natalie , Nadkarni Vinay , Nishisaki Akira
Published: November 2018

Objectives:

It is unknown if variation in tracheal intubation practice and outcomes exist across PICUs in different geographical regions. We hypothesized there would be differences in the process of care and adverse outcomes for tracheal intubation across PICUs in six different geographical regions (New Zealand, Japan, Singapore, Germany, India, and North America).

Design:

Prospective multicenter pediatric tracheal intubation database (National Emergency Airway Registry for Children)

Setting:

Six non-North American (International) and 36 North American PICUs.

Events:

All PICU tracheal intubation encounters from July 2014 to June 2017

Measurements and Main Results:

Adverse tracheal intubation–associated events and desaturation occurrence (oxygen saturation < 80%) were evaluated. A total of 1,134 and 9,376 TIs from International and North American PICUs were reported, respectively: primary tracheal intubation 9,060, endotracheal tube change 1,450. The proportion of tracheal intubations for endotracheal tube change was greater in International PICUs (37% vs 11%; p < 0.001). Median age for International tracheal intubations was younger compared with North America (0 yr [interquartile range, 0–2 yr] vs 1 yr (0–7 yr); p < 0.001). Among primary tracheal intubations, the most common indication was respiratory (International 67%, North American 63%; p = 0.049). Direct laryngoscopy was the most common device in both International (86%) and North American (74%) tracheal intubations. Occurrence of any adverse tracheal intubation–associated event was New Zealand 8%, Japan 17%, Singapore 9%, Germany 17%, and India 6%; International 11% versus North American 14%; p value equals to 0.003. Desaturation was reported less commonly in International PICUs: 13% versus North American 17%; p equals to 0.001. International PICUs used cuffed endotracheal tube less often (52% vs 95%; p < 0.001). Proportion of cuffed endotracheal tube use per PICU was inversely correlated with the rate of tube change (r = –0.67; p < 0.001).

Conclusions:

There were both similarities and differences in tracheal intubation practice and outcomes across international PICUs. Fewer adverse tracheal intubation–associated events were reported from International versus North American PICUs. International PICUs used cuffed endotracheal tube less often and had higher proportion of endotracheal tube change.
Positive Airway Pressure Versus High-Flow Nasal Cannula for Prevention of Extubation Failure in Infants After Congenital Heart Surgery*
Authors: Richter Robert P. , Alten Jeffrey A. , King R. Wilson , Gans Asaf D. , Rahman AKM Fazlur , Kalra Yuvraj , Borasino Santiago
Published: November 2018

Objectives:

Compare the impact of initial extubation to positive airway pressure versus high-flow nasal cannula on postoperative outcomes in neonates and infants after congenital heart surgery.

Design:

Retrospective cohort study with propensity-matched analysis.

Setting:

Cardiac ICU within a tertiary care children’s hospital.

Patients:

Patients less than 6 months old initially extubated to either high-flow nasal cannula or positive airway pressure after cardiac surgery with cardiopulmonary bypass were included (July 2012 to December 2015).

Interventions:

None.

Measurements and Main Results:

Of 258 encounters, propensity matching identified 49 pairings of patients extubated to high-flow nasal cannula versus positive airway pressure. Extubation failure was 12% for all screened encounters. After matching, there was no difference in extubation failure rate between groups (positive airway pressure 16% vs high-flow nasal cannula 10%; p = 0.549). However, compared with high-flow nasal cannula, patients initially extubated to positive airway pressure experienced greater resource utilization: longer time to low-flow nasal cannula (83 vs 28 hr; p = 0.006); longer time to room air (159 vs 110 hr; p = 0.013); and longer postsurgical hospital length of stay (22 vs 14 d; p = 0.015).

Conclusions:

In this pediatric cohort, primary extubation to positive airway pressure was not superior to high-flow nasal cannula with respect to prevention of extubation failure after congenital heart surgery. Compared with high-flow nasal cannula, use of positive airway pressure was associated with increased hospital resource utilization. Prospective initiatives aimed at establishing best clinical practice for postoperative noninvasive respiratory support are needed.
Comparing Assessments of Physical Functional Independence in Older Adults With Mobility Limitations
Authors: Mortenson W. Ben , Fuhrer Marcus J. , Bilkey Jessica , Jutai Jeffrey , Alkadri Jamal , Aziz Joseph , Demers Louise
Published: November 2018

Objectives

The aims of the study were (1) to assess the agreement and correlation between self-reported functional independence and observations of family caregivers in a heterogeneous population of community-dwelling older adults with disabilities and (2) to determine how self-reports and caregiver reports correlate with evaluator rated functional independence over time.

