bluuebunny/crossref_metadata_2025 huggingface dataset:
Incidence, Risk Factors, and Treatment of Proximally Migrated Pancreatic Stents
Authors: Gokbulut Volkan , Kaplan Mustafa , Odemis Bulent , Disibeyaz Selcuk , Parlak Erkan , Kilic Zeki M.Y. , Oztas Erkin
Published: June 2021

Aim:

The aim of this study was to investigate the incidence, risk factors, and treatment strategies of proximally migrated pancreatic stents.

Materials and Methods:

The data of 626 sessions of 421 patients with pancreatic duct stenting were retrospectively analyzed between 2010 and 2018, and patients with proximally migrated stents were included in the study.

Results:

Of 626 stents examined, 77 migrated proximally (12%). The migration rate (MR) was 16%, 2%, and 7%, respectively, in patients treated with chronic pancreatitis, malignancy, and pancreatic leakage indication. The MR was 14% in procedures with pancreatic duct stenosis, 21% in procedures with pancreatic sphincterotomy, and 27% in procedures performed from minor papillae. The MR of the 5, 7, and 10 Fr stents was 4%, 17%, and 10%, respectively. Of the 77 migrated stents, 64 were successfully removed (83%). This success rate (SR) was 84% in procedures with chronic pancreatitis indication, 83% in procedures with pancreatic duct stenosis, 79% in procedures with sphincterotomy, and 75% in procedures performed from minor papillae. The SR of the 5, 7, and 10 Fr stents was 100%, 79%, and 92%, respectively. It was also determined that 33 stents were fractured and migrated (43%). The SR of the fractured stents was 76%. Moreover, of the stents that were successfully removed, 35 were removed with forceps (55%) and 15 (23%) were removed with a balloon. Furthermore, in 47 cases, the stent was removed in the first session (73%). Acute pancreatitis occurred in 5 patients (8%) and perforation occurred in 1 patient (2%).

Conclusion:

In this study, it was shown that proximal migration of pancreatic stents is frequent and most of these stents can be removed successfully.
Quantifying year-round nocturnal bird migration with a fluid dynamics model
Authors: Nussbaumer Raphaël , Bauer Silke , Benoit Lionel , Mariethoz Grégoire , Liechti Felix , Schmid Baptiste
Published: June 2021

To understand the influence of biomass flows on ecosystems, we need to characterize and quantify migrations at various spatial and temporal scales. Representing the movements of migrating birds as a fluid, we applied a flow model to bird density and velocity maps retrieved from the European weather radar network, covering almost a year. We quantified how many birds take-off, fly, and land across Western Europe to (1) track bird migration waves between nights, (2) cumulate the number of birds on the ground and (3) quantify the seasonal flow into and out of the study area through several regional transects. Our results identified several migration waves that crossed the study area in 4 days only and included up to 188 million (M) birds that took-off in a single night. In spring, we estimated that 494 M birds entered the study area, 251 M left it, and 243 M birds remained within the study area. In autumn, 314 M birds entered the study area while 858 M left it. In addition to identifying fundamental quantities, our study highlights the potential of combining interdisciplinary data and methods to elucidate the dynamics of avian migration from nightly to yearly time scales and from regional to continental spatial scales.
Homeostatic swimming of zooplankton upon crowding: the case of the copepod
Centropages typicus
Authors: Uttieri Marco , Hinow Peter , Pastore Raffaele , Bianco Giuseppe , Ribera d’Alcalá Maurizio , Mazzocchi Maria Grazia
Published: June 2021

Crowding has a major impact on the dynamics of many material and biological systems, inducing effects as diverse as glassy dynamics and swarming. While this issue has been deeply investigated for a variety of living organisms, more research remains to be done on the effect of crowding on the behaviour of copepods, the most abundant metazoans on Earth. To this aim, we experimentally investigate the swimming behaviour, used as a dynamic proxy of animal adaptations, of males and females of the calanoid copepod
Centropages typicus
at different densities of individuals (10, 50 and 100 ind. l
−1
) by performing three-dimensional single-organism tracking. We find that the
C. typicus
motion is surprisingly unaffected by crowding over the investigated density range. Indeed, the mean square displacements as a function of time always show a crossover from ballistic to Fickian regime, with poor variations of the diffusion constant on increasing the density. Close to the crossover, the displacement distributions display exponential tails with a nearly density-independent decay length. The trajectory fractal dimension,
D
3D
≅ 1.5, and the recently proposed ‘ecological temperature’ also remain stable on increasing the individual density. This suggests that, at least over the range of animal densities used, crowding does not impact on the characteristics of
C. typicus
swimming motion, and that a homeostatic mechanism preserves the stability of its swimming performance.
A paradox of traffic and extra cars in a city as a collective behaviour
Authors: Prieto Curiel Rafael , González Ramírez Humberto , Quiñones Domínguez Mauricio , Orjuela Mendoza Juan Pablo
Published: June 2021

