bluuebunny/crossref_metadata_2025 huggingface dataset:
Unsupervised manifold learning of collective behavior
Authors: Titus Mathew , Hagstrom George , Watson James R.
Published: February 2021

Collective behavior is an emergent property of numerous complex systems, from financial markets to cancer cells to predator-prey ecological systems. Characterizing modes of collective behavior is often done through human observation, training generative models, or other supervised learning techniques. Each of these cases requires knowledge of and a method for characterizing the macro-state(s) of the system. This presents a challenge for studying novel systems where there may be little prior knowledge. Here, we present a new unsupervised method of detecting emergent behavior in complex systems, and discerning between distinct collective behaviors. We require only metrics,d(1),d(2), defined on the set of agents,X, which measure agents’ nearness in variables of interest. We apply the method of diffusion maps to the systems (X,d(i)) to recover efficient embeddings of their interaction networks. Comparing these geometries, we formulate a measure of similarity between two networks, called the map alignment statistic (MAS). A large MAS is evidence that the two networks are codetermined in some fashion, indicating an emergent relationship between the metricsd(1)andd(2). Additionally, the form of the macro-scale organization is encoded in the covariances among the two sets of diffusion map components. Using these covariances we discern between different modes of collective behavior in a data-driven, unsupervised manner. This method is demonstrated on a synthetic flocking model as well as empirical fish schooling data. We show that our state classification subdivides the known behaviors of the school in a meaningful manner, leading to a finer description of the system’s behavior.
OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations
Authors: Lu Wei , Bueno Carlos , Schafer Nicholas P. , Moller Joshua , Jin Shikai , Chen Xun , Chen Mingchen , Gu Xinyu , Davtyan Aram , de Pablo Juan J. , Wolynes Peter G.
Published: February 2021

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM’s Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM’s Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen’s early Nobel prize winning experiments by using OpenMM’s Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology.
Evaluating epidemic forecasts in an interval format
Authors: Bracher Johannes , Ray Evan L. , Gneiting Tilmann , Reich Nicholas G.
Published: February 2021

For practical reasons, many forecasts of case, hospitalization, and death counts in the context of the current Coronavirus Disease 2019 (COVID-19) pandemic are issued in the form of central predictive intervals at various levels. This is also the case for the forecasts collected in theCOVID-19 Forecast Hub(https://covid19forecasthub.org/). Forecast evaluation metrics like the logarithmic score, which has been applied in several infectious disease forecasting challenges, are then not available as they require full predictive distributions. This article provides an overview of how established methods for the evaluation of quantile and interval forecasts can be applied to epidemic forecasts in this format. Specifically, we discuss the computation and interpretation of the weighted interval score, which is a proper score that approximates the continuous ranked probability score. It can be interpreted as a generalization of the absolute error to probabilistic forecasts and allows for a decomposition into a measure of sharpness and penalties for over- and underprediction.
Signatures of neutral evolution in exponentially growing tumors: A theoretical perspective
Authors: Tung Hwai-Ray , Durrett Rick
Published: February 2021

Recent work of Sottoriva, Graham, and collaborators have led to the controversial claim that exponentially growing tumors have a site frequency spectrum that follows the 1/f law consistent with neutral evolution. This conclusion has been criticized based on data quality issues, statistical considerations, and simulation results. Here, we use rigorous mathematical arguments to investigate the site frequency spectrum in the two-type model of clonal evolution. If the fitnesses of the two types are λ0 < λ1, then the site frequency spectrum is c/fα where α = λ0/λ1. This is due to the advantageous mutations that produce the founders of the type 1 population. Mutations within the growing type 0 and type 1 populations follow the 1/f law. Our results show that, in contrast to published criticisms, neutral evolution in an exponentially growing tumor can be distinguished from the two-type model using the site frequency spectrum.
A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways
Authors: Garrido-Rodriguez Martín , Lopez-Lopez Daniel , Ortuno Francisco M. , Peña-Chilet María , Muñoz Eduardo , Calzado Marco A. , Dopazo Joaquin
Published: February 2021

MIGNON is a workflow for the analysis of RNA-Seq experiments, which not only efficiently manages the estimation of gene expression levels from raw sequencing reads, but also calls genomic variants present in the transcripts analyzed. Moreover, this is the first workflow that provides a framework for the integration of transcriptomic and genomic data based on a mechanistic model of signaling pathway activities that allows a detailed biological interpretation of the results, including a comprehensive functional profiling of cell activity. MIGNON covers the whole process, from reads to signaling circuit activity estimations, using state-of-the-art tools, it is easy to use and it is deployable in different computational environments, allowing an optimized use of the resources available.
Thermal performance of the Chagas disease vector, Triatoma infestans, under thermal variability
Authors: Clavijo-Baquet Sabrina , Cavieres Grisel , González Avia , Cattan Pedro E. , Bozinovic Francisco
Published: February 2021