Design

Data were drawn from a larger, randomized controlled trial examining the effects of a caregiver-inclusive intervention on outcomes of care recipients and their family caregivers. Functional independence measures were obtained using a self-report version of the Functional Independence Measure (care recipient self-reported Functional Independence Measure, caregiver self-reported Functional Independence Measure) and the Functional Autonomy Measurement System (evaluator perspective). They were administered at baseline (preintervention) and after the intervention at 6, 22, and 58 wks.

Results

Bivariate correlation analyses of 90 dyads consisting of older care recipients and their family caregivers reported moderate to very strong correlations between the three functional independence measures across all time points (r
S = 0.45–0.91, P < 0.01). Bland-Altman analyses revealed a small systematic bias between care recipient and caregiver assessments of functional independence, with participants reporting higher scores across all time points (mean difference = 2.00–2.97).

Conclusions

There is substantial consistency among the self-assessed, caregiver-assessed, and evaluator assessed functional independence of older adults. Caregivers may be used as proxies for community-dwelling older adults without severe cognitive impairments with functional limitations.

To Claim CME Credits

Complete the self-assessment activity and evaluation online at http://www.physiatry.org/JournalCME

CME Objectives

After reviewing this article, readers will be able to: (1) Describe the strength of association between self-reported functional independence and observations of family caregivers in a heterogeneous population of community-dwelling older adults with disabilities over time; (2) Describe the level of agreement between self-reported functional independence and observations of family caregivers over time; and (3) Describe the associations among self-reported, caregiver reported and evaluator rated functional independence over time.

Level

Advanced

Accreditation

The Association of Academic Physiatrists is accredited by the Accreditation Council for Continuing Medical Education to provide continuing medical education for physicians.

The Association of Academic Physiatrists designates this Journal-based CME activity for a maximum of 1.0 AMA PRA Category 1 Credit(s)™. Physicians should only claim credit commensurate with the extent of their participation in the activity.
The Value of Histology in the Diagnosis of Tuberculous Spondylodiscitis
Authors: Romdhane Emna , Rammeh Soumaya , Riahi Hend , Chebbi Yosra , Mouna Chelli Bouaziz , Achour Wafa , Slim-Saidi Leila , Benaissa Hanène Tiouiri , Ladeb Mohamed Fethi
Published: November 2018

Background

Tuberculous spondylodiscitis (TS) is the most common form of musculoskeletal tuberculosis. Currently, histology is widely used to distinguish tuberculous from nontuberculous disease.

Objectives

The aim of the present study was to assess the accuracy of histology compared with bacteriology in the diagnosis of TS.

Methods

This is a single-center case series carried out from January 2014 to February 2018 in a pathology department. It included 121 discovertebral biopsies of infective spondylodiscitis. The measures of diagnostic accuracy of histology were determined taking bacteriology as criterion standard.

Results

Among the 121 cases, 55 (45.4%) were diagnosed as TS by histological and/or bacteriological findings, 17 (30.9%) were classified as definite TS by bacteriology, and the remaining 38 (69.1%) had positive histology and negative bacteriology. There were 2 false-negatives, which histologically displayed suppuration without granuloma, and 3 false-positives; in one case, histology displayed granulomas without necrosis and culture isolated Brucella. In the 2 others, histology revealed granulomas with caseous-like necrosis and microbiology isolated fungal species. The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of histology in the diagnosis of TS were 88.2%, 93.4%, 83.3%, 95.5%, and 92%, respectively.

Conclusions

Histology is proved to be an accurate diagnostic tool in TS. Suppurative forms of TS without granuloma are rare and represent the main cause of false-negative histology. Suggestive histology of TS does not rule out fungal and brucellar spondylodiscitis. Caseous necrosis is not pathognomonic of tuberculosis. Fungal infection can also exhibit such type of necrosis.
Individually Body Weight–Adapted Contrast Media Application in Computed Tomography Imaging of the Liver at 90 kVp
Authors: Martens Bibi , Hendriks Babs M.F. , Eijsvoogel Nienke G. , Wildberger Joachim E. , Mihl Casper
Published: November 2018

Objectives

The aim of the present study was to evaluate the attenuation and image quality (IQ) of a body weight–adapted contrast media (CM) protocol compared with a fixed injection protocol in computed tomography (CT) of the liver at 90 kV.