Promoting walking or cycling and reducing cars’ use is one of the city planners’ main targets, contributing to a sustainable transport method. Yet, the number of vehicles worldwide is increasing as fast as the population, and motorized mobility has become the primary transport method in most cities. Here, we consider modal share as an emergent behaviour of personal decisions. All individuals minimize their commuting time and reach an equilibrium under which no person is willing to change their transportation mode. In terms of the minimum travel time, the best-case scenario is used to determine the extra commuting time and the excess cars, computed as a social inefficiency. Results show that commuting times could increase up to 25% with many more vehicles than optimum. Paradoxically, all individuals trying to minimize their time could collectively reach the maximum commuting times in the extreme case, with all individuals driving during rush hour.
Temporal discounting mediates the relationship between socio-economic status and social trust
Authors: Guillou Léonard , Grandin Aurore , Chevallier Coralie
Published: June 2021

Social trust and income are associated both within and across countries, such that higher income typically correlates with increased trust. While this correlation is well-documented, the psychological mechanisms sustaining this relationship remain poorly understood. One plausible candidate is people’s temporal discounting: on the one hand, trust has a strong time component—it exposes the individual to immediate costs in exchange of uncertain and delayed benefits; on the other hand, temporal discounting is robustly influenced by income. The goal of our studies was to test whether temporal discounting mediates the relationship between income and trust and whether experimentally manipulating perceived income has a downstream impact on temporal discounting and trust. To do so, participants who underestimated their relative income position received information about their true position in the income distribution in order to correct their misperception. Our results indicate that temporal discounting partially mediates the effect of income on social trust in a pre-registered online study on British participants (N= 855). However, receiving a positive information shock on one’s income position had no impact on either temporal discounting or social trust. In a second pre-registered study, we replicated the finding that temporal discounting partially mediates the effect of income on social trust in a representative sample of the British population (N= 1130).
Past thermal conditions affect hunting behaviour in larval antlions
Authors: Miler Krzysztof , Czarnoleski Marcin
Published: June 2021

Some sit-and-wait predators, such as antlion larvae, construct traps to capture passing prey. The location of these traps depends on many abiotic and biotic factors, including temperature and the presence of conspecifics, which probably stimulate behaviours that minimize the costs and maximize the benefits of trap building. Here, we exposed second instar antlion larvae to elevated temperatures of 25°C (mild treatment) or 31°C (harsh treatment) for one month and then transferred them to common conditions (20°C) to examine the effects of previous thermal treatment on aggregation tendency and trap size. We predicted that antlions that experienced harsh conditions would subsequently increase the neighbouring distance and trap diameter to reduce competition with conspecifics and improve prey capture success, compensating for past conditions. In contrast with these predictions, antlions exposed to harsh conditions displayed a trend in the opposite direction, towards the decreased neighbouring distance. Furthermore, some of these antlions also built smaller traps. We discuss possible reasons for our results. The effects of previous thermal exposure have rarely been considered in terms of trap construction in antlions. Described effects may possibly apply to other sit-and-wait predators and are significant considering that many of these predators are long-lived.
Comparison of the bactericidal effects of quinolones against low-susceptible Haemophilus influenzae
Authors: Mizoi Kosei , Wajima Takeaki , Tanaka Emi , Nakaminami Hidemasa , Noguchi Norihisa
Published: June 2021

The increasing incidence of

Haemophilus influenzae

with decreased susceptibility to quinolones (quinolone low-susceptible

H. influenzae

) in Japan has raised concerns about therapeutic failure. Thus, assessment of effective antimicrobial agents is necessary to establish an effective therapeutic strategy against resulting infections. In this study, in vitro bactericidal effects of quinolones on low-susceptible

H. influenzae

strains were evaluated using time-kill curve analysis. For tosufloxacin, log reduction values for low-susceptible strains were significantly lower than those for susceptible strains at both Cmax and 1/2 Cmax. Conversely, although the log reduction values were lower for susceptible strains, the Cmax of levofloxacin and β-lactams (amoxicillin and cefditoren) indicated bactericidal effects. In addition, higher concentrations of tosufloxacin at 2×Cmax and 4×Cmax had bactericidal effects on not only susceptible but also low-susceptible strains. These data strongly suggest that we should consider the presence of low-susceptible strains and reconsider the appropriate dosage of tosufloxacin for treatment, especially for paediatric patients.
SplitStrains, a tool to identify and separate mixed Mycobacterium tuberculosis infections from WGS data
Authors: Gabbassov Einar , Moreno-Molina Miguel , Comas Iñaki , Libbrecht Maxwell , Chindelevitch Leonid
Published: June 2021

The occurrence of multiple strains of a bacterial pathogen such as

M. tuberculosis

or

C. difficile

within a single human host, referred to as a mixed infection, has important implications for both healthcare and public health. However, methods for detecting it, and especially determining the proportion and identities of the underlying strains, from WGS (whole-genome sequencing) data, have been limited. In this paper we introduce SplitStrains, a novel method for addressing these challenges. Grounded in a rigorous statistical model, SplitStrains not only demonstrates superior performance in proportion estimation to other existing methods on both simulated as well as real

M. tuberculosis

data, but also successfully determines the identity of the underlying strains. We conclude that SplitStrains is a powerful addition to the existing toolkit of analytical methods for data coming from bacterial pathogens and holds the promise of enabling previously inaccessible conclusions to be drawn in the realm of public health microbiology.
Predicting thermal injury patient outcomes in a Tertiary-Care Burn Centre, Pakistan
Authors: Bajwa Mohammad Suleman , Sohail Muhammad , Ali Hamza , Nazir Umer , Bashir Muhammad Mustehsan
Published: June 2021

Objectives

To explore candidate parameters for their ability to predict survival and length of hospital stay (LOS) in thermal burns patients, to prepare multivariate predictive models for these two outcomes, and to compare performance of native models to other models.