Vector-borne diseases (VBD) are particularly susceptible to climate change because most of the diseases’ vectors are ectotherms, which themselves are susceptible to thermal changes. The Chagas disease is one neglected tropical disease caused by the protozoan parasite, Trypanosoma cruzi. One of the main vectors of the Chagas disease in South America is Triatoma infestans, a species traditionally considered to be restricted to domestic or peridomestic habitats, but sylvatic foci have also been described along its distribution. The infestation of wild individuals, together with the projections of environmental changes due to global warming, urge the need to understand the relationship between temperature and the vector’s performance. Here, we evaluated the impact of temperature variability on the thermal response of T. infestans. We acclimated individuals to six thermal treatments for five weeks to then estimate their thermal performance curves (TPCs) by measuring the walking speed of the individuals. We found that the TPCs varied with thermal acclimation and body mass. Individuals acclimated to a low and variable ambient temperature (18°C ± 5°C) exhibited lower performances than those individuals acclimated to an optimal temperature (27°C ± 0°C); while those individuals acclimated to a low but constant temperature (18°C ± 0°C) did not differ in their maximal performance from those at an optimal temperature. Additionally, thermal variability (i.e., ± 5°C) at a high temperature (30°C) increased performance. These results evidenced the plastic response of T. infestans to thermal acclimation. This plastic response and the non-linear effect of thermal variability on the performance of T. infestans posit challenges when predicting changes in the vector’s distribution range under climate change.
Tracking individual honeybees among wildflower clusters with computer vision-facilitated pollinator monitoring
Authors: Ratnayake Malika Nisal , Dyer Adrian G. , Dorin Alan
Published: February 2021

Monitoring animals in their natural habitat is essential for advancement of animal behavioural studies, especially in pollination studies. Non-invasive techniques are preferred for these purposes as they reduce opportunities for research apparatus to interfere with behaviour. One potentially valuable approach is image-based tracking. However, the complexity of tracking unmarked wild animals using video is challenging in uncontrolled outdoor environments. Out-of-the-box algorithms currently present several problems in this context that can compromise accuracy, especially in cases of occlusion in a 3D environment. To address the issue, we present a novel hybrid detection and tracking algorithm to monitor unmarked insects outdoors. Our software can detect an insect, identify when a tracked insect becomes occluded from view and when it re-emerges, determine when an insect exits the camera field of view, and our software assembles a series of insect locations into a coherent trajectory. The insect detecting component of the software uses background subtraction and deep learning-based detection together to accurately and efficiently locate the insect among a cluster of wildflowers. We applied our method to track honeybees foraging outdoors using a new dataset that includes complex background detail, wind-blown foliage, and insects moving into and out of occlusion beneath leaves and among three-dimensional plant structures. We evaluated our software against human observations and previous techniques. It tracked honeybees at a rate of 86.6% on our dataset, 43% higher than the computationally more expensive, standalone deep learning model YOLOv2. We illustrate the value of our approach to quantify fine-scale foraging of honeybees. The ability to track unmarked insect pollinators in this way will help researchers better understand pollination ecology. The increased efficiency of our hybrid approach paves the way for the application of deep learning-based techniques to animal tracking in real-time using low-powered devices suitable for continuous monitoring.
High-throughput analysis of lung immune cells in a combined murine model of agriculture dust-triggered airway inflammation with rheumatoid arthritis
Authors: Gaurav Rohit , Mikuls Ted R. , Thiele Geoffrey M. , Nelson Amy J. , Niu Meng , Guda Chittibabu , Eudy James D. , Barry Austin E. , Wyatt Todd A. , Romberger Debra J. , Duryee Michael J. , England Bryant R. , Poole Jill A.
Published: February 2021

Rheumatoid arthritis (RA)-associated lung disease is a leading cause of mortality in RA, yet the mechanisms linking lung disease and RA remain unknown. Using an established murine model of RA-associated lung disease combining collagen-induced arthritis (CIA) with organic dust extract (ODE)-induced airway inflammation, differences among lung immune cell populations were analyzed by single cell RNA-sequencing. Additionally, four lung myeloid-derived immune cell populations including macrophages, monocytes/macrophages, monocytes, and neutrophils were isolated by fluorescence cell sorting and gene expression was determined by NanoString analysis. Unsupervised clustering revealed 14 discrete clusters among Sham, CIA, ODE, and CIA+ODE treatment groups: 3 neutrophils (inflammatory, resident/transitional, autoreactive/suppressor), 5 macrophages (airspace, differentiating/recruited, recruited, resident/interstitial, and proliferative airspace), 2 T-cells (differentiating and effector), and a single cluster each of inflammatory monocytes, dendritic cells, B-cells and natural killer cells. Inflammatory monocytes, autoreactive/suppressor neutrophils, and recruited/differentiating macrophages were predominant with arthritis induction (CIA and CIA+ODE). By specific lung cell isolation, several interferon-related and autoimmune genes were disproportionately expressed among CIA and CIA+ODE (e.g.Oasl1,Oas2,Ifit3,Gbp2,Ifi44, andZbp1), corresponding to RA and RA-associated lung disease. Monocytic myeloid-derived suppressor cells were reduced, while complement genes (e.g.C1s1andCfb) were uniquely increased in CIA+ODE mice across cell populations. Recruited and inflammatory macrophages/monocytes and neutrophils expressing interferon-, autoimmune-, and complement-related genes might contribute towards pro-fibrotic inflammatory lung responses following airborne biohazard exposures in setting of autoimmune arthritis and could be predictive and/or targeted to reduce disease burden.
Predicting the rental value of houses in household surveys in Tanzania, Uganda and Malawi: Evaluations of hedonic pricing and machine learning approaches
Authors: Embaye Weldensie T. , Zereyesus Yacob Abrehe , Chen Bowen
Published: February 2021