Materials and Methods

One hundred ninety-nine consecutive patients referred for abdominal CT imaging in portal venous phase were included. Group 1 (n = 100) received a fixed CM dose with a total iodine load (TIL) of 33 g I at a flow rate of 3.5 mL/s, resulting in an iodine delivery rate (IDR) of 1.05 g I/s. Group 2 (n = 99) received a body weight–adapted CM protocol with a dosing factor of 0.4 g I/kg with a subsequent TIL adapted to the patients' weight. Injection time of 30 seconds was kept identical for all patients. Therefore, flow rate and IDR changed with different body weight. Patients were divided into 3 weight categories; 70 kg or less, 71 to 85 kg, and 86 kg or greater. Attenuation (HU) in 3 segments of the liver, signal-to-noise ratio, and contrast-to-noise ratio were used to evaluate objective IQ. Subjective IQ was assessed by a 5-point Likert scale. Differences between groups were statistically analyzed (P < 0.05 was considered statistically significant).

Results

No significant differences in baseline characteristics were found between groups. The CM volume and TIL differed significantly between groups (P < 0.01), with mean values in group 1 of 110 mL and 33 g I, and in group 2 of 104.1 ± 21.2 mL and 31.2 ± 6.3 g I, respectively. Flow rate and IDR were not significantly different between groups (P > 0.05). Body weight–adapted protocoling led to more homogeneous enhancement of the liver parenchyma compared with a fixed protocol with a mean enhancement per weight category in group 2 of 126.5 ± 15.8, 128.2 ± 15.3, and 122.7 ± 21.2 HU compared with that in group 1 of 139.9 ± 21.4, 124.6 ± 24.8, and 116.2 ± 17.8 HU, respectively.

Conclusions

Body weight–adapted CM injection protocols result in more homogeneous enhancement of the liver parenchyma at 90 kV in comparison to a fixed CM volume with comparable objective and subjective IQ, whereas overall CM volume can be safely reduced in more than half of patients.
Spatiotemporal proteomics uncovers cathepsin-dependent host cell death during bacterial infection
Authors: Selkrig Joel , Li Nan , Bobonis Jacob , Hausmann Annika , Sueki Anna , Imamura Haruna , El Debs Bachir , Sigismondo Gianluca , Florea Bogdan I. , Overkleeft Herman S. , Beltrao Pedro , Hardt Wolf-Dietrich , Krijgsveld Jeroen , Typas Athanasios
Published: November 2018

Immune cells need to swiftly and effectively respond to invading pathogens. This response relies heavily on rapid protein synthesis and accurate cellular targeting to ensure pathogen destruction. In return, pathogens intercept this response to ensure their survival and proliferation. To gain insight into this dynamic interface, we combined click-chemistry with pulsed stable isotope labeling of amino acids (pSILAC-AHA) in cell culture to quantify the newly synthesised host proteome during macrophage infection with the model intracellular bacterial pathogen,Salmonella entericaTyphimurium (STm). We monitored newly synthesised proteins across different host cell compartments and infection stages, and used available proteomics data in response to lipopolysaccharide to deconvolute theSTm-specific response. Within this rich resource, we detected aberrant trafficking of lysosomal proteases to the extracellular space and the nucleus, the latter of which correlated with signatures of cell death. Pharmacological cathepsin inhibition suppressed Caspase-11 dependent macrophage cell death, thus demonstrating an active role for cathepsins duringSTm induced pyroptosis. Our study illustrates that resolving host proteome dynamics during infection can drive the discovery of biological mechanisms at the host-microbe interface.
REM sleep: unique associations with behavior, corticosterone regulation and apoptotic pathways in chronic stress in mice
Authors: Nollet Mathieu , Hicks Harriet , McCarthy Andrew P. , Wu Huihai , Möller-Levet Carla S. , Laing Emma E. , Malki Karim , Lawless Nathan , Wafford Keith A. , Dijk Derk-Jan , Winsky-Sommerer Raphaelle
Published: November 2018