Methods

A retrospective cohort study was undertaken based on record review. Data was extracted from files of patients admitted to a tertiary-care burn centre in Lahore, Pakistan from January 1, 2020 to October 31, 2020. Univariate preselection was used to prepare multivariate logistic regression models for each outcome of interest (survival and LOS). Multivariate models were tested and compared to other models.

Results

Increasing TBSA of burn was positively associated with reduced survival and prolonged length of stay. Advancing age and full-thickness burns independently predicted decreased survival. Burn etiology showed prognostic value: petrol-flame burns predicted decreased survival and prolonged LOS; scald was associated with improved survival-odds and shorter LOS. The Survival-model consisted of (1) Baux score, (2) TBSA>40% and (3) serum albumin <3.5g/dl (AUC=0.968, Nagelkerke R2=0.797). The LOS-model consisted of (1) TBSA2 and (2) serum albumin concentration (AUC= 0.832, Nagelkerke R2 =0.408). In tests of discrimination and calibration, native models prepared for survival and LOS outcomes outperformed other models applicable to our dataset.

Conclusion

Data from a South Asian burn center has been used to explore factors influencing prognosis for their utility in predictive models for survival and the duration of hospital stay. The significant prognostic roles of TBSA, age, inhalational injury, burn-depth, etiology of burn, anatomic site of burn, hypoalbuminemia and other biochemical parameters were observed. These tools hold significance in guiding healthcare policy and in communications with patients and their families.
Delay of molecular SARS-CoV-2 testing and turnaround time in Mexico and Colombia
Authors: Núñez Isaac , Belaunzarán-Zamudio Pablo F. , Caro-Vega Yanink
Published: June 2021

Objective

To quantify the delay in SARS-CoV-2 real time polymerase chain reaction (RT-PCR) testing and test result reporting in Mexico and Colombia, and to assess the relation between margination status and these delays.

Methods

We quantified time in days from symptom onset until testing (latency one) and delay in test results report (latency two) using freely available country-wide open data from Mexico and Colombia. Directed acyclic graphs were built to determine which associations were appropriate to assess. Stratification by margination status, state and hospitalization status was used to determine corresponding associations.

Results

In almost all the study period latency two was longer than latency one. Median latency one was 3 (IQR 0-6) days and latency two 7 (IQR 4-11) days in Colombia, while in Mexico they were 3 (IQR 1-5) days and 4 (IQR 3-6) days. In Colombia, worse margination status prolonged latency two. In Mexico, a lower number and percentage of point-of-care (POC) tests in areas with worse margination.

Conclusion

POC tests must be used as a widespread means to reduce latency two, and until then should be prioritized in areas with longer latency two. An unequal distribution of this resource should be avoided.
T-cell mediated immunity after AZD1222 vaccination: A polyfunctional spike-specific Th1 response with a diverse TCR repertoire
Authors: Swanson Phillip A. , Padilla Marcelino , Hoyland Wesley , McGlinchey Kelly , Fields Paul A. , Bibi Sagida , Faust Saul N. , McDermott Adrian B. , Lambe Teresa , Pollard Andrew J. , Durham Nicholas M. , Kelly Elizabeth J.
Published: June 2021

AZD1222 (ChAdOx1 nCoV-19), a replication-deficient simian adenovirus-vectored vaccine, has demonstrated safety, efficacy, and immunogenicity against coronavirus disease 2019 (COVID-19) in clinical trials and real-world studies. We characterized CD4+ and CD8+ T-cell responses induced by AZD1222 vaccination in peripheral blood mononuclear cells (PBMCs) from 280 unique vaccine recipients aged 18–85 years who enrolled in the phase 2/3 COV002 trial. Total spike-specific CD4+ T cell helper type 1 (Th1) and CD8+ T-cell responses were significantly increased in AZD1222-vaccinated adults of all ages following two doses of AZD1222. CD4+ Th2 responses following AZD1222 vaccination were not detected. Furthermore, AZD1222-specific Th1 and CD8+ T cells both displayed a high degree of polyfunctionality in all adult age groups. T-cell receptor (TCR) β sequences from vaccinated participants mapped against TCR sequences known to react to SARS-CoV-2 revealed substantial breadth and depth across the SARS-CoV-2 spike protein for the AZD1222-induced CD4+ and CD8+ T-cell responses. Overall, AZD1222 vaccination induced a robust, polyfunctional Th1-dominated T-cell response, with broad CD4+ and CD8+ T-cell coverage across the SARS-CoV-2 spike protein.

One Sentence Summary

Polyfunctional CD4+ and CD8+ T-cell responses are elicited against the SARS-CoV-2 spike protein following vaccination with AZD1222
Assessing the Impact of Mental Health Difficulties on Young People’s Daily Lives: Protocol for a Scoping Umbrella Review of Measurement Instruments
Authors: Krause Karolin Rose , Chung Sophie , Rodak Terri , Cleverley Kristin , Butcher Nancy J , Szatmari Peter
Published: June 2021

Introduction

An important consideration for determining the severity of mental health symptoms is their impact on youth’s daily lives. Those wishing to assess life impact face several challenges: First, various measurement instruments are available, including of global functioning, health-related quality of life (HRQoL), and well-being. Existing reviews have tended to focus on one of these domains; consequently, a comprehensive overview is lacking. Second, the extent to which such instruments truly capture distinct concepts is unclear. Third, many available scales conflate symptoms and their impact, thus undermining much needed analyses of associations between the two.