Housing value is a major component of the aggregate expenditure used in the analyses of welfare status of households in the development economics literature. Therefore, an accurate estimation of housing services is important to obtain the value of housing in household surveys. Data show that a significant proportion of households in a typical Living Standard Measurement Survey (LSMS), adopted by the Word Bank and others, are self-owned. The standard approach to predict the housing value for such surveys is based on the rental cost of the house. A hedonic pricing applying an Ordinary Least Squares (OLS) method is normally used to predict rental values. The literature shows that Machine Learning (ML) methods, shown to uncover generalizable patterns based on a given data, have better predictive power over OLS applied in other valuation exercises. We examined whether or not a class of ML methods (e.g. Ridge, LASSO, Tree, Bagging, Random Forest, and Boosting) provided superior prediction of rental value of housing over OLS methods accounting for spatial autocorrelations using household level survey data from Uganda, Tanzania, and Malawi, across multiple years. Our results showed that the Machine Learning methods (Boosting, Bagging, Forest, Ridge and LASSO) are the best models in predicting house values using out-of-sample data set for all the countries and all the years. On the other hand, Tree regression underperformed relative to the various OLS models, over the same data sets. With the availability of abundant data and better computing power, ML methods provide viable alternative to predicting housing values in household surveys.
The Abbreviated Science Anxiety Scale: Psychometric properties, gender differences and associations with test anxiety, general anxiety and science achievement
Authors: Megreya Ahmed M. , Szűcs Denes , Moustafa Ahmed A.
Published: February 2021

Science anxiety refers to students’ negative emotions about learning science. Across two studies, we investigated the psychometric properties of the newly developed Abbreviated Science Anxiety Scale (ASAS), which was adapted from the modified Abbreviated Math Anxiety Scale (m-AMAS) (Carey E., 2017). Using a sample of students in grades 7 to 10 (N = 710), Study 1 reported a two-factor structure of the ASAS (learning science anxiety and science evaluation anxiety) and negative associations between the ASAS factors and science achievement. Study 2 replicated this two-factor model in students in grades 11 and 12 (N = 362) and found that students in the “Arts” track were more anxious about science than those in “Sciences” track. Both studies consistently reported positive inter-correlations between the ASAS factors, with good internal reliabilities and modest meaningful associations with test anxiety and general anxiety, suggesting that science anxiety might be a distinct construct. Further, female students had higher science anxiety (especially science evaluation anxiety) than male students, even when test anxiety and general anxiety were considered in models. In summary, the ASAS is a brief, valid, and reliable instrument that can be used to guide and improve science education.
Outcomes within a year following first ever stroke in Tanzania
Authors: Tessua Kezia Kodawa , Munseri Patricia , Matuja Sarah Shali
Published: February 2021

Background

Stroke contributes to a significant proportion of deaths and disability worldwide, with a high fatality rate within 30 days following a first ever stroke. We describe the outcomes within one year among patients who succumbed a first ever stroke and survived the first 30 days.

Methods

Participants were patients who survived after 30 days from succumbing a first ever stroke admitted at the Muhimbili University of Health and Allied Sciences Academic Medical Center. Stroke survivors or their next of kin were contacted at one year after succumbing a first stroke to determine the outcomes. We assessed participants’ vital status and level of disability using the modified Rankin scale. Assessment on utilization of stroke secondary preventive measures among survivors was done by an interviewer-based questionnaire that assessed the number of times participants attended follow up clinics, medication refill and adherence. Participants were examined for waist-hip ratio, body mass index and blood pressure. Cholesterol levels were assessed at one year post first stroke for survivors. Outcomes were summarized as proportions, survival at one year was estimated by using the Kaplan Meier analysis and Cox regression analysis was performed to determine for predictors of mortality.