One of sleep’s putative functions is mediation of adaptation to waking experiences. Chronic stress is a common waking experience, however, which specific aspect of sleep is most responsive, and how sleep changes relate to behavioral disturbances and molecular correlates remain unknown. We quantified sleep, physical, endocrine and behavioral variables and the brain and blood transcriptome in mice exposed to nine weeks of unpredictable chronic mild stress (UCMS). Comparing 46 phenotypical variables revealed that rapid-eye-movement sleep (REMS), corticosterone regulation and coat state were most responsive to UCMS. REMS theta oscillations were enhanced whereas delta oscillations in non-REMS were unaffected. Transcripts affected by UCMS in the prefrontal cortex, hippocampus, hypothalamus and blood were associated with inflammatory and immune responses. A machine learning approach controlling for unspecific UCMS effects identified transcriptomic predictors for specific phenotypes and their overlap. Transcriptomic predictor sets for the inter-individual variation in REMS continuity and theta activity shared many pathways with corticosterone regulation and in particular pathways implicated in apoptosis, including mitochondrial pathways. Predictor sets for REMS and anhedonia, one of the behavioral changes following UCMS, shared pathways involved in oxidative stress, cell proliferation and apoptosis. RNA predictor sets for non-NREMS parameters showed no overlap with other phenotypes. These novel data identify REMS as a core and early element of the response to chronic stress, and identify apoptotic pathways as a putative mechanism by which REMS mediates adaptation to stressful waking experiences.

Significance Statement

Sleep is responsive to experiences during wakefulness and is altered in stress-related disorders. Whether sleep changes primarily concern rapid-eye-movement sleep (REMS) or non-REM sleep, and how they correlate with stress hormones, behavioral and transcriptomic responses remained unknown. We demonstrate using unpredictable chronic (9-weeks) mild stress that REMS is the most responsive of all the measured sleep characteristics, and correlates with deficiency in corticosterone regulation. An unbiased machine learning, controlling for unspecific effects of stress, revealed that REMS correlated with RNA predictor sets enriched in apoptosis including mitochondrial pathways. Several pathways were shared with predictors of corticosterone and behavioral responses. This unbiased approach point to apoptosis as a molecular mechanism by which REMS mediates adaptation to an ecologically relevant waking experience.
Functional network dynamics in a neurodevelopmental disorder of known genetic origin
Authors: Hawkins Erin , Akarca Danyal , Zhang Mengya , Brkic Diandra , Woolrich Mark , Baker Kate , Astle Duncan
Published: November 2018

Cognitive processing depends on the temporal co-ordination of functional brain networks. This fundamental aspect of neurophysiology potentially bridges the genetic regulation of neuronal activity and developmental cognitive impairments. We investigated brain network dynamics in a neurodevelopmental disorder of known genetic origin, by comparing individuals with ZDHHC9-associated intellectual disability to individuals with no known impairment. We used Hidden Markov Modelling on magnetoencephalography (MEG) data, at rest and during auditory oddball stimulation, to characterise transient network dynamics. At rest, network dynamics distinguished the groups, with ZDHHC9 participants showing longer state activation. Crucially, ZDHHC9 gene expression levels predicted the group differences across networks, supporting an association between molecular pathology and neurophysiology. In contrast, network dynamics during auditory oddball stimulation did not show this association. We demonstrate a link between brain network dynamics and regional gene expression, and present a valuable method for understanding the real-time neural mechanisms linking genetic variation to cognitive difficulties.
Spatio-Genetic and Phenotypic Modelling Elucidates Resistance and Re-Sensitisation to Treatment in Heterogeneous Melanoma
Authors: Hodgkinson Arran , Cam Laurent Le , Trucu Dumitru , Radulescu Ovidiu
Published: November 2018