Methods and analysis

A scoping umbrella review will examine existing reviews of life impact measures for use with 6-24-year-olds in the context of mental health and well-being research. We will systematically search five bibliographic databases (MEDLINE, Embase, APA PsycINFO, CINAHL, Web of Science), and conduct systematic record screening, data extraction and charting based on methodological guidance by the Joanna Briggs Institute (JBI). Data synthesis will involve the tabulation of scale characteristics, feasibility, and measurement properties, and the use of summary statistics to synthesize how these instruments operationalize life impact.

Ethics and dissemination

This study will provide a comprehensive road map for researchers and clinicians seeking to assess life impact in youth mental health, providing guidance in navigating available measurement options. We will seek to publish the findings in a leading peer-reviewed journal in the field. Formal research ethics approval will not be required.

Registration details

This protocol was registered prospectively with the Open Science Framework (osf.io/jfqdv).

Strengths and Limitations of this Study

Umbrella review methodology will enable a higher-level synthesis of existing review efforts, thus generating a comprehensive map of available measurement instruments and research findings about their properties.

Our methodological approach is based on the JBI guidelines for scoping reviews, umbrella reviews, and psychometric reviews.

This review is based on a rigorous systematic search developed and executed by a health science librarian.

We will only include studies published in the English language since 1990.

As this is a scoping umbrella review designed to map available measurement instruments, the quality and risk of bias of included review articles will not be systematically assessed.
A Delphi study to establish a consensus definition and clinical reporting guidelines for Mesenchymal Stromal Cells
Authors: Renesme Laurent , Cobey Kelly D , Lê Maxime , Lalu Manoj M , Thébaud Bernard
Published: June 2021

Introduction

Despite being more than two decades of research, Mesenchymal Stromal Cell (MSC) treatments are still struggling to cross the translational gap. Two key issues that likely contribute to these failures are i) the lack of clear definition for MSC and ii) poor quality of reporting in MSC clinical studies. To address these issues, we propose a modified Delphi study to establish a consensus definition for MSC and clinical reporting guidelines for MSC.

Methods and analysis

We will conduct a three-round international modified Delphi Survey. Findings from a recent scoping review examining how MSC are defined and reported in preclinical and clinical studies were used to draft the initial survey for round one of our Delphi. Participants will include a ‘core group’ of individuals as well as researchers whose work was captured in our scoping review. The core group will include stakeholders from different research fields including developmental biology, translational science, research methods, regulatory practices, scholarly journal editing, and industry. The first two survey rounds will be online, and the final round will take place in person. Each participant will be asked to rate their agreement on potential MSC definition characteristics and reporting items using a Likert scale. After each round, we will analyse data to determine which items have reached consensus for inclusion/exclusion, and then develop a revised questionnaire for any new items, or items that did not reach consensus.

Ethics and dissemination

This study received ethical approval from the Ottawa Health Research Network Research Ethics Board. To support the dissemination of our findings, we will use an evidence-based ‘integrated knowledge translation’ approach to engage knowledge users from the inception of the research. This will allow us to develop a tailored end-of-project knowledge translation plan to support and ensure dissemination and implementation of the Delphi results.

Strengths and limitations of this study

We proposed to address the current limitations in MSC experimental and clinical research with a rigorous and methodological consensus building method (Delphi method) that will allow for structured communication on controversial issues.

To support dissemination and implementation of our results, we will engage stakeholders and end-users from the inception of the project – such as patient partners – and will develop a tailored end of project knowledge translation plan (integrated knowledge translation approach) in order to overcome historical issues related to community uptake.

To address the main limitations of a Delphi method (e.g., lack of participation, no in-person interaction or information exchange), we use a modified Delphi survey with a Core group of stakeholders and a face-to-face meeting.
Molecular Genetic Analysis of SARS-CoV-2 Lineages in Armenia
Authors: Avetyan Diana , Hakobyan Siras , Nikoghosyan Maria , Khachatryan Gisane , Sirunyan Tamara , Muradyan Nelli , Zakharyan Roksana , Chavushyan Andranik , Ghazaryan Hovsep , Melkonyan Ani , Stepanyan Ani , Hayrapetyan Varduhi , Atshemyan Sofi , Martirosyan Gevorg , Melik-Andreasyan Gayane , Sargsyan Shushan , Ghazazyan Armine , Aleksanyan Naira , Nersisyan Lilit , Arakelyan Arsen
Published: June 2021

