bluuebunny/crossref_metadata_2025 huggingface dataset:
Bashing irreproducibility withshournal
Authors: Kirchner Tycho , Riege Konstantin , Hoffmann Steve
Published: August 2020

1

The Linux shell is arguably one of the most important computational tools across various scientific disciplines. Its high flexibility makes it the platform of choice for many file operations and smaller scripting tasks. Also, many stand-alone programs are called from the Linux shell - typically followed by multiple command-line parameters. However, in larger analysis projects, keeping track of the work quickly becomes challenging, as a typical shell workflow involves the iterative execution of commands with many parameters, modification of scripts, and editing of configuration files. Too often, researchers find themselves in the uncomfortable position that a computational result generated a few weeks ago can no longer be reproduced, despite having taken great care documenting the work manually. On the other hand, there is a lack of tools able to record the researcher’s shell activity automatically with reasonably low runtime- and storage overhead. To close this critical gap, we developedshournal, a program that tightly integrates with the Linux shell and automatically records every shell command along with the files it reads or writes. Besides logging command- and file metadata, such as working directory, file path, and checksums,shournalcan be configured to archive scripts or configuration files that are not regularly under version control viagitorsvn.
Setting Limits on Neural Network’s Predictive Capacity in T1D Blood Glucose Concentration
Authors: Chuna Thomas
Published: August 2020

The ability to anticipate changes in blood glucose (BG) concentration would have a great impact on Type 1 diabetics (T1D). In order to create T1D treatment plans, patients collect a BG concentration time series. It has been demonstrated that various types of recurrent neural networks, such as Long Short Term Memory (LSTM), have success forecasting T1D BG concentrations. However, limited work has been done to characterize the T1D time series or set limits on neural network’s predictive capacity. In this work, a T1D patient’s 14 day BG concentration time series is studied. First, I test the time series stationarity. Then I use auto-correlation analysis, spectral analysis, and Gaussian process regression to characterize the T1D BG time series. Finally, the LSTM’s prediction quality is quantified and interpreted at different prediction intervals. The success or failure of the LSTM’s predictions are interpreted using the characterization of the time series.
Measurement lessons of a repeated cross-sectional household food insecurity survey during the COVID-19 pandemic in Mexico
Authors: Gaitán-Rossi P. , Vilar-Compte M. , Teruel G. , Pérez-Escamilla R.
Published: August 2020

Objective

To validate the telephone modality of the Latin American and Caribbean Food Security Scale (ELCSA) included in three waves of a phone survey to estimate the monthly household food insecurity (HFI) prevalence during the COVID-19 pandemic in Mexico.

Design

We examined the reliability and internal validity of the ELCSA scale in three repeated waves of a cross-sectional surveys with Rasch models. We estimated the monthly prevalence of food insecurity in the general population and in households with and without children, and compared them with a national 2018 survey. We tested concurrent validity by testing associations of HFI with socioeconomic status and anxiety.

Setting

ENCOVID-19 is a monthly telephone cross-sectional survey collecting information on the well-being of Mexican households during the pandemic lockdown. Surveys used probabilistic samples and we used data from April (n=833), May (n=850), and June 2020 (n=1,674).

Participants

Mexicans 18 years or older who had a mobile telephone.

Results

ELCSA had adequate model fit and HFI was associated, within each wave, with more poverty and anxiety. The COVID-19 lockdown was associated with an important reduction in food security; decreasing stepwise from 38.9% in 2018 to 24.9% in June 2020 in households with children.

Conclusions

Telephone surveys are a feasible strategy to monitor food insecurity with ELCSA
Seroprevalence of SARS-CoV-2 in Niger State: A Pilot Cross Sectional Study
Authors: Majiya Hussaini , Aliyu-Paiko Mohammed , Balogu Vincent T , Musa Dickson A , Salihu Ibrahim M , Kawu Abdullahi A , Bashir Yakubu I , Sani Aishat A , John Baba , Muhammad Amina T , Jibril Fatima L , Bala Ezekiel , Obaje Nuhu G , Aliyu Yahaya B. , Muhammad Ramatu G , Mohammed Hadiza , Gimba Usman N , Uthman Abduljelili , Liman Hadiza M , Sule Alfa A , Joseph Kolo J , Makusidi Mohammed M , Isah Mohammed D , Abdullahi Ibrahim , Ndagi Umar , Waziri Bala , Bisallah Chindo I , Dadi-Mamud Naomi J , Ibrahim Kolo , Adamu Abu Kasim
Published: August 2020

Background

Coronavirus Disease 2019 (COVID-19) Pandemic caused by SARS-CoV-2 is ongoing causing human and socioeconomic losses.

Objective

To know how far the virus has spread in Niger State, Nigeria, a pilot study was carried out to determine the SARS-CoV-2 seroprevalence, patterns, dynamics, and risk factors in the state.

Methods

A cross sectional study design and Clustered-Stratified-Random sampling strategy were used to select 185 test participants across the state. SARS-CoV-2 IgG and IgM Rapid Test Kits (Colloidal gold immunochromatography lateral flow system) were used to determine the presence or absence of the antibodies to the virus in the blood of sampled participants across Niger State as from 26th June 2020 to 30th June 2020. The test kits were validated using the blood samples of some of the Nigeria Center for Disease Control (NCDC) confirmed positive and negative COVID-19 cases in the State. SARS-CoV-2 IgG and IgM Test results were entered into the EPIINFO questionnaire administered simultaneously with each test. EPIINFO was then used for to calculate arithmetic mean and percentage, odd ratio, chi-square, and regression at 95% Confidence Interval of the data generated.