Although novel targeted therapies have significantly improved the overall survival of patients with advanced melanoma, understanding and combatting drug resistance remains a major clinical challenge. Using partial differential equations, we describe the evolution of a cellular population through time, space, and phenotype dimensions, in the presence of various drug species. We then use this framework to explore models in which resistance is attained by either mutations (irreversible) or plasticity (reversible). Numerical results suggest that punctuated evolutionary assumptions are more consistent with results obtained from murine melanoma models than gradual evolution. Furthermore, in the context of an evolving tumour cell population, sequencing the treatment, for instance applying immunotherapy before BRAF inhibitors, can increase treatment effectiveness. However, drug strategies which showed success within a spatially homogeneous tumour environment were unsuccessful under heterogeneous conditions, suggesting that spatio-environmental heterogeneity may be the greatest challenge to tumour therapies. Plastic metabolic models are additionally capable of reproducing the characteristic resistant tumour volume curves and predicting re-sensitisation to secondary waves of treatment observed in patient derived xenograft (PDX) melanomas treated with MEK and BRAF inhibitors. Nevertheless, secondary relapse due to a pre-adapted subpopulation, remaining after the first wave of treatment, results in a more rapid development of resistance. Our model provides a framework through which tumour resistance can be understood and would suggest that carefully phased treatments may be able to overcome the development of long-term resistance in melanoma.
Genetic structure in the wood mouse and the bank vole: contrasting patterns in a human-modified and highly fragmented landscape
Authors: Biello Roberto , Brunelli Andrea , Sozio Giulia , Havenstein Katja , Mortelliti Alessio , Ketmaier Valerio , Bertorelle Giorgio
Published: November 2018

Habitat fragmentation related to human activities modifies the distribution and the demographic trajectory of a species, often leading to genetic erosion and increased extinction risks. Understanding the impact of fragmentation on different species that co-exist in the same area becomes extremely important. Here we estimated the impact produced by different natural and anthropic landscape features on gene flow patterns in two sympatric species sampled in the same locations. Our main goal was to identify shared and private factors in the comparison among species. 199 bank voles and 194 wood mice were collected in 15 woodlands in a fragmented landscape, and genotyped at 8 and 7 microsatellites, respectively. Genetic variation and structure were analysed with standard approaches. Effective migration surfaces, isolation by resistance analysis, and regression with randomization were used to study isolation by distance and to estimate the relative importance of land cover elements on gene flow. Genetic structure was similarly affected by isolation by distance in these species, but the isolation-by-resistance analysis suggests that i) the wood mouse has constrained patterns of dispersal across woodland patches and facilitated connectivity in cultivated areas; ii) the bank vole connectivity is hindered by urban areas, while permeability is facilitated by the presence of woodlands, and cultivated terrains. Habitat loss and fragmentation can therefore influence genetic structure of small sympatric mammal species in different ways, and predicting the genetic consequences of these events using only one species may be misleading.
DeepTCR: a deep learning framework for understanding T-cell receptor sequence signatures within complex T-cell repertoires
Authors: Sidhom John-William , Larman H. Benjamin , Ross-MacDonald Petra , Wind-Rotolo Megan , Pardoll Drew M. , Baras Alexander S.
Published: November 2018

Deep learning algorithms have been utilized to achieve enhanced performance in pattern-recognition tasks, such as in image and vocal recognition1,2. The ability to learn complex patterns in data has tremendous implications in the genomics and immunology worlds, where sequence motifs become learned ‘features’ that can be used to predict functionality, guiding our understanding of disease and basic biology3–6. T-cell receptor (TCR) sequencing assesses the diversity of the adaptive immune system, where complex structural patterns in the TCR can be used to model its antigenic interaction. We present DeepTCR, a broad collection of unsupervised and supervised deep learning methods able to uncover structure in highly complex and large TCR sequencing data by learning a joint representation of a given TCR by its CDR3 sequences, V/D/J gene usage, and HLA background in which the T-cells reside. We demonstrate the utility of deep learning to provide an improved ‘featurization’ of the TCR across multiple human and murine datasets, including improved classification of antigen-specific TCR’s in both unsupervised and supervised learning tasks, understanding immunotherapy-related shaping of repertoire in the murine setting, and predicting response to checkpoint blockade immunotherapy from pre-treatment tumor biopsies in a clinical trial of melanoma. Our results show the flexibility and capacity for deep neural networks to handle the complexity of high-dimensional TCR genomic data for both descriptive and predictive purposes across basic science and clinical research.
Genetic dissection of the different roles of hypothalamic kisspeptin neurons in regulating female reproduction
Authors: Wang Luhong , Vanacker Charlotte , Burger Laura L. , Barnes Tammy , Shah Yatrik M. , Myers Martin G. , Moenter Suzanne M.
Published: November 2018