Sequencing of SARS-CoV-2 provides essential information into viral evolution, transmission, and epidemiology. Short-read next-generation sequencing platforms are currently the gold-standard approaches characterized by the highest accuracy. Meanwhile, Oxford Nanopore’s long-read sequencing devices show great promise, offering comparable accuracy, fast turnaround time, and reduced cost. In this study, we performed whole-genome sequencing and molecular-genetic characterization of SARS-CoV-2 from clinical specimens using an amplicon-based nanopore sequencing approach. Lineage and phylogenetic analysis identified the most prevalent lineages at different time points (B.1.1.163, B.1.1.208, B.1.1, and since March 2021 - B.1.1.7). In addition, we evaluated the possible effect of identified mutations on the efficacy of recommended primers and probes used for PCR detection of SARS-CoV-2. In summary, a high-quality SARS-CoV-2 genome can be acquired by nanopore sequencing and it can serve as an efficient and affordable alternative to short-read next-generation sequencing and be used for epidemiologic surveillance and molecular-genetic analyses of the virus.
White Blood Cell and Platelet Dynamics Define Human Inflammatory Recovery
Authors: Foy Brody H , Sundt Thor , Carlson Jonathan C T , Aguirre Aaron D , Higgins John M
Published: June 2021

Inflammation is the physiologic reaction to cellular and tissue damage caused by pathologic processes including trauma, infection, and ischemia1. Effective inflammatory responses integrate molecular and cellular functions to prevent further tissue damage, initiate repair, and restore homeostasis, while futile or dysfunctional responses allow escalating injury, delay recovery, and may hasten death2. Elevation of white blood cell count (WBC) and altered levels of other acute phase reactants are cardinal signs of inflammation, but the dynamics of these changes and their resolution are not established3,4. Patient responses appear to vary dramatically with no clearly defined signs of good prognosis, leaving physicians reliant on qualitative interpretations of laboratory trends4,5.

We retrospectively, observationally studied the human acute inflammatory response to trauma, ischemia, and infection by tracking the longitudinal dynamics of cellular and serum markers in hospitalized patients. Unexpectedly, we identified a conserved pattern of recovery defined by co-regulation of WBC and platelet (PLT) populations. Across all inflammatory conditions studied, recovering patients followed a consistent WBC-PLT trajectory shape that is well-approximated by exponential WBC decay and delayed linear PLT growth. This recovery trajectory shape may represent a fundamental archetype of human physiologic response at the cellular population scale, and provides a generic approach for identifying high-risk patients: 32x relative risk of adverse outcomes for cardiac surgery patients, 9x relative risk of death for COVID-19, and 5x relative risk of death for myocardial infarction.
Reduction in severity of all-cause gastroenteritis requiring hospitalisation in children vaccinated against rotavirus in Malawi
Authors: Mandolo Jonathan J. , Henrion Marc Y. R. , Mhango Chimwemwe , Chinyama End , Wachepa Richard , Kanjerwa Oscar , Malamba-Banda Chikondi , Shawa Isaac T. , Hungerford Daniel , Kamng’ona Arox W. , Iturriza-Gomara Miren , Cunliffe Nigel A. , Jere Khuzwayo C.
Published: June 2021

Background

Rotavirus is the major cause of severe gastroenteritis in children aged <5 years. Introduction of Rotarix® rotavirus vaccine (RV1) in Malawi in 2012 has reduced rotavirus-associated hospitalisations and diarrhoeal mortality. However, RV1 impact on gastroenteritis severity remains unknown. We conducted a hospital-based surveillance study to assess RV1 impact on gastroenteritis severity in children aged <5 years, in Malawi.

Methods

Stool samples were collected from children hospitalised with acute gastroenteritis from December 2011 – October 2019. Gastroenteritis severity was determined using Ruuska and Vesikari scores. Rotavirus was detected in stool using Enzyme Immunoassay. Rotavirus genotypes were determined using nested RT-PCR. Associations between RV1 vaccination and gastroenteritis severity were investigated using adjusted linear regression.

Results

In total, 3,159 children were recruited. After adjusting for Mid-Upper Arm Circumference, age, weight, gender and receipt of other vaccines, all-cause gastroenteritis severity scores were 2.21 units lower (95% CI 1.85, 2.56; p<0.001) among RV1-vaccinated (n=2,224) compared to RV1-unvaccinated children (n=935); the decrease was comparable between rotavirus-positive and rotavirus-negative cases in all age groups. The reduction in severity score was observed against every rotavirus genotype, although the magnitude was smaller among those infected with G12P[6] compared to the remaining genotypes (p=0.011). Other than RV1 vaccination, age was the only variable associated with gastroenteritis severity. Each one-year increment in age was associated with a decrease of 0.43 severity score (95% CI 0.26, 0.60; p<0.001).

Conclusion

Our findings provide additional evidence of RV1 impact in a high disease burden, low-income country, lending further support to Malawi’s rotavirus vaccine programme.

In a long-term hospital-based surveillance study in Malawi, we found evidence of the reduction in gastroenteritis severity among hospitalised RV1-vaccinated children infected with both homotypic and heterotypic rotavirus strains and off-target RV1 vaccine effects against non-rotavirus diarrhoeal severity.
Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag
Authors: Akdogan-Ozdilek Bagdeser , Duval Katherine L , Meng Fanju W , Murphy Patrick J , Goll Mary G
Published: June 2021

Background

Cell fate decisions are governed by interactions between sequence-specific transcription factors and a dynamic chromatin landscape. Zebrafish offer a powerful system for probing the mechanisms that drive these cell fate choices, especially in the context of early embryogenesis. However, technical challenges associated with conventional methods for chromatin profiling have slowed progress toward understanding the exact relationships between chromatin changes, transcription factor binding, and cellular differentiation during zebrafish embryogenesis.