Results

The seroprevalence of SARS-CoV-2 in Niger State was found to be 25.41% and 2.16% for the positive IgG and IgM respectively. Seroprevalence among age groups, gender and by occupation varied widely. COVID-19 asymptomatic rate in the state was found to be 46.81%. The risk analyses showed that the chances of infection are almost the same for both urban and rural dwellers in the state. However, health care workers, those that experienced flu-like symptoms and those that have had contact with person (s) that travelled out of Nigeria in the last six (6) months (February -June 2020) are twice (2 times) at risk of being infected with the virus. More than half (54.59%) of the participants in this study did not practice social distancing at any time since the pandemic started. Discussions about knowledge, practice and attitude of the participants are included.

Conclusion

The observed Niger State SARS-CoV-2 seroprevalence and infection patterns means that the virus is widely spread, far more SARS CoV-2 infections occurred than the reported cases and high asymptomatic COVID-19 across the state.
A comparative analysis between a SIRD compartmental model and the Richards growth model
Authors: Macêdo Antônio M. S. , Brum Arthur A. , Duarte-Filho Gerson C. , Almeida Francisco A. G. , Ospina Raydonal , Vasconcelos Giovani L.
Published: August 2020

We propose a compartmental SIRD model with time-dependent parameters that can be used to give epidemiological interpretations to the phenomenological parameters of the Richards growth model. We illustrate the use of the map between these two models by fitting the fatality curves of the COVID-19 epidemic data in Italy, Germany, Sweden, Netherlands, Cuba, and Japan.
Descriptive analysis of the Autism Spectrum Quotient (AQ) in a sample of Brazilian adults
Authors: Alves Ana Luíza Costa , de Paula Jonas Jardim , de Miranda Débora Marques , Romano-Silva Marco Aurélio
Published: August 2020

Background

The Autism Spectrum Disorder is characterized by the presence of difficulties in social interaction, inflexible, repetitive and/or stereotyped behaviors and interests. The Autism Spectrum Quotient (AQ) is a self-report instrument with 50 items created to quantify autistic traits in individuals older than 18 years with average or above-average intelligence.

Objectives

The principal aim was to present a brief descriptive analysis of the AQ in a heterogeneous sample of Brazilian adults, also, to measure the clinical validity of the scale.

Method

We recruited all the participants in Brazil (N=1024). Then we described the distribution in the general population (N=385) and investigated the AQ accuracy in a sample of autistic adults (N=32).

Results

Our results suggested that autism traits were normally distributed in the population, but Brazilian adults have shown a different profile from the original study. Further, we found that 24 adults from the sample had a clinical score on the AQ, compatible with their previous autism diagnosis.

Discussion

Our population probably reports more symptoms compared to other because the original clinical score represents a lower percentile in our sample. Also, future work will be required to adequate the use of the AQ in the Brazilian population.
Mathematical Analysis, Model and Prediction of COVID-19 Data
Authors: Tong Yit C.
Published: August 2020

A simple and effective mathematical procedure for the description of observed COVID-19 data and calculation of future projections is presented. An exponential function E(t) with a time-varying Growth Constant k(t) is used. E(t) closely approximates observed COVID-19 Daily Confirmed Cases with NRMSD’s of 1 to 2%. An example of prediction of future cases is presented. The Effective Growth Rates of a discrete SIR model were estimated on the basis of k(t) for COVID-19 data for Germany, and were found to be consistent with those reported in a previous study (1). The proposed procedure, which involves less than ten basic algebraic, logarithm and exponentiation operations for each data point, is suitable for use in promoting interdisciplinary research, exchange and sharing of information.
Sleep Abnormalities in the Synaptopathies – SYNGAP1-related Intellectual Disability and Phelan-McDermid syndrome
Authors: Smith-Hicks Constance , Stowe Robert C. , McCormack Maria , Holder J. Lloyd
Published: August 2020

Neurodevelopmental disorders are frequently associated with sleep disturbances. One class of neurodevelopmental disorders, the genetic synaptopathies, is caused by mutations in genes encoding proteins found at the synapse. Mutations in these genes cause derangement of synapse development and function. We utilized a validated sleep instrument, Children’s Sleep Habits Questionnaire (CSHQ) to discover what sleep abnormalities occur in individuals with two synaptopathies – Phelan-McDermid syndrome (PMD) and SYNGAP1-related Intellectual Disability (SYNGAP1-ID) when compared with healthy controls. We found both PMD and SYNGAP1-ID have significant sleep abnormalities with SYNGAP1-ID having greater severity of sleep disturbance than PMD. We found that sleep disturbances were more severe for both disorders in individuals 10 years and older compared with those less than 10 years old. Individuals with either disorder were more likely to use sleep aids than healthy controls.