The brain regulates fertility through gonadotropin-releasing hormone (GnRH) neurons. Estradiol induces negative feedback on pulsatile GnRH/luteinizing hormone (LH) release and positive feedback generating preovulatory GnRH/LH surges. Negative and positive feedback are postulated to be mediated by kisspeptin neurons in arcuate and anteroventral periventricular (AVPV) nuclei, respectively. Kisspeptin-specific ERα knockout mice exhibit disrupted LH pulses and surges. This knockout approach is neither location-specific nor temporally-controlled. We utilized CRISPR-Cas9 to disrupt ERα in adulthood. Mice with ERα disruption in AVPV kisspeptin neurons have typical reproductive cycles but blunted LH surges, associated with decreased excitability of these neurons. Mice with ERα knocked down in arcuate kisspeptin neurons showed disrupted cyclicity, associated with increased glutamatergic transmission to these neurons. These observations suggest activational effects of estradiol regulate surge generation and maintain cyclicity through AVPV and arcuate kisspeptin neurons, respectively, independent from its role in the development of hypothalamic kisspeptin neurons or puberty onset.

Significant Statement

The brain regulates fertility through gonadotropin-releasing hormone (GnRH) neurons. Ovarian estradiol regulates GnRH pulses (negative feedback) and the GnRH surge release that ultimately triggers ovulation (positive feedback). Kisspeptin neurons in the arcuate and anteroventral periventricular nuclei are postulated to convey negative and positive feedback to GnRH neurons, respectively. Kisspeptin-specific ERα knockout mice exhibited disrupted negative and positive feedback. However, it is not clear what roles each kisspeptin population plays, and not possible to separate their roles during development vs adulthood in this model. Here we utilized CRISPR-Cas9 to disrupt ERα in each population in adulthood. We found activational effects of estradiol regulate surge generation and maintain cyclicity through AVPV and arcuate kisspeptin neurons, respectively, independent from estradiol action during development.
Transcriptional Feedback Disruption Yields Escape-Resistant Antivirals
Authors: Chaturvedi Sonali , Wolf Marie , Vardi Noam , Du Kelvin , Glazier Joshua , Ke Ruian , Chan Matilda F. , Perelson Alan S. , Weinberger Leor S.
Published: November 2018

From microbes to cancers, drug-resistant ‘escape’ variants cause significant morbidity and mortality1–7. Here we present proof-of-concept that disruption of viral auto-regulatory (feedback) circuits strongly inhibits viral replication and confers an extremely high barrier to the evolution of resistance. Using DNA duplexes, we develop single-molecule ‘feedback-circuit disruptors’ that interfere with transcriptional negative feedback in human herpesviruses (both Herpes Simplex Virus 1 and Cytomegalovirus) thereby increasing viral transcription factors to cytotoxic levels. Feedback disruptors exhibit low-nanomolar to picomolar IC-50’s, reduce viral replication >100-fold in culture and in mice, and synergize with the standard-of-care antivirals. Strikingly, no feedback-disruptor escape mutants evolved over >60 days of culture, in contrast to approved antivirals to which resistance rapidly evolved. Overall, the results demonstrate that molecular targeting of feedback circuitry could yield escape-resistant antivirals, potentially enabling development of a new class of antimicrobials.
Semi-in vitro Reconstitution of Roseocin, a Two-Component Lantibiotic from an Actinomycete
Authors: Singh Mangal , Sareen Dipti
Published: November 2018

Lantibiotics are lanthionine containing peptide natural products that belong to the class of ribosomally synthesized and post-translationally modified peptides (RiPPs). Recent expansion in the availability of microbial genomic data and in silico analysis tools have accelerated the discovery of these promising alternatives to antibiotics. Following the genome-mining approach, a biosynthetic gene cluster for a putative two-component lantibiotic roseocin was identified in the genome of an Actinomycete, Streptomyces roseosporus NRRL 11379. Post-translationally modified lanthipeptides of this cluster were obtained by heterologous expression of the genes in E. coli, and were in vitro reconstituted to their bioactive form. The two lanthipeptides displayed antimicrobial activity against Gram-positive bacteria only synergistically, a property reminiscent of two-component lantibiotics. Structural analysis of the α-component identified a disulfide bridge flanking two of its four thioether bridges and the β-component having six thioether bridges with its C-terminus extended than the previously known two-component lantibiotics.
De novo profiling of RNA viruses inAnophelesmalaria vector mosquitoes from forest ecological zones in Senegal and Cambodia
Authors: Belda Eugeni , Minkeu Ferdinand Nanfack , Eiglmeier Karin , Carissimo Guillaume , Holm Inge , Diallo Mawlouth , Diallo Diawo , Vantaux Amélie , Kim Saorin , Sharakhov Igor V. , Vernick Kenneth D.
Published: November 2018

Background

Mosquitoes are colonized by a large but mostly uncharacterized natural virome of RNA viruses.Anophelesmosquitoes are efficient vectors of human malaria, and the composition and distribution of the natural RNA virome may influence the biology and immunity ofAnophelesmalaria vector populations.