Results

To overcome these challenges, we adapted the chromatin profiling methods CUT&RUN and CUT&Tag for use in zebrafish, and applied these methods to generate high resolution enrichment maps for H3K4me3, H3K27me3, H3K9me3, RNA polymerase II, and the histone variant H2A.Z from mid gastrula stage embryos. Using this data, we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation, provide evidence for an evolving H2A.Z landscape during embryo development, and demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences.

Conclusions

Our results demonstrate the power of combining CUT&RUN and CUT&Tag methods with the strengths of the zebrafish system to define emerging chromatin landscapes in the context of vertebrate embryogenesis.
The Imaging and Molecular Annotation of Xenografts and Tumours (IMAXT) High Throughput Data and Analysis Infrastructure
Authors: González-Solares Eduardo A. , Dariush Ali , González-Fernández Carlos , Yoldaş Aybüke Küpcü , Sa’d Mohammad Al , Millar Neil , Whitmarsh Tristan , Chornay Nicholas , Falciatori Ilaria , Fatemi Atefeh , Goodwin Daniel , Kuett Laura , Mulvey Claire M. , Páez Ribes Marta , Qosaj Fatime , Roth Andrew , Vázquez-García Ignacio , Watson Spencer S. , Windhager Jonas , Aparicio Samuel , Bodenmiller Bernd , Boyden Ed , Caldas Carlos , Harris Owen , Shah Sohrab P. , Tavaré Simon ,   CRUK IMAXT Grand Challenge Team, Bressan Dario , Hannon Gregory J. , Walton Nicholas A.
Published: June 2021

With the aim of producing a 3D representation of tumours, IMAXT uses a large variety of modalities in order to acquire tumour samples and produce a map of every cell in the tumour and its host environment. With the large volume and variety of data produced in the project we develop automatic data workflows and analysis pipelines and introduce a research methodology where scientists connect to a cloud environment to perform analysis close to where data are located instead of bringing data to their local computers. Here we present the data and analysis infrastructure, discuss the unique computational challenges and describe the analysis chains developed and deployed to generate molecularly annotated tumour models. Registration is achieved by use of a novel technique involving spherical fiducial marks that are visible in all imaging modalities used within IMAXT.
Proteome-wide probing of the dual NMT-dependent myristoylation tradeoff unveils potent, mechanism-based suicide inhibitors
Authors: Rivière Frédéric , Dian Cyril , Dutheil Rémi F. , Giglione Carmela , Meinnel Thierry
Published: June 2021

N-myristoyltransferases (NMTs) catalyze protein myristoylation, a major and ubiquitous lipid modification. Originally thought to modify only N-terminal glycine α-amino groups (G-myristoylation), NMTs are now known to modify lysine ε-amino groups (K-myristoylation), the significance of which is uncertain. Here we exploited systematic structural proteomics analyses and a novel pipeline involving the Shigella IpaJ protease to discriminate K- and G-myristoylation with unprecedented accuracy and identify the specific features driving each modification. NMT-dependent K-myristoylation occurs post-translationally and only on lysines 1, 2, or 3 following G-myristoylation or caspase cleavage. Direct interactions between the substrate’s reactive amino group and the NMT catalytic base slow K-myristoylation catalysis. IpaJ unmasked novel K-myristoylation sites in a dozen human proteins. The unique properties of NMT-driven K-myristoylation allowed us to design potent, mechanism-based suicide NMT inhibitors. These analyses unravel the respective paths towards K-myristoylation, G-myristoylation, or NMT inhibition, which rely on a very subtle tradeoff embracing the chemical landscape around the reactive group.

SIGNIFICANCE STATEMENT

We report the specific and unique elements guiding N-myristoyltransferase to either alpha or epsilon myristoylation, allowing us to establish the post-translational nature of N-myristoyltransferase-dependent lysine myristoylation and design novel, potent N-myristoyltransferase inhibitors.
Evolutionary plasticity of SH3 domain binding by Nef proteins of the HIV-1/SIVcpz lentiviral lineage
Authors: Zhao Zhe , Fagerlund Riku , Sauter Daniel , Tossavainen Helena , Permi Perttu , Kirchhoff Frank , Saksela Kalle
Published: June 2021

The accessory protein Nef of human and simian immunodeficiency viruses (HIV and SIV) is an important pathogenicity factor known to interact with cellular protein kinases and other signaling proteins. A canonical SH3 domain binding motif in Nef is required for most of these interactions. For example, HIV-1 Nef activates the tyrosine kinase Hck by tightly binding to its SH3 domain. An archetypal contact between a negatively charged SH3 residue and a highly conserved arginine in Nef (Arg77) plays a key role here. Combining structural analyses with functional assays, we here show that Nef proteins have also developed a distinct structural strategy - termed the “R-clamp” - that favors the formation of this salt bridge via buttressing Arg77. Comparison of evolutionarily diverse Nef proteins revealed that several distinct R-clamps have evolved that are functionally equivalent but differ in the side chain compositions of Nef residues 83 and 120. Whereas a similar R-clamp design is shared by Nef proteins of HIV-1 groups M, O, and P, as well as SIVgor, the Nef proteins of SIV from the Eastern chimpanzee subspecies (SIVcpzP.t.s.) exclusively utilize another type of R-clamp. By contrast, SIV of Central chimpanzees (SIVcpzP.t.t.) and HIV-1 group N strains show more heterogenous R-clamp design principles, including a non-functional evolutionary intermediate of the aforementioned two classes. These data add to our understanding of the structural basis of SH3 binding and kinase deregulation by Nef, and provide an interesting example of primate lentiviral protein evolution.