Furthermore, review of polysomnography studies for individuals with SYNGAP1-ID revealed significant reduction in rapid eye movement (REM) sleep content and delayed REM latency demonstrating abnormalities in sleep architecture. In conclusion, sleep disturbances are a significant phenotype in the synaptopathies PMD and SYNGAP1-ID. Improved sleep is a viable clinical endpoint for future clinical trials for these neurodevelopmental disorders.
Performing Qualitative Mask Fit Testing without a Commercial Kit: Fit Testing Which can be Performed at Home and at Work
Authors: O’Kelly Eugenia , Arora Anmol , Pearson Charlotte , Ward James , Clarkson P. John
Published: August 2020

Introduction

Qualitative fit testing is a popular method of ensuring the fit of sealing face masks such as N95 and FFP3 masks. Increased demand due to the COVID-19 pandemic has led to shortages in testing equipment and has forced many institutions to abandon fit testing. Three key materials are required for qualitative fit testing: the test solution, nebulizer, and testing hood. Accessible alternatives to the testing solution have been studied. This exploratory qualitative study evaluates alternatives to the nebulizer and hoods for performing qualitative fit testing.

Methods

Four devices were trialed to replace the test kit nebulizer. Two enclosures were tested for their ability to replace the test hood. Three researchers evaluated promising replacements under multiple mask fit conditions to assess functionality and accuracy.

Results

The aroma diffuser and smaller enclosures allowed participants to perform qualitative fit tests quickly and with high accuracy.

Discussion & Conclusion

Aroma diffusers show significant promise in their ability to allow individuals to quickly, easily, and inexpensively perform qualitative fit testing. Our findings indicate that aroma diffusers and homemade testing hoods may allow for qualitative fit testing when conventional apparatus is unavailable. Additional research is needed to evaluate the safety and reliability of these devices.
Social Behaviors Associated with a Positive COVID-19 Test Result
Authors: Speaker Sidra , Doherty Christine , Pfoh Elizabeth R. , Dunn Aaron , Hair Bryan , Shaker Victoria , Daboul Lynn , Rothberg Michael B.
Published: August 2020

Objective

To compare behaviors of individuals who tested positive for COVID-19 relative to non-infected individuals.

Methods

We sent COVID positive cases and age/gender matched controls a survey regarding their social behaviors via MyChart (online patient portal). We called cases if they did not complete the electronic survey within two days. Data was collected from May-June 2020. Survey responses for cases without a close contact and controls were compared using Pearson chi-square or Fisher’s Exact tests as appropriate.

Results

A total of 339 participants completed the survey (113 cases, 226 controls); 45 (40%) cases had known contact with COVID-19. Cases were more likely to have recently traveled (4% vs. 0%, p=0.01) or to work outside the home (40% vs. 25%, p=0.02). There was no difference in the rates of attending private or public gatherings, mask/glove use, hand-washing, cleaning surfaces and cleaning mail/groceries between cases and controls.

Conclusions

Sixty percent of cases had no known contact with COVID-19, indicating ongoing community transmission and underlining the importance of contact tracing. The greater percentage of cases who work outside the home provides further evidence for social distancing.
Extended lifetime of respiratory droplets in a turbulent vapour puff and its implications on airborne disease transmission
Authors: Chong Kai Leong , Ng Chong Shen , Hori Naoki , Yang Rui , Verzicco Roberto , Lohse Detlef
Published: August 2020

To mitigate the COVID-19 pandemic, it is key to slow down the spreading of the life-threatening coronavirus (SARS-CoV-2). This spreading mainly occurs through virus-laden droplets expelled at speaking, screaming, shouting, singing, coughing, sneezing, or even breathing [1–7]. To reduce infections through such respiratory droplets, authorities all over the world have introduced the so-called “2-meter distance rule” or “6-foot rule”. However, there is increasing empirical evidence, e.g. through the analysis of super-spreading events [6, 8–11], that airborne transmission of the coronavirus over much larger distances plays a major role [1–3, 7, 12–15], with tremendous implications for the risk assessment of coronavirus transmission. It is key to better and fundamentally understand the environmental ambient conditions under which airborne transmission of the coronavirus is likely to occur, in order to be able to control and adapt them. Here we employ direct numerical simulations of a typical respiratory aerosol in a turbulent jet of the respiratory event within a Lagrangian-Eulerian approach [16–18] with 5000 droplets, coupled to the ambient velocity, temperature, and humidity fields to allow for exchange of mass and heat [19] and to realistically account for the droplet evaporation under different ambient conditions. We found that for an ambient relative humidity of 50% the lifetime of the smallest droplets of our study with initial diameter of 10 µm gets extended by a factor of more than 30 as compared to what is suggested by the classical picture of Wells [20, 21], due to collective effects during droplet evaporation and the role of the respiratory humidity [22], while the larger droplets basically behave ballistically. With increasing ambient relative humidity the extension of the lifetimes of the small droplets further increases and goes up to 150 times for 90% relative humidity, implying more than two meters advection range of the respiratory droplets within one second. Smaller droplets live even longer and travel further. Our results may explain why COVID-19 superspreading events can occur for large ambient relative humidity such as in cooled-down meat-processing plants [10] or in pubs with poor ventilation. We anticipate our tool and approach to be starting points for larger parameter studies and for optimizing ventilation and indoor humidity controlling concepts, which in the upcoming autumn and winter both will be key in mitigating the COVID-19 pandemic.
Total testosterone is not associated with lean mass or handgrip strength in pre-menopausal females: findings from the NHANES
Authors: Alexander Sarah E. , Abbott Gavin , Aisbett Brad , Wadley Glenn D. , Hnatiuk Jill A. , Lamon Séverine
Published: August 2020

Testosterone is a naturally occurring hormone that has been positively associated with lean mass and strength in males. Whether endogenous testosterone is related to lean mass and strength in females is unknown.