Results

Anophelesvectors of human malaria were sampled in forest village sites in Senegal and Cambodia, includingAnopheles funestus, Anopheles gambiaegroup sp., andAnopheles coustaniin Senegal, andAnopheles hyrcanusgroupsp., Anopheles maculatusgroupsp., andAnopheles dirusin Cambodia. Small and long RNA sequences were depleted of mosquito host and de novo assembled to yield non-redundant contigs longer than 500 nucleotides. Analysis of the assemblies by sequence similarity to known virus families yielded 125 novel virus sequences, 39 from SenegalAnophelesand 86 from Cambodia. Important monophyletic virus clades in theBunyaviralesandMononegaviralesorders are found in theseAnophelesfrom Africa and Asia. Small RNA size and abundance profiles were used to cluster non-host RNA assemblies that were unclassified by sequence similarity. 39 unclassified non-redundant contigs >500 nucleotides strongly matched a pattern of classic RNAi processing of viral replication intermediates, and 1566 unclassified contigs strongly matched a pattern consistent with piRNAs. Analysis of piRNA expression inAnopheles coluzziiafter infection with O’nyong nyong virus (familyTogaviridae) suggests that virus infection can specifically alter abundance of some piRNAs.

Conclusions

RNA viruses ubiquitously colonize Anopheles vectors of human malaria worldwide. At least some members of the mosquito virome are monophyletic with other arthropod viruses. However, high levels of collinearity and similarity of Anopheles viruses at the peptide level is not necessarily matched by similarity at the nucleotide level, indicating thatAnophelesfrom Africa and Asia are colonized by closely related but clearly diverged virome members. The interplay between small RNA pathways and the virome may represent an important part of the homeostatic mechanism maintaining virome members in a commensal or nonpathogenic state, and host-virome interactions could influence variation in malaria vector competence.
A Framework to Incorporate D-trace Loss into Compositional Data Analysis
Authors: He Shun , Deng Minghua
Published: November 2018

The development of high-throughput sequencing technologies for 16S rRNA gene profiling provides higher quality compositional data for microbe communities. Inferring the direct interaction network under a specific condition and understanding how the network structure changes between two different environmental or genetic conditions are two important topics in biological studies. However, the compositional nature and high dimensionality of the data are challenging in the context of network and differential network recovery. To address this problem in the present paper, we proposed a framework to incorporate the data transformations developed for compositional data analysis into D-trace loss for network and differential network estimation, respectively. The sparse matrix estimators are defined as the minimizer of the corresponding lasso penalized loss. This framework is characterized by its straightforward application based on the ADMM algorithm for numerical solution. Simulations show that the proposed method outperforms other state-of-the-art methods in network and differential network inference under different scenarios. Finally, as an illustration, our method is applied to a mouse skin microbiome data.

Author summary

Inferring the direct interactions among microbes and how these interactions change under different conditions are important to understand community-wide dynamics. The compositional nature and high dimensionality are two distinctive features of microbial data, which invalidate traditional correlation analysis and challenge interaction network estimation. In this study, we set up a framework that combines data transformation with D-trace loss to infer the direct interaction network and differential network from compositional data. Simulations and real data analysis show that our proposed methods lead to results with higher accuracy and stability.
Protein composition of the occlusion bodies of Epinotia aporema granulovirus
Authors: Masson Tomás , Fabre María Laura , Ferrelli María Leticia , Pidre Matías Luis , Romanowski Víctor
Published: November 2018