AUTHOR SUMMARY

Viral replication depends on interactions with a plethora of host cell proteins. Cellular protein interactions are typically mediated by specialized binding modules, such as the SH3 domain. To gain access to host cell regulation viruses have evolved to contain SH3 domain binding sites in their proteins, a notable example of which is the HIV-1 Nef protein. Here we show that during the primate lentivirus evolution the structural strategy that underlies the avid binding of Nef to cellular SH3 domains, which we have dubbed the R-clamp, has been generated via alternative but functionally interchangeable molecular designs. These patterns of SH3 recognition depend on the amino acid combinations at the positions corresponding to residues 83 and 120 in the consensus HIV-1 Nef sequence, and are distinctly different in Nef proteins from SIVs of Eastern and Central chimpanzees, gorillas, and the four groups of HIV-1 that have independently originated from the latter two. These results highlight the evolutionary plasticity of viral proteins, and have implications on therapeutic development aiming to interfere with SH3 binding of Nef.
SIA: Selection Inference Using the Ancestral Recombination Graph
Authors: Hejase Hussein A. , Mo Ziyi , Campagna Leonardo , Siepel Adam
Published: June 2021

Detecting signals of selection from genomic data is a central problem in population genetics. Coupling the rich information in the ancestral recombination graph (ARG) with a powerful and scalable deep learning framework, we developed a novel method to detect and quantify positive selection: Selection Inference using the Ancestral recombination graph (SIA). Built on a Long Short-Term Memory (LSTM) architecture, a particular type of a Recurrent Neural Network (RNN), SIA can be trained to explicitly infer a full range of selection coefficients, as well as the allele frequency trajectory and time of selection onset. We benchmarked SIA extensively on simulations under a European human demographic model, and found that it performs as well or better as some of the best available methods, including state-of-the-art machine-learning and ARG-based methods. In addition, we used SIA to estimate selection coefficients at several loci associated with human phenotypes of interest. SIA detected novel signals of selection particular to the European (CEU) population at the MC1R and ABCC11 loci. In addition, it recapitulated signals of selection at the LCT locus and several pigmentation-related genes. Finally, we reanalyzed polymorphism data of a collection of recently radiated southern capuchino seedeater taxa in the genus Sporophila to quantify the strength of selection and improved the power of our previous methods to detect partial soft sweeps. Overall, SIA uses deep learning to leverage the ARG and thereby provides new insight into how selective sweeps shape genomic diversity.
Prevalence of white matter pathways coming into a single diffusion MRI voxel orientation: the bottleneck issue in tractography
Authors: Schilling Kurt G , Tax Chantal M.W. , Rheault Francois , Landman Bennett , Anderson Adam , Descoteaux Maxime , Petit Laurent
Published: June 2021

Characterizing and understanding the limitations of diffusion MRI fiber tractography is a prerequisite for methodological advances and innovations which will allow these techniques to accurately map the connections of the human brain. The so-called “crossing fiber problem” has received tremendous attention and has continuously triggered the community to develop novel approaches for disentangling distinctly oriented fiber populations. Perhaps an even greater challenge occurs when multiple white matter bundles converge within a single voxel, or throughout a single brain region, and share the same parallel orientation, before diverging and continuing towards their final cortical or sub-cortical terminations. These so-called “bottleneck” regions contribute to the ill-posed nature of the tractography process, and lead to both false positive and false negative estimated connections. Yet, as opposed to the extent of crossing fibers, a thorough characterization of bottleneck regions has not been performed. The aim of this study is to quantify the prevalence of bottleneck regions. To do this, we use diffusion tractography to segment known white matter bundles of the brain, and assign each bundle to voxels they pass through and to specific orientations within those voxels (i.e. fixels). We demonstrate that bottlenecks occur in greater than 50-70% of fixels in the white matter of the human brain. We find that all projection, association, and commissural fibers contribute to, and are affected by, this phenomenon, and show that even regions traditionally considered “single fiber voxels” often contain multiple fiber populations. Together, this study shows that a majority of white matter presents bottlenecks for tractography which may lead to incorrect or erroneous estimates of brain connectivity or quantitative tractography (i.e., tractometry), and underscores the need for a paradigm shift in the process of tractography and bundle segmentation for studying the fiber pathways of the human brain.
Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4
Authors: Neijenhuis Tim , van Keulen Siri C. , Bonvin Alexandre M.J.J.
Published: June 2021