Results

We recruited 130 first stroke survivors. Mortality within one year was 53/130 (40.8%) and disability rate measured by Modified Rankin Scale with scores of 3–5 was 29/77 (37.7%) among survivors. Factors associated with mortality were residual disability HR = 8.60, {95% CI (1.16–63.96)}, severe stroke, HR = 2.67 {95% CI (1.44–4.95)} and residing in Dar-es-Salaam HR = 2.15 {95% (CI 1.06–4.36)}. Non-adherence rates to antihypertensives, antiplatelets and statins was 11/73 (15.1%), 9/23 (39.1%) and 18/22 (81.8%) respectively. Attendance rates of follow-up clinics among all survivors and physiotherapy among survivors with disability are 45/77 (58.4%) and 16/29 (55.2%) respectively.

Conclusions

The mortality and disability rates within a year following a first ever stroke among 30 days stroke survivors is high. Secondary stroke preventive measures should be enhanced to mitigate stroke adverse outcomes. Community outreach programs could be useful interventions in preventing the adverse outcomes of stroke.
A prospective study on the use of ultralow-dose computed tomography with iterative reconstruction for the follow-up of patients liver and renal abscess
Authors: Seo Nieun , Park Mi-Suk , Choi Jun Yong , Yeom Joon-Sup , Kim Myeong-Jin , Chung Yong Eun , Ku Nam Su
Published: February 2021

Background

Radiation dose reduction is a major concern in patients who undergo computed tomography (CT) to follow liver and renal abscess.

Objectives

The purpose of this study is to investigate the feasibility of ultralow-dose CT with iterative reconstruction (IR) to follow patients with liver and renal abscess.

Methods

This prospective study included 18 patients who underwent ultralow-dose CT with IR to follow abscesses (liver abscesses in 10 patients and renal abscesses in 8 patients; ULD group). The control group consisted of 14 patients who underwent follow-up standard-dose CT for liver abscesses during the same period. The objective image noise was evaluated by measuring standard deviation (SD) in the liver and subcutaneous fat to select a specific IR for qualitative analysis. Two radiologists independently evaluated subjective image quality, noise, and diagnostic confidence to evaluate abscess using a five-point Likert scale. Qualitative parameters were compared between the ULD and control groups with the Mann-Whitney U test.

Results

The mean CT dose index volume and dose length product of standard-dose CT were 8.7 ± 1.8 mGy and 555.8 ± 142.8 mGy·cm, respectively. Mean dose reduction of ultralow-dose CT was 71.8% compared to standard-dose CT. After measuring SDs, iDose level 5, which showed similar SD to standard-dose CT in both the subcutaneous fat and liver (P = 0.076, and P = 0.124), was selected for qualitative analysis. Ultralow-dose CT showed slightly worse subjective image quality (P < 0.001 for reader 1, and P = 0.005 for reader 2) and noise (P = 0.004 for reader 1, and P = 0.001 for reader 2) than standard-dose CT. However, the diagnostic confidence of ultralow-dose CT for evaluating abscess was comparably excellent to standard-dose CT (P = 0.808 for reader 1, and P = 0.301 for reader 2).

Conclusions

Ultralow-dose CT with IR can be used in the follow-up of liver and renal abscess with comparable diagnostic confidence.
Ecological correlates of chimpanzee (Pan troglodytes schweinfurthii) density in Mahale Mountains National Park, Tanzania
Authors: Chitayat Adrienne B. , Wich Serge A. , Lewis Matthew , Stewart Fiona A. , Piel Alex K.
Published: February 2021

Understanding the ecological factors that drive animal density patterns in time and space is key to devising effective conservation strategies. In Tanzania, most chimpanzees (~75%) live outside national parks where human activities threaten their habitat’s integrity and connectivity. Mahale Mountains National Park (MMNP), therefore, is a critical area for chimpanzees (Pan troglodytes schweinfurthii) in the region due to its location and protective status. Yet, despite its importance and long history of chimpanzee research (>50 years), a park-wide census of the species has never been conducted. The park is categorized as a savanna-woodland mosaic, interspersed with riparian forest, wooded grassland, and bamboo thicket. This heterogeneous landscape offers an excellent opportunity to assess the ecological characteristics associated with chimpanzee density, a topic still disputed, which could improve conservation plans that protect crucial chimpanzee habitat outside the park. We examined the influence of fine-scale vegetative characteristics and topographical features on chimpanzee nest density, modeling nest counts using hierarchical distance sampling. We counted 335 nests in forest and woodland habitats across 102 transects in 13 survey sites. Nests were disproportionately found more in or near evergreen forests, on steep slopes, and in feeding tree species. We calculated chimpanzee density in MMNP to be 0.23 ind/km2, although density varied substantially among sites (0.09–3.43 ind/km2). Density was associated with factors related to the availability of food and nesting trees, with topographic heterogeneity and the total basal area of feeding tree species identified as significant positive predictors. Species-rich habitats and floristic diversity likely play a principal role in shaping chimpanzee density within a predominately open landscape with low food abundance. Our results provide valuable baseline data for future monitoring efforts in MMNP and enhance our understanding of this endangered species’ density and distribution across Tanzania.
Pediatric fever in neutropenia with bacteremia—Pathogen distribution and in vitro antibiotic susceptibility patterns over time in a retrospective single-center cohort study
Authors: Stergiotis Melina , Ammann Roland A. , Droz Sara , Koenig Christa , Agyeman Philipp Kwame Abayie
Published: February 2021

Background

Fever in neutropenia (FN) is a potentially life-threatening complication of chemotherapy in pediatric cancer patients. The current standard of care at most institutions is emergency hospitalization and empirical initiation of broad-spectrum antibiotic therapy.