Within family Baculoviridae, members of the Betabaculovirus genus are employed as biocontrol agents against lepidopteran pests, either alone or in combination with selected members of the Alphabaculovirus genus. Epinotia aporema granulovirus (EpapGV) is a fast killing betabaculovirus that infects the bean shoot borer (E. aporema) and is a promising biopesticide. Because occlusion bodies (OBs) play a key role in baculovirus horizontal transmission, we investigated the composition of EpapGV OBs. Using mass spectrometry-based proteomics we could identify 56 proteins that are included in the OBs during the final stages of larval infection. Our data provides experimental validation of several annotated hypothetical coding sequences. Proteogenomic mapping against genomic sequence detected a previously unannotated ac110-like core gene and a putative translation fusion product of ORFs epap48 and epap49. Comparative studies of the proteomes available for the family Baculoviridae highlight the conservation of core gene products as parts of the occluded virion. Two proteins specific for betabaculoviruses (Epap48 and Epap95) are incorporated into OBs. Moreover, quantification based on emPAI values showed that Epap95 is one of the most abundant components of EpapGV OBs.
A metapopulation model for the 2018 Ebola virus disease outbreak in Equateur province in the Democratic Republic of the Congo
Authors: Meakin Sophie R. , Tildesley Mike J. , Davis Emma , Keeling Matt J.
Published: November 2018

Ebola virus disease (EVD) is a viral haemorrhagic fever with high mortality that has caused a number of severe outbreaks in Central and West Africa. Although the majority previous outbreaks have been relatively small, the result of managing outbreaks places huge strains on already limited resources. Mathematical models matched to early case reporting data can be used to identify outbreaks that are at high risk of spreading. Here we consider the EVD outbreak in Equateur Province in the Democratic Republic of the Congo, which was declared on 8 May 2018. We use a simple stochastic metapopulation model to capture the dynamics in the three affected health zones: Bikoro, Iboko and Wangata. We are able to rapidly simulate a large number of realisations and use approximate Bayesian computation, a likelihood-free method, to determine parameters by matching between reported and simulated cases. This method has a number of advantages over more traditional likelihood-based methods as it is less sensitive to errors in the data and is a natural extension to the prediction framework. Using data from 8 to 25 May 2018 we are able to capture the exponential increases in the number of cases in three locations (Bikoro, Iboko and Wangata), although our estimated basic reproductive ratio is higher than for previous outbreaks. Using additional data until 08 July 2018 we are able to detect a decrease in transmission such that the reproductive ratio falls below one. We also estimate the probability of transmission to Kinshasa. We believe this method of fitting models to data offers a generic approach that can deliver rapid results in real time during a range of future outbreaks.
Effect of the Crystal Size of Biogenic Hydroxyapatites on IR and Raman Spectra
Authors: Londoño-Restrepo S.M. , Zubieta-Otero L. F. , Jeronimo-Cruz R. , Mondragon M. A. , Rodriguez-García M. E.
Published: November 2018

This work focuses on the analysis of the impact that raw and calcined biogenic hydroxyapatite crystal size has on the Raman and infrared spectra. To this end, bovine, porcine, and human bones samples were defatted and deproteinized as well as calcinated at 720°C and then analyzed through Raman and Infrared spectroscopies, Transmission Electron Microscopy (TEM), Inductively Coupled Plasma (ICP), and Scanning Electron Microscopy (SEM). Raman and IR spectra for raw samples showed broad bands while after calcination bands became narrow and well defined. TEM images showed that all raw crystallites are nano-plates with a high crystalline quality contrary to the so far well-established concept that biogenic hydroxyapatites have low crystalline quality. This fact confirmed that the broad Raman and infrared bands of raw clean bones come from nanocrystal-plates. SEM analysis confirmed the increase in the size of the crystals after calcination from nano to sub-micron dimensions due to a coalescence phenomenon.
Inference of clonal selection in cancer populations using single-cell sequencing data
Authors: Skums Pavel , Tsivina Vyacheslau , Zelikovsky Alex
Published: November 2018

Intra-tumor heterogeneity is one of the major factors influencing cancer progression and treatment outcome. However, evolutionary dynamics of cancer clone populations remain poorly understood. Quantification of clonal selection and inference of fitness landscapes of tumors is a key step to understanding evolutionary mechanisms driving cancer. These problems could be addressed using single cell sequencing, which provides an unprecedented insight into intra-tumor heterogeneity allowing to study and quantify selective advantages of individual clones. Here we present SCIFIL, a computational tool for inference of fitness landscapes of heterogeneous cancer clone populations from single cell sequencing data. SCIFIL allows to estimate maximum likelihood fitnesses of clone variants, measure their selective advantages and order of appearance by fitting an evolutionary model into the tumor phylogeny. We demonstrate the accuracy and utility of our approach on simulated and experimental data. SCIFIL can be used to provide new insight into the evolutionary dynamics of cancer. Its source code is available athttps://github.com/compbel/SCIFIL