Objective

To examine the relationship between endogenous testosterone concentration and lean mass and handgrip strength in healthy, pre-menopausal females.

Methods

Secondary data from the 2013-2014 National Health and Nutrition Examination Survey (NHANES)were used. Females were aged 18-40 (n=753, age 30 ± 6 yr, mean ± SD) and pre-menopausal. Multivariate linear regression models were used to examine associations between total testosterone, height-adjusted lean mass and handgrip strength.

Results

Mean ± SD testosterone concentration was 1.0 ± 0.6 nmol·L-1 and mean free androgen index (FAI) was 0.02 ± 0.02. Mean fat-free mass index (FFMI) was 16.4 ± 3.0 kg·m-2 and mean handgrip strength was 61.7 ± 10.5 kg. In females, testosterone was not associated with FFMI (β=0.08; 95%CI: −0.02, 0.18; p=0.11) or handgrip strength (β=0.03; 95%CI: −0.11, 0.17; p=0.67) in a statistically significant manner. Conversely, FAI was positively associated with FFMI (β=0.17; 95%CI: 0.01, 0.33; p=0.04) but not handgrip strength (β=0.19; 95%CI: −0.02, 0.21; p=0.10).

Conclusions

These findings indicate that FAI, but not total testosterone, is associated with FFMI in females. The small coefficients however suggest that FAI only accounts for a minor proportion of the variance in FFMI, highlighting the complexity of the regulation of lean mass in female physiology. FAI nor total testosterone are associated with handgrip strength in females when testosterone concentrations are not altered pharmacologically.
Regional ventilation characteristics during non-invasive respiratory support in preterm infants
Authors: Thomson J , Rüegger CM , Perkins EJ , Pereira-Fantini PM , Farrell O , Owen LS , Tingay DG
Published: August 2020

Objective

To determine the regional ventilation characteristics during non-invasive ventilation in stable preterm infants. The secondary aims were to explore the relationship between indicators of ventilation homogeneity and other clinical measures of respiratory status.

Design

Prospective observational study.

Setting

Two tertiary neonatal intensive care units.

Patients

Forty stable preterm infants born <30 weeks gestation receiving either CPAP (n=32) or nHF(n=8) if <36 weeks corrected gestation, and extubated for at least 24 hours at time of study.

Interventions

Continuous electrical impedance tomography imaging of regional ventilation during 60-minutes of quiet breathing on clinician-determined non-invasive settings.

Main outcome measures

Gravity-dependent and right-left centre of ventilation (CoV), percentage of whole lung tidal volume by lung region, and percentage of lung unventilated were determined for 120 artefact-free breaths/infant (4770 breaths included). Oxygen saturation, heart and respiratory rates were also measured.

Results

Ventilation was greater in the right lung (mean (SD) CoVRL 69.1 (14.9)%) and the gravity non-dependent lung; ideal-actual CoV 1.4 (4.5). The central third of the lung received the most tidal volume, followed by the non-dependent and dependent regions (p<0.0001 repeated measure ANOVA). Ventilation inhomogeneity was associated with worse SpO2/FiO2, (p=0.031, r2 0.12; linear regression). In those infants that later developed bronchopulmonary dysplasia (n=25) SpO2/FiO2 was worse and non-dependent ventilation inhomogeneity greater than in those that did not (both p<0.05; t test Welch correction).

Conclusions

There is high breath-by-breath variability in regional ventilation patterns during NIV in preterm infants. Ventilation favoured the gravity non-dependent lung, with ventilation inhomogeneity associated with worse oxygenation.
Seasonal climate variations promote bacterial α-diversity in soil
Authors: Zhao Xin-Feng , Shu Wen-Sheng , Hao Yi-Qi
Published: August 2020

Ecological theory suggests that temporal environmental fluctuations can contribute greatly to diversity maintenance. Given bacteria’s short generation time and rapid responses to environmental change, seasonal climate fluctuations are very likely to play an important role in maintaining the extremely high α-diversity of soil bacterial community, which has been unfortunately neglected in previous studies. Here, with in-depth analyses of two previously published soil bacterial datasets at global scale, we found that soil bacterial α-diversity was positively correlated with both seasonal variations of temperature and precipitation. Furthermore, piecewise structural equation models showed that seasonal variations of temperature or precipitation directly promoted soil bacterial α-diversity in each dataset. However, it is noteworthy that the importance of seasonal climate variations might be underestimated in the above analyses, due to the high level of environmental variations irrelevant to climate seasonality among sampling sites and the lack of sampling across seasons. Supplementary analyses of a previously published wheat cropland dataset with samples collected in both summer and winter across North China Plain was conducted. Similarly, we found that bacterial α-diversity was positively correlated with seasonal climate variations, but much stronger, though the range of seasonal climate variations was much smaller compared to the two global datasets. Collectively, these findings implied that fluctuation-dependent mechanisms of diversity maintenance presumably operate in soil bacterial communities. Based on existing evidence, we speculated that the storage effect may be the main mechanism responsible for diversity maintenance in soil bacterial community, but rigorous experimental tests are needed in the future.
Advances in mixed cell deconvolution enable quantification of cell types in spatially-resolved gene expression data
Authors: Danaher Patrick , Kim Youngmi , Nelson Brenn , Griswold Maddy , Yang Zhi , Piazza Erin , Beechem Joseph M.
Published: August 2020