Methods

We analyzed in retrospect FN episodes with bacteremia in pediatric cancer patients in a single center cohort from 1993 to 2012. We assessed the distribution of pathogens, the in vitro antibiotic susceptibility patterns, and their trends over time.

Results

From a total of 703 FN episodes reported, we assessed 134 FN episodes with bacteremia with 195 pathogens isolated in 102 patients. Gram-positive pathogens (124, 64%) were more common than Gram-negative (71, 36%). This proportion did not change over time (p = 0.26). Coagulase-negative staphylococci (64, 32%), viridans group streptococci (42, 22%), Escherichia coli (33, 17%), Klebsiella spp. (10, 5%) and Pseudomonas aeruginosa (nine, 5%) were the most common pathogens. Comparing the in vitro antibiotic susceptibility patterns, the antimicrobial activity of ceftriaxone plus amikacin (64%; 95%CI: 56%-72%), cefepime (64%; 95%CI 56%-72%), meropenem (64%; 95%CI 56%-72), and piperacillin/tazobactam (62%; 95%CI 54%-70%), respectively, did not differ significantly. The addition of vancomycin to those regimens would have increased significantly in vitro activity to 99% for ceftriaxone plus amikacin, cefepime, meropenem, and 96% for piperacillin/tazobactam (p < 0.001).

Conclusions

Over two decades, we detected a relative stable pathogen distribution and found no relevant trend in the antibiotic susceptibility patterns. Different recommended antibiotic regimens showed comparable in vitro antimicrobial activity.
Birth outcomes, pregnancy complications, and postpartum mental health after the 2013 Calgary flood: A difference in difference analysis
Authors: Hetherington Erin , Adhikari Kamala , Tomfohr-Madsen Lianne , Patten Scott , Metcalfe Amy
Published: February 2021

Background

In June 2013, the city of Calgary, Alberta and surrounding areas sustained significant flooding which resulted in large scale evacuations and closure of businesses and schools. Floods can increase stress which may negatively impact perinatal outcomes and mental health, but previous research is inconsistent. The objectives of this study are to examine the impact of the flood on pregnancy health, birth outcomes and postpartum mental health.

Methods

Linked administrative data from the province of Alberta were used. Outcomes included preterm birth, small for gestational age, a new diagnoses of preeclampsia or gestational hypertension, and a diagnosis of, or drug prescription for, depression or anxiety. Data were analyzed using a quasi-experimental difference in difference design, comparing flooded and non-flooded areas and in affected and unaffected time periods. Multivariable log binomial regression models were used to estimate risk ratios, adjusted for maternal age. Marginal probabilities for the difference in difference term were used to show the potential effect of the flood.

Results

Participants included 18,266 nulliparous women for the pregnancy outcomes, and 26,956 women with infants for the mental health analysis. There were no effects for preterm birth (DID 0.00, CI: -0.02, 0.02), small for gestational age (DID 0.00, CI: -0.02, 0.02), or new cases of preeclampsia (DID 0.00, CI: -0.01, 0.01). There was a small increase in new cases of gestational hypertension (DID 0.02, CI: 0.01, 0.03) in flood affected areas. There were no differences in postpartum anxiety or depression prescriptions or diagnoses.

Conclusion

The Calgary 2013 flood was associated with a minor increase in gestational hypertension and not other health outcomes. Universal prenatal care and magnitude of the disaster may have minimized impacts of the flood on pregnant women.
Client-care provider interaction during labour and birth as experienced by women: Respect, communication, confidentiality and autonomy
Authors: van der Pijl Marit S. G. , Kasperink Marlies , Hollander Martine H. , Verhoeven Corine , Kingma Elselijn , de Jonge Ank
Published: February 2021

Introduction

Respectful Maternity Care is important for achieving a positive labour and birth experience. Client-care provider interaction—specifically respect, communication, confidentiality and autonomy—is an important aspect of Respectful Maternity Care. The aim of this study was twofold: (1) to assess Dutch women’s experience of respect, communication, confidentiality and autonomy during labour and birth and (2) to identify which client characteristics are associated with experiencing optimal respect, communication, confidentiality and autonomy.

Methods

Pregnant women and women who recently gave birth in the Netherlands were recruited to fill out a validated web-based questionnaire (ReproQ). Mean scores per domain (scale 1–4) were calculated. Domains were dichotomised in non-optimal (score 1, 2,3) and optimal client-care provider interaction (score 4), and a multivariable logistic regression analysis was performed.