A wide range of cellular processes require the formation of multimeric protein complexes. The rise of cryo-electron microscopy (cryo-EM) has enabled the structural characterization of these protein assemblies. The produced density maps can, however, still suffer from limited resolution, impeding the process of resolving structures at atomic resolution. In order to solve this issue, monomers can be fitted into low-to-medium resolution maps. Unfortunately, the produced models frequently contain atomic clashes at the protein-protein interfaces (PPIs) as intermolecular interactions are typically not considered during monomer fitting. Here, we present a refinement approach based on HADDOCK2.4 to remove intermolecular clashes and optimize PPIs. A dataset of 14 cryo-EM complexes was used to test eight protocols. The best performing protocol, consisting of a semi-flexible simulated annealing refinement with restraints on the centroids of the monomers, was able to decrease intermolecular atomic clashes by 98% without significantly deteriorating the quality of the cryo-EM density fit.
PI(4,5)P2 controls slit diaphragm formation and endocytosis in Drosophila nephrocytes
Authors: Gass Maximilian , Borkowsky Sarah , Lotz Marie-Luise , Schröter Rita , Nedvetsky Pavel , Luschnig Stefan , Rohlmann Astrid , Missler Markus , Krahn Michael P.
Published: June 2021

Drosophila nephrocytes are an emerging model system for mammalian podocytes and podocyte-associated diseases. Like podocytes, nephrocytes exhibit characteristics of epithelial cells, but the role of phospholipids in polarization of these cells is yet unclear. In epithelia phosphatidylinositol(4,5)bisphosphate (PI(4,5)P2) and phosphatidylinositol(3,4,5)-trisphosphate (PI(3,4,5)P3) are asymmetrically distributed in the plasma membrane and determine apical-basal polarity. Here we demonstrate that both phospholipids are present in the plasma membrane of nephrocytes, but only PI(4,5)P2 accumulates at slit diaphragms. Knockdown of Skittles, a phosphatidylinositol(4)phosphate 5-kinase, which produces PI(4,5)P2, abolished slit diaphragm formation and led to strongly reduced endocytosis. Notably, reduction in PI(3,4,5)P3 by overexpression of PTEN or expression of a dominant-negative phosphatidylinositol-3-Kinase did not affect nephrocyte function, whereas enhanced formation of PI(3,4,5)P3 by constitutively active phosphatidylinositol-3-Kinase resulted in strong slit diaphragm and endocytosis defects by ectopic activation of the Akt/mTOR pathway. Thus, PI(4,5)P2 but not PI(3,4,5)P3 is essential for slit diaphragm formation and nephrocyte function. However, PI(3,4,5)P3 has to be tightly controlled to ensure nephrocyte development.
Genetic code expansion in the engineered organism Vmax X2: High yield and exceptional fidelity
Authors: Santiago Sebasthian , Ad Omer , Shah Bhavana , Zhang Zhongqi , Zhang Xizi , Chatterjee Abhishek , Schepartz Alanna
Published: June 2021

We report that the recently introduced commercial strain of V. natriegens (Vmax X2) supports robust unnatural amino acid mutagenesis, generating exceptional yields of soluble protein containing up to 5 non-canonical α-amino acids (ncAA). The isolated yields of ncAA-containing superfolder green fluorescent protein (sfGFP) expressed in Vmax X2 are up to 25-fold higher than those achieved using commercial expression strains (Top10 and BL21) and more than10-fold higher than those achieved using two different genomically recoded E. coli strains that lack endogenous UAG stop codons and release factor 1 and have been optimized for improved fitness and preferred growth temperature (C321.ΔA.opt and C321.ΔA.exp). In addition to higher yields of soluble protein, Vmax X2 cells also generate proteins with significantly lower levels of mis-incorporated natural α-amino acids at the UAG-programmed position, especially in cases where the ncAA is an imperfect substrate for the chosen orthogonal aminoacyl tRNA synthetase (aaRS). This increase in fidelity implies that use of Vmax X2 cells as the expression host can obviate the need for time-consuming directed evolution experiments to improve specific activity of highly desirable but imperfect ncAA substrates.
Transcription Factor Activation Profiles (TFAP) identify compounds promoting differentiation of Acute Myeloid Leukemia cell lines
Authors: Riccio Federica , Micarelli Elisa , Secci Riccardo , Giuliani Giulio , Vumbaca Simone , Massacci Giorgia , Castagnoli Luisa , Fuoco Claudia , Cesareni Gianni
Published: June 2021

Repurposing of drugs for new therapeutic use has received considerable attention for its potential to reduce time and cost of drug development. Here we present a new strategy to identify chemicals that are likely to induce differentiation of leukemic cells. As Acute Myeloid Leukemia (AML) is the result of a block in myeloid differentiation, finding new drugs that are capable of inducing blast terminal maturation is considered a valuable strategy. We used data from the Connectivity Map (CMap) to identify drugs that could be repositioned for their potential to activate transcription factors that mediate myeloid differentiation. Compounds promoting the activation of transcription factors that play a positive role in myeloid differentiation were considered candidate pro-differentiation drugs. This approach yielded a list of chemicals ranked according to the potential to activate transcription factors that induce differentiation of leukemic progenitor cells. Drugs that are already used in differentiation therapy, such as for instance all-trans retinoic acid (ATRA) are in the top positions of this ranked list. To validate our strategy, we tested thein vitrodifferentiation potential of 22 candidate compounds using the HL-60 human cell line as a myeloid differentiation model. Ten out of 22 compounds, ranking high in the inferred list, were confirmed to induce significant differentiation of HL-60. Some of these compounds are known to trigger the DNA damage response, thus identifying this process as a target to modulate myeloid differentiation. These results underscore the potential of our approach to accelerate the drug discovery process. The method that we have developed is highly versatile and it can be adapted to different drug repurposing projects.