We introduce SpatialDecon, an algorithm for quantifying cell populations defined by single cell RNA sequencing within the regions of spatially-resolved gene expression studies. It obtains cell abundance estimates that are spatially-resolved, granular, and paired with highly multiplexed gene expression data.

SpatialDecon incorporates several advancements in the field of gene expression deconvolution. We propose an algorithm based in log-normal regression, attaining sometimes dramatic performance improvements over classical least-squares methods. We compile cell profile matrices for 27 tissue types. We identify genes whose minimal expression by cancer cells makes them suitable for immune deconvolution in tumors. And we provide a lung tumor dataset for benchmarking immune deconvolution methods.

In a lung tumor GeoMx DSP experiment, we observe a spatially heterogeneous immune response in intricate detail and identify 7 distinct phenotypes of the localized immune response. We then demonstrate how cell abundance estimates give crucial context for interpreting gene expression results.
Different activation signatures in the primary sensorimotor and higher-level regions for haptic three-dimensional curved surface exploration
Authors: Yang Jiajia , Molfese Peter J. , Yu Yinghua , Handwerker Daniel A. , Chen Gang , Taylor Paul A. , Ejima Yoshimichi , Wu Jinglong , Bandettini Peter A.
Published: August 2020

Haptic object perception begins with continuous exploratory contacts, and the human brain needs to accumulate sensory information continuously over time. However, it is still unclear how the primary sensorimotor cortex (PSC) interacts with these higher-level regions during haptic exploration across time. This functional magnetic resonance imaging (fMRI) study investigates time-dependent haptic object processing by examining brain activity during haptic 3D curve and roughness estimation. For this experiment, we designed sixteen haptic stimuli (4 kinds of curve × 4 kinds of roughness) for the haptic curve and roughness estimation tasks. Twenty participants were asked to move their right index and middle fingers along with the surface twice and to estimate one of the two features--roughness or curvature--dependent on the task instruction. We found that the brain activity in several higher-level regions (e.g., bilateral posterior parietal cortex) linearly increased with curvature through the haptic exploration phase. Surprisingly, we found that the contralateral PSC was parametrically modulated by the number of curves only during the late exploration phase, but not during the early exploration phase. In contrast, we found no similar parametric modulation activity patterns for haptic roughness estimation in either the contralateral PSC or in the higher-level regions. Together, our findings suggest that haptic 3D object perception is processed across the cortical hierarchy, while the contralateral PSC interacts with other higher-level regions across time in a manner that is dependent upon object features.

Highlights

We observed the brain activity of haptic object perception using parametric stimuli.

Haptic curve estimation showed parametric modulation across the cortical hierarchy.

Curve parametric modulation in the sensorimotor cortex showed time dependency.

Roughness parametric modulation showed very little dependency in any regions of the brain.

These findings reflect the nature of time-dependent haptic object processing in the brain.
Plant community associations with environmental variables in a semi-deciduous tropical forest of the Dominican Republic
Authors: Martínez Batlle José Ramón , van der Hoek Yntze
Published: August 2020

Despite being increasingly threatened by human-induced disturbances, dry forests remain the least studied and protected forest types in the Caribbean region. In contrast to many other forest systems in the world, we have little knowledge of the site-specific variation in vegetation communities within these forests, nor understand how plant species distribution is determined by environmental variables, including among them geological attributes. Here, we assessed the associations between plant communities and habitat types in a semi-deciduous forest of the Dominican Republic. We collected vegetation data from 23 sites within the Ocoa river basin, which we classified into six groups with a Random Forest algorithm, lithology, geomorphology, topography, and last decade history of forest loss as predictor variables. We established three main clusters: one group which encompassed sites with forest over a limestone substrate, four groups of sites with forests over a marlstone substrate with varied degrees of steepness and forest loss history, and one group that gathered all sites with forest over an alluvial substrate. In order to measure the associations of plant communities with groups of sites, we used the indicator value index (IndVal), which indicates whether a plant species is found in one or multiple habitat types, and the phi coefficient of association, which measures species preferences for habitats. We found that 16 species of woody plants are significantly associated with groups of sites by means of their indices. Our findings suggest that the detection of plant species associations with our selection of environmental variables is possible using a combination of indices. We show that there is considerable variation in plant community composition within the semi-deciduous forest studied, and suggest that conservation planning should focus on protection of this variation, while considering the significance and variability of geodiversity as well. In addition, we propose that our indicator groups facilitate vegetation mapping in nearby dry forests, where it is difficult to conduct thorough vegetation or environmental surveys. In short, our analyses hold potential for the development of site-specific management and protection measures for threatened semi-deciduous forests in the Caribbean.
Social integration predicts survival in female white-faced capuchin monkeys
Authors: Kajokaite Kotrina , Whalen Andrew , Koster Jeremy , Perry Susan
Published: August 2020