Results

Of the 1367 recruited women, 804 respondents completed the questionnaire and 767 respondents completed enough questions to be included for analysis. Each domain had a mean score above 3.5. The domain confidentiality had the highest proportion of optimal scores (64.0%), followed by respect (53.3%), communication (45.1%) and autonomy (36.2%). In all four domains, women who gave birth at home with a community midwife had a higher proportion of optimal scores than women who gave birth in the hospital with a (resident) obstetrician or hospital-based midwife. Lower education level, being multiparous and giving birth spontaneously were also significantly associated with a higher proportion of optimal scores in (one of) the domains.

Discussion

This study shows that on average women scored high on experienced client-care provider interaction in the domains respect, communication, confidentiality and autonomy. At the same time, client-care provider interaction in the Netherlands still fell short of being optimal for a large number of women, in particular regarding women’s autonomy. These results show there is still room for improvement in client-care provider interaction during labour and birth.
In silico analysis suggests less effective MHC-II presentation of SARS-CoV-2 RBM peptides: Implication for neutralizing antibody responses
Authors: Castro Andrea , Ozturk Kivilcim , Zanetti Maurizio , Carter Hannah
Published: February 2021

SARS-CoV-2 antibodies develop within two weeks of infection, but wane relatively rapidly post-infection, raising concerns about whether antibody responses will provide protection upon re-exposure. Here we revisit T-B cooperation as a prerequisite for effective and durable neutralizing antibody responses centered on a mutationally constrained RBM B cell epitope. T-B cooperation requires co-processing of B and T cell epitopes by the same B cell and is subject to MHC-II restriction. We evaluated MHC-II constraints relevant to the neutralizing antibody response to a mutationally-constrained B cell epitope in the receptor binding motif (RBM) of the spike protein. Examining common MHC-II alleles, we found that peptides surrounding this key B cell epitope are predicted to bind poorly, suggesting a lack MHC-II support in T-B cooperation, impacting generation of high-potency neutralizing antibodies in the general population. Additionally, we found that multiple microbial peptides had potential for RBM cross-reactivity, supporting previous exposures as a possible source of T cell memory.
Effect of number and placement of EEG electrodes on measurement of neural tracking of speech
Authors: Montoya-Martínez Jair , Vanthornhout Jonas , Bertrand Alexander , Francart Tom
Published: February 2021

Measurement of neural tracking of natural running speech from the electroencephalogram (EEG) is an increasingly popular method in auditory neuroscience and has applications in audiology. The method involves decoding the envelope of the speech signal from the EEG signal, and calculating the correlation with the envelope of the audio stream that was presented to the subject. Typically EEG systems with 64 or more electrodes are used. However, in practical applications, set-ups with fewer electrodes are required. Here, we determine the optimal number of electrodes, and the best position to place a limited number of electrodes on the scalp. We propose a channel selection strategy based on an utility metric, which allows a quick quantitative assessment of the influence of a channel (or a group of channels) on the reconstruction error. We consider two use cases: a subject-specific case, where the optimal number and position of the electrodes is determined for each subject individually, and a subject-independent case, where the electrodes are placed at the same positions (in the 10-20 system) for all the subjects. We evaluated our approach using 64-channel EEG data from 90 subjects. In the subject-specific case we found that the correlation between actual and reconstructed envelope first increased with decreasing number of electrodes, with an optimum at around 20 electrodes, yielding 29% higher correlations using the optimal number of electrodes compared to all electrodes. This means that our strategy of removing electrodes can be used to improve the correlation metric in high-density EEG recordings. In the subject-independent case, we obtained a stable decoding performance when decreasing from 64 to 22 channels. When the number of channels was further decreased, the correlation decreased. For a maximal decrease in correlation of 10%, 32 well-placed electrodes were sufficient in 91% of the subjects.
Barriers and facilitators to prudent antibiotic prescribing for acute respiratory tract infections: A qualitative study with general practitioners in Malta
Authors: Saliba-Gustafsson Erika A. , Nyberg Anna , Borg Michael A. , Rosales-Klintz Senia , Stålsby Lundborg Cecilia
Published: February 2021

Background

Antibiotic resistance is a leading global public health concern and antibiotic use is a key driver. Effective interventions are needed to target key stakeholders, including general practitioners (GPs). In Malta, little is known about factors that influence GPs’ antibiotic prescribing, making it challenging to implement targeted interventions. We therefore aimed to explore GPs’ understanding of antibiotic use and resistance, and describe their perceived barriers and facilitators to prudent antibiotic prescribing for acute respiratory tract infections in Malta.

Methods

Face-to-face individual semi-structured interviews were held with a quota sample of 20 GPs in 2014. Interviews were audio recorded and transcribed verbatim, and later analysed iteratively using manifest and latent content analysis. Findings were collated in a socioecological model to depict how GPs as individuals are embedded within larger social systems and contexts, and how each component within this system impacts their prescribing behaviour.

Findings

We found that GPs’ antibiotic prescribing decisions are complex and impacted by numerous barriers and facilitators at the individual, interpersonal, organisational, community, and public policy level. Predominant factors found to impact GPs’ antibiotic prescribing included not only intrinsic GP factors such as knowledge, awareness, experience, and misconceptions, but also several external factors. At the interpersonal level, GPs’ perceived patient demand and behaviour to be a persistent issue that impacts their prescribing decisions. Similarly, some GPs found pressure from drug reps to be concerning despite being considered an important source of information. Organisational and public policy-level issues such as lack of access to relevant antibiotic prescribing guidelines and current antibiotic resistance data from the community, were also considered major barriers to appropriate antibiotic prescribing. Utilisation of diagnostic testing was found to be low and GPs’ perceptions on the introduction of rapid point-of-care tests to support antibiotic prescription decisions, were mixed.

Conclusion

This study revealed the complexity of the antibiotic prescribing decision and the numerous barriers and facilitators that impact it, visualised through a socioecological model. Addressing GPs’ antibiotic prescribing practices will require targeted and coordinated implementation activities at all levels to change behaviour and address misconceptions, whilst also improving the physical and social environment.

Trial registration number

NCT03218930;https://clinicaltrials.gov/ct2/show/NCT03218930.
Climate change, hunger and rural health through the lens of farming styles: An agent-based model to assess the potential role of peasant farming
Authors: Lloyd Simon J. , Chalabi Zaid
Published: February 2021

Undernutrition is a major contributor to the global-burden of disease, and global-level health impact models suggest that climate change-mediated reductions in food quantity and quality will negatively affect it. These models, however, capture just some of the processes that will shape future nutrition. We adopt an alternative standpoint, developing an agent-based model in which producer-consumer smallholders practice different ‘styles of farming’ in the global food system. The model represents a hypothetical rural community in which ‘orphan’ (subsistence) farmers may develop by adopting an ‘entrepreneurial’ style (highly market-dependent) or by maintaining a ‘peasant’ style (agroecology). We take a first look at the question: how might patterns of farming styles—under various style preference, climate, policy, and price transmission scenarios—impact on hunger and health-supporting conditions (incomes, work, inequality, ‘real land productivity’) in rural areas? imulations without climate change or agricultural policy found that style preference patterns influence production, food price, and incomes, and there were trade-offs between them. For instance, entrepreneurial-oriented futures had the highest production and lowest prices but were simultaneously those in which farms tended towards crisis. Simulations with climate change and agricultural policy found that peasant-orientated agroecology futures had the highest production, prices equal to or lower than those under entrepreneurial-oriented futures, and better supported rural health. There were, however, contradictory effects on nutrition, with benefits and harms for different groups. Collectively the findings suggest that when attempting to understand how climate change may impact on future nutrition and health, patterns of farming styles—along with the fates of the households that practice them—matter. These issues, including the potential role of peasant farming, have been neglected in previous global-level climate-nutrition modelling but go to the heart of current debates on the future of farming: thus, they should be given more prominence in future work.
Resource selection of a nomadic ungulate in a dynamic landscape
Authors: Stratmann Theresa S. M. , Dejid Nandintsetseg , Calabrese Justin M. , Fagan William F. , Fleming Christen H. , Olson Kirk A. , Mueller Thomas
Published: February 2021

Nomadic movements are often a consequence of unpredictable resource dynamics. However, how nomadic ungulates select dynamic resources is still understudied. Here we examined resource selection of nomadic Mongolian gazelles (Procapra gutturosa) in the Eastern Steppe of Mongolia. We used daily GPS locations of 33 gazelles tracked up to 3.5 years. We examined selection for forage during the growing season using the Normalized Difference Vegetation Index (NDVI). In winter we examined selection for snow cover which mediates access to forage and drinking water. We studied selection at the population level using resource selection functions (RSFs) as well as on the individual level using step-selection functions (SSFs) at varying spatio-temporal scales from 1 to 10 days. Results from the population and the individual level analyses differed. At the population level we found selection for higher than average NDVI during the growing season. This may indicate selection for areas with more forage cover within the arid steppe landscape. In winter, gazelles selected for intermediate snow cover, which may indicate preference for areas which offer some snow for hydration but not so much as to hinder movement. At the individual level, in both seasons and across scales, we were not able to detect selection in the majority of individuals, but selection was similar to that seen in the RSFs for those individuals showing selection. Difficulty in finding selection with SSFs may indicate that Mongolian gazelles are using a random search strategy to find forage in a landscape with large, homogeneous areas of vegetation. The combination of random searches and landscape characteristics could therefore obscure results at the fine scale of SSFs. The significant results on the broader scale used for the population level RSF highlight that, although individuals show uncoordinated movement trajectories, they ultimately select for similar vegetation and snow cover.
Impact of positive biphasic pressure during low and high inspiratory efforts in Pseudomonas aeruginosa-induced pneumonia
Authors: da Cruz Daniela G. , de Magalhães Raquel F. , Padilha Gisele A. , da Silva Mariana C. , Braga Cassia L. , Silva Adriana R. , Gonçalves de Albuquerque Cassiano F. , Capelozzi Vera L. , Samary Cynthia S. , Pelosi Paolo , Rocco Patricia R. M. , Silva Pedro L.
Published: February 2021