Across multiple species of social mammals, a growing number of studies have found that that individual sociality is associated with survival. In long-lived species, like primates, lifespan is one of the main components of fitness. We used 18 years of data from the Lomas Barbudal Monkey project to quantify social integration in 11 capuchin (Cebus capucinus) groups and tested whether female survivorship was associated with females’ tendencies to interact with three types of partners: (1) all group members, (2) adult females, (3) adult males. We found strong evidence that females who engaged more with other females in affiliative interactions and foraged in close proximity experienced increased survivorship. We found some weak evidence that females might also benefit from engaging in more support in agonistic contexts with other females. These benefits were evident in models that account for the females’ rank and group size. Female interactions with all group members also increased survival, but the estimates of the effects were more uncertain. In interactions with adult males, only females who provided more grooming to males survived longer. The results presented here suggest that social integration may result in survival-related benefits. Females might enjoy these benefits through exchanging grooming for other currencies, such as coalitionary support or tolerance.
A quick and easy way to estimate entropy and mutual information for neuroscience
Authors: Zbili Mickael , Rama Sylvain
Published: August 2020

Abstract

Calculations of entropy of a signal or mutual information between two variables are valuable analytical tools in the field of neuroscience. They can be applied to all types of data, capture nonlinear interactions and are model independent. Yet the limited size and number of recordings one can collect in a series of experiments makes their calculation highly prone to sampling bias. Mathematical methods to overcome this so-called “sampling disaster” exist, but require significant expertise, great time and computational costs. As such, there is a need for a simple, unbiased and computationally efficient tool for estimating the level of entropy and mutual information. In this paper, we propose that application of entropy-encoding compression algorithms widely used in text and image compression fulfill these requirements. By simply saving the signal in PNG picture format and measuring the size of the file on the hard drive, we can estimate entropy changes through different conditions. Furthermore, with some simple modifications of the PNG file, we can also estimate the evolution of mutual information between a stimulus and the observed responses through different conditions. We first demonstrate the applicability of this method using white-noise-like signals. Then, while this method can be used in all kind of experimental conditions, we provide examples of its application in patch-clamp recordings, detection of place cells and histological data. Although this method does not give an absolute value of entropy or mutual information, it is mathematically correct, and its simplicity and broad use make it a powerful tool for their estimation through experiments.
Towards A 3D Chromosome Shape Alphabet
Authors: Soto Carlos , Bryner Darshan , Neretti Nicola , Srivastava Anuj
Published: August 2020

The study of the 3-dimensional (3D) structure of chromosomes – the largest macromolecules in biology – is one of the most challenging to date in structural biology. Here, we develop a novel representation of chromosomes, as sequences ofshape lettersfrom a finiteshape alphabet, which provides a compact and efficient way to analyze ensembles of chromosome shape data, akin to the analysis of texts in a language by using letters. We construct aChromosome Shape Alphabet(CSA) from an ensemble of chromosome 3D structures inferred from Hi-C data – via SIMBA3D or other methods – by segmenting curves based on topologically associating domains (TADs) boundaries, and by clustering all TADs’ 3D structures into groups of similar shapes. The median shapes of these groups, with some pruning and processing, form theChromosome Shape Letters(CSLs) of the alphabet. We provide a proof-of-concept for these CSLs by reconstructing independent test curves using only CSLs (and corresponding transformations) and comparing these reconstructions with the original curves. Finally, we demonstrate how CSLs can be used to summarize the variability of shapes in an ensemble of chromosome 3D structures using generalized sequence logos.
Immunosuppressive role of PGE2 during human tuberculosis
Authors: Pellegrini Joaquín Miguel , Tateosian Nancy Liliana , Morelli María Paula , Rollandelli Agustín , Amiano Nicolás Oscar , Palmero Domingo , Levi Alberto , Ciallella Lorena , Colombo María Isabel , García Verónica Edith
Published: August 2020

Prostaglandin E2 (PGE2), an active lipid compound derived from arachidonic acid, regulates different stages of the immune response of the host during several pathologies such as chronic infections or cancer. Manipulation of PGE2 levels was proposed as an approach for countering the Type I IFN signature of tuberculosis (TB), but very limited information exists about this pathway in patients with active TB. Here, we demonstrated that PGE2 exerts a potent immunosuppressive action during the immune response of the human host againstM. tuberculosis. Thus, we showed that PGE2 inhibited both lymphoproliferation and cytokine production of proinflammatory cytokines, together with a significant reduction of the surface expression of several immunological receptors in human cells. However, PGE2 promoted the autophagic flux of antigen-stimulated monocytes, even in the presence of IFNα. In this way, the attenuation of inflammation and immunopathology caused by an excessive immune response emerges as an attractive therapeutic target. Together, our findings contribute to the knowledge ofMtb-resistance mediated by PGE2 and highlight the potential of this lipid mediator as a tool to improve anti-TB treatment.
Proteogenomic analysis unveils the HLA Class I presented immunopeptidome in melanoma and EGFR mutant lung adenocarcinoma
Authors: Qi Yue A. , Maity Tapan K. , Cultraro Constance M. , Misra Vikram , Zhang Xu , Ade Catherine , Gao Shaojian , Milewski David , Nguyen Khoa D. , Ebrahimabadi Mohammad H. , Hanada Ken-ichi , Khan Javed , Sahinalp Cenk , Yang James C. , Guha Udayan
Published: August 2020

Immune checkpoint inhibitor and adoptive lymphocyte transfer-based therapies have shown great therapeutic potential for cancers with high tumor mutation burden (TMB). Here, we employed mass spectrometry (MS)-based proteogenomic large-scale profiling to identify potential immunogenic human leukocyte antigen (HLA) Class I-presented peptides in both melanoma, a “hot tumor” with high TMB, and EGFR mutant lung adenocarcinoma, a “cold tumor” with low TMB. We identified several classes of neopeptides, including mutated neoantigens and more than 1000 post-translationally modified peptides representing 58 different PTMs. We constructed a cancer germline (CG) antigen database with 285 antigens and identified 42 Class I-presented CG antigens. Finally, we developed a non-canonical peptide discovery pipeline to identify 44 lncRNA-derived peptides and validated Class I binding for select neopeptides. We provide direct evidence of HLA Class I presentation of a large number of neopeptides for potential vaccine or adoptive cell therapy in melanoma and mutant EGFR lung cancer.
Gut microbiome composition predicts summer core range size in a generalist and specialist ungulate
Authors: Wolf J.F. , Kriss K.D. , MacAulay K.M. , Munro K. , Patterson B.R. , Shafer A.B.A.
Published: August 2020

The gut microbiome of animals varies by age, diet, and habitat, and directly influences individual health. Similarly, variation in an individual’s home range can lead to differences in feeding strategies and fitness. Ungulates (hooved mammals) exhibit species-specific microbiomes and habitat use patterns: here, we combined gut microbiome and movement data to assess relationships between space use and the gut microbiome in a specialist and a generalist ungulate. We captured and GPS radiocollared 24 mountain goats (Oreamnos americanus) and 34 white-tailed deer (Odocoileus virginianus). We collected fecal samples and conducted high-throughput sequencing of the 16S rRNA gene. Using GPS data, we estimated core (50%) and home range (95%) sizes and calculated proportional use for several important habitat types. We generated metrics related to gut diversity and key bacterial ratios. We hypothesize that largerFirmicutestoBacteroidesratios confer body size or fat advantages that allow for larger home ranges, and that relationships between gut diversity and disproportionate habitat use is stronger in mountain goats due to their restricted niche relative to white-tailed deer.FirmicutestoBacteroidesratios were positively correlated with core range area in both species. Mountain goats exhibited a negative relationship between gut diversity and use of two key habitat types (treed areas and escape terrain), whereas no relationships were detected in white-tailed deer. This is the first study to relate core range size to the gut microbiome in wild ungulates and is an important proof of concept that advances the information that can be gleaned from non-invasive sampling.
Evidence for an extreme founding effect in a highly successful invasive species
Authors: Kratzer Kateryna V. , van der Marel Annemarie , Garroway Colin , López-Darias Marta , Petersen Stephen D. , Waterman Jane M.
Published: August 2020

The adaptive potential of invasive species is thought to decrease during founding events due to reduced genetic diversity, limiting the new population’s ability to colonize novel habitats. Barbary ground squirrels (Atlantoxerus getulus) were purportedly introduced as a single breeding pair to the island of Fuerteventura but have expanded to over a million individuals spread across the island in just over 50 years. We estimated the number of founders and measured the level of genetic diversity in this population using the mitochondrial displacement loop and microsatellite markers. Island samples (n= 19) showed no variation in the d-loop, suggesting a single founding female, while Moroccan samples (n= 6) each had unique mitochondrial haplotypes. The microsatellite data of the island population (n= 256 individuals) revealed a small effective population size, low levels of heterozygosity, and high levels of inbreeding, supporting a founding population size of two to three individuals. Our results suggest thatA. getulushas undergone an intense genetic bottleneck during their colonization of the island. They are one of the few species where introduction effort does not explain invasion success, although further investigation may explain how they have avoided the worst expected effects following an extreme genetic bottleneck.
Effect of sublethal prenatal endotoxaemia on murine placental transport systems and lipid homeostasis
Authors: Reginatto MW , Fontes KN , Monteiro VRS , Silva NL , Andrade CBV , Gomes HR , Imperio GE , Bloise FF , Kluck G , Atella GC , Matthews SG , Bloise E , Ortiga-Carvalho TM
Published: August 2020