Background

During pneumonia, normal alveolar areas coexist adjacently with consolidated areas, and high inspiratory efforts may predispose to lung damage. To date, no study has evaluated different degrees of effort during Biphasic positive airway pressure (BIVENT) on lung and diaphragm damage in experimental pneumonia, though largely used in clinical setting. We aimed to evaluate lung damage, genes associated with ventilator-induced lung injury (VILI) and diaphragmatic injury, and blood bacteria in pressure-support ventilation (PSV), BIVENT with low and high inspiratory efforts in experimental pneumonia.

Material and methods

Twenty-eight male Wistar rats (mean ± SD weight, 333±78g) were submitted Pseudomonas aeruginosa-induced pneumonia. After 24-h, animals were ventilated for 1h in: 1) PSV; 2) BIVENT with low (BIVENTLow-Effort); and 3) BIVENT with high inspiratory effort (BIVENTHigh-Effort). BIVENT was set at Phigh to achieve VT = 6 ml/kg and Plow at 5 cmH2O (n = 7/group). High- and low-effort conditions were obtained through anaesthetic infusion modulation based on neuromuscular drive (P0.1). Lung mechanics, histological damage score, blood bacteria, and expression of genes related to VILI in lung tissue, and inflammation in diaphragm tissue.

Results

Transpulmonary peak pressure and histological damage score were higher in BIVENTHigh-Effort compared to BIVENTLow-Effort and PSV [16.1 ± 1.9cmH2O vs 12.8 ± 1.5cmH2O and 12.5 ± 1.6cmH2O, p = 0.015, and p = 0.010; median (interquartile range) 11 (9–13) vs 7 (6–9) and 7 (6–9), p = 0.021, and p = 0.029, respectively]. BIVENTHigh-Effort increased interleukin-6 expression compared to BIVENTLow-Effort (p = 0.035) as well as expressions of cytokine-induced neutrophil chemoattractant-1, amphiregulin, and type III procollagen compared to PSV (p = 0.001, p = 0.001, p = 0.004, respectively). Tumour necrosis factor-α expression in diaphragm tissue and blood bacteria were higher in BIVENTHigh-Effort than BIVENTLow-Effort (p = 0.002, p = 0.009, respectively).

Conclusion

BIVENT requires careful control of inspiratory effort to avoid lung and diaphragm damage, as well as blood bacteria. P0.1 might be considered a helpful parameter to optimize inspiratory effort.
Histological outcomes in HPV-screened elderly women in Denmark
Authors: St-Martin Gry , Viborg Petra Hall , Andersen Ane Birgitte Telén , Andersen Berit , Christensen Jette , Ejersbo Dorthe , Heje Hanne Nørgaard , Jochumsen Kirsten Marie , Johansen Tonje , Larsen Lise Grupe , Lynge Elsebeth , Serizawa Reza Rafiolsadat , Waldstrøm Marianne
Published: February 2021

Introduction

Danish women exit cervical cancer screening at age 65 years, but 23% of cervical cancer cases occur beyond this age. In addition, due to gradual implementation of cervical cancer screening, older women are underscreened by today´s standards. A one-time screening with HPV test was therefore offered to Danish women born before 1948.

Methods

Register based study reporting histology diagnoses and conizations in women found HPV positive in the one-time screening. Number and proportion of women with severe or non-severe histology results were calculated for screened and HPV-positive women by age group or region of residence. Number of women with biopsy and/or conization per case of cervical intraepithelial neoplasia (CIN) grade 2 or worse (CIN2+) or CIN3+ were also calculated by age groups and region.

Results

4,479 (4.1% of screened women) had positive HPV test. 94% of these had one or more additional tests. 2,785 (62%) of HPV-positive women had histology results, and conization was performed in 1,076 (24% of HPV-positive and 1% of all screened women). HPV positivity and CIN3+ detection varied little between regions, but the proportions of HPV positive women undergoing histology varied between regions from 40% to 86% and the proportion with conization from 13% to 36%. Correspondingly, the number of histologies and conizations per CIN3+ detected varied from 5.9 to 11.2 and 1.8 to 4.7, respectively. In total, 514 CIN2+ (0.47% of screened women, 11% of HPV-positive) and 337 CIN3+ (0.31% of screened women, 7.5% of HPV-positive) were diagnosed, including 37 cervical cancer cases.

Discussion

HPV screening of insufficiently screened birth cohorts can potentially prevent morbidity and mortality from cervical cancer but longer follow-up is needed to see if cancer incidence declines in the screened women in the coming years. Management strategies differed among regions which influenced the proportions undergoing biopsy/conization.