Infection alters the expression of transporters that mediate the placental exchange of xenobiotics, lipids and cytokines. We hypothesized that lipopolysaccharide (LPS) modifies the expression of placental transport systems and lipid homeostasis. LPS (150 μg/kg; i.p.) treatments were administered for 4 h or 24 h, animals were euthanized at gestational days (GD) 15.5 or 18.5, and maternal blood, foetuses and placentae were collected. Increased rates of foetal demise were observed at GD15.5 following LPS treatment, whereas at GD18.5, high rates of early labour occurred and were associated with distinct proinflammatory responses. LPS did not alter ABC transporter mRNA expression but decreased Fabppm at GD15.5 (LPS-4 h) and increased Fat/Cd36 lipid transporter mRNA at GD18.5 (LPS-4 h). At the protein level, breast cancer-related protein (BCRP) and Abcg1 levels were decreased in the placental labyrinth zone (Lz) at GD15.5, whereas P-glycoprotein (P-gp) and Bcrp Lz-immunostaining was decreased at GD18.5. In the placental junctional zone (Jz), P-gp, Bcrp and Abcg1 levels were higher at GD18.5. Specific maternal plasma and placental changes in triacylglycerol, free fatty acid, cholesterol, cholesterol ester and monoacylglycerol levels were detected in a gestational age-dependent manner. In conclusion, LPS-induced foetal death and early labour were associated with altered placental ABC and lipid transporter expression and deranged maternal plasma and placental lipid homeostasis. These changes likely modify foetal xenobiotic exposure and placental lipid exchange in cases of bacterial infection.
Cortical thickness estimation in individuals with cerebral small vessel disease, focal atrophy, and chronic stroke lesions
Authors: Ozzoude Miracle , Ramirez Joel , Raamana Pradeep , Holmes Melissa F. , Walker Kirstin , Scott Christopher J.M. , Goubran Maged , Kwan Donna , Tartaglia Maria C. , Beaton Derek , Saposnik Gustavo , Hassan Ayman , Lawrence-Dewar Jane , Dowlatshahi Dariush , Strother Stephen C. , Symons Sean , Bartha Robert , Swartz Richard H. , Black Sandra E. ,   on behalf of the ONDRI Investigators
Published: August 2020

Background

Regional changes to cortical thickness in individuals with neurodegenerative and cerebrovascular diseases can be estimated using specialised neuroimaging software. However, the presence of cerebral small vessel disease, focal atrophy, and cortico-subcortical stroke lesions, pose significant challenges that increase the likelihood of misclassification errors and segmentation failures.

Purpose

The main goal of this study was to examine a correction procedure developed for enhancing FreeSurfer’s cortical thickness estimation tool, particularly when applied to the most challenging MRI obtained from participants with chronic stroke and cerebrovascular disease, with varying degrees of neurovascular lesions and brain atrophy.

Methods

In 155 cerebrovascular disease patients enrolled in the Ontario Neurodegenerative Disease Research Initiative (ONDRI), FreeSurfer outputs were compared between a fully automated, unmodified procedure and a corrected procedure that accounted for potential sources of error due to atrophy and neurovascular lesions. Quality control (QC) measures were obtained from both procedures. Association between cortical thickness and global cognitive status as assessed by the Montreal Cognitive Assessment (MoCA) score was also investigated from both procedures.

Results

Corrected procedures increased ‘Acceptable’ QC ratings from 18% to 76% for the cortical ribbon and from 38% to 92% for tissue segmentation. Corrected procedures reduced ‘Fail’ ratings from 11% to 0% for the cortical ribbon and 62% to 8% for tissue segmentation. FreeSurfer-based segmentation of T1-weighted white matter hypointensities were significantly greater in the corrected procedure (5.8mL vs. 15.9mL, p<0.001). The unmodified procedure yielded no significant associations with global cognitive status, whereas the corrected procedure yielded positive associations between MoCA total score and clusters of cortical thickness in the left superior parietal (p=0.018) and left insula (p=0.04) regions. Further analyses with the corrected cortical thickness results and MoCA subscores showed a positive association between left superior parietal cortical thickness and Attention (p<0.001).

Conclusions

These findings suggest that correction procedures that account for brain atrophy and neurovascular lesions can significantly improve FreeSurfer’s segmentation results, reduce failure rates, and potentially increase sensitivity to examine brain-behaviour relationships. Future work will examine relationships between cortical thickness, cerebral small vessel disease, and neurodegenerative disease in the ONDRI study.
Immune gene expression covaries with gut microbiome composition in stickleback
Authors: Fuess Lauren , Haan Stijn den , Ling Fei , Weber Jesse N. , Steinel Natalie C. , Bolnick Daniel I.
Published: August 2020

Commensal microbial communities have immense effects on their vertebrate hosts, contributing to a number of physiological functions as well as host fitness. In particular, host immunity is strongly linked to microbiota composition through poorly understood bi-directional links. Gene expression may be a potential mediator of these links between microbial communities and host function. However few studies have investigated connections between microbiota composition and expression of host immune genes in complex systems. Here we leverage a large study of laboratory-raised fish from the speciesGasterosteus aculeatus(three-spined stickleback) to document correlations between gene expression and microbiome composition. First, we examined correlations between microbiome alpha diversity and gene expression. Our results demonstrate robust positive associations between microbial alpha diversity and expression of host immunity. Next, we examined correlations between host gene expression and abundance of microbial taxa. We identified 15 microbial families that were highly correlated to host gene expression. These families were all tightly correlated to host expression of immune genes and processes, falling into one of three categories: those positively correlated, negatively correlated, and neutrally related to immune processes. Furthermore, we highlight several important immune processes that are commonly associated with abundance of these taxons, including both macrophage and B cell functions. Further functional characterization of microbial taxa will help disentangle the mechanisms of the correlations described here. In sum, our study supports prevailing hypotheses of intimate links between host immunity and gut microbiome composition.