Biological Literature Research Articles

P > .05: The incorrect interpretation of "not significant" results is a significant problem.

Statistically nonsignificant (p > .05) results from a null hypothesis significance test (NHST) are often mistakenly interpreted as evidence that the null hypothesis is true-that there is "no effect" or "no difference." However, many of these results occur because the study had low statistical power to detect an effect. Power below 50% is common, in which case a result of no statistical significance is more likely to be incorrect than correct. The inference of "no effect" is not valid even if power is high. NHST assumes that the null hypothesis is true; p is the probability of the data under the assumption that there is no effect. A statistical test cannot confirm what it assumes. These incorrect statistical inferences could be eliminated if decisions based on p values were replaced by a biological evaluation of effect sizes and their confidence intervals. For a single study, the observed effect size is the best estimate of the population effect size, regardless of the p value. Unlike p values, confidence intervals provide information about the precision of the observed effect. In the biomedical and pharmacology literature, methods have been developed to evaluate whether effects are "equivalent," rather than zero, as tested with NHST. These methods could be used by biological anthropologists to evaluate the presence or absence of meaningful biological effects. Most of what appears to be known about no difference or no effect between sexes, between populations, between treatments, and other circumstances in the biological anthropology literature is based on invalid statistical inference.

Global analysis of a model of competition in the chemostat with internal inhibitor

A model of two microbial species in a chemostat competing for a single resource in the presence of an internal inhibitor is considered. The model is a four-dimensional system of ordinary differential equations. Using general growth rate functions of the species, we give a complete analysis for the existence and local stability of all steady states. We describe the behavior of the system with respect to the operating parameters represented by the dilution rate and the input concentrations of the substrate. The operating diagram has the operating parameters as its coordinates and the various regions defined in it correspond to qualitatively different asymptotic behavior: washout, competitive exclusion of one species, coexistence of the species, bistability, multiplicity of positive steady states. This bifurcation diagram which determines the effect of the operating parameters, is very useful to understand the model from both the mathematical and biological points of view, and is often constructed in the mathematical and biological literature.

SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts.

Thanks to recent efforts by the text mining community, biocurators have now access to plenty of good tools and Web interfaces for identifying and visualizing biomedical entities in literature. Yet, many of these systems start with a PubMed query, which is limited by strong Boolean constraints. Some semantic search engines exploit entities for Information Retrieval, and/or deliver relevance-based ranked results. Yet, they are not designed for supporting a specific curation workflow, and allow very limited control on the search process. The Swiss Institute of Bioinformatics Literature Services (SIBiLS) provide personalized Information Retrieval in the biological literature. Indeed, SIBiLS allow fully customizable search in semantically enriched contents, based on keywords and/or mapped biomedical entities from a growing set of standardized and legacy vocabularies. The services have been used and favourably evaluated to assist the curation of genes and gene products, by delivering customized literature triage engines to different curation teams. SIBiLS (https://candy.hesge.ch/SIBiLS) are freely accessible via REST APIs and are ready to empower any curation workflow, built on modern technologies scalable with big data: MongoDB and Elasticsearch. They cover MEDLINE and PubMed Central Open Access enriched by nearly 2 billion of mapped biomedical entities, and are daily updated.

Agent-based and continuous models of hopper bands for the Australian plague locust: How resource consumption mediates pulse formation and geometry.

Locusts are significant agricultural pests. Under favorable environmental conditions flightless juveniles may aggregate into coherent, aligned swarms referred to as hopper bands. These bands are often observed as a propagating wave having a dense front with rapidly decreasing density in the wake. A tantalizing and common observation is that these fronts slow and steepen in the presence of green vegetation. This suggests the collective motion of the band is mediated by resource consumption. Our goal is to model and quantify this effect. We focus on the Australian plague locust, for which excellent field and experimental data is available. Exploiting the alignment of locusts in hopper bands, we concentrate solely on the density variation perpendicular to the front. We develop two models in tandem; an agent-based model that tracks the position of individuals and a partial differential equation model that describes locust density. In both these models, locust are either stationary (and feeding) or moving. Resources decrease with feeding. The rate at which locusts transition between moving and stationary (and vice versa) is enhanced (diminished) by resource abundance. This effect proves essential to the formation, shape, and speed of locust hopper bands in our models. From the biological literature we estimate ranges for the ten input parameters of our models. Sobol sensitivity analysis yields insight into how the band's collective characteristics vary with changes in the input parameters. By examining 4.4 million parameter combinations, we identify biologically consistent parameters that reproduce field observations. We thus demonstrate that resource-dependent behavior can explain the density distribution observed in locust hopper bands. This work suggests that feeding behaviors should be an intrinsic part of future modeling efforts.

Influence of endothelial glycocalyx layer microstructure upon its role as a mechanotransducer

The endothelial glycocalyx layer (EGL) is a brush-like layer that lines the internal surfaces of blood vessels. It is thought to serve a number of physiological functions, including as a mechanotransducer of fluid loadings to the vessel wall. However, the fragility of the EGL makes it difficult to examine experimentally, and so there is much value in theoretical models that can help to explain the dynamical behaviour of the EGL. Most previous models have employed mixture theory to mechanically describe the layer, which treats the EGL as a isotropic linearly poroelastic layer. However, there is increasing experimental evidence to suggest that the EGL has a well-defined organisational structure that might not necessarily be well captured by such mixture theory descriptions. We therefore employ homogenisation theory to incorporate into the models some of the possible EGL microstructure suggested by the current biological literature. We explore how mechanotransduction varies under the different possible EGL microstructures, which potentially has important consequences to our understanding of how structural changes to the EGL might affect a vessel’s ability to respond to hemodynamical cues. We also find that, whereas mechanotransduction through the solid components of the EGL is dominated by the fluid tractions applied at the lumen–EGL interface, the component carried through its fluid phase is most sensitive to pressure gradients within the bulk EGL. This is relevant, since it is known that the underlying endothelial cells respond differently to these two different forms of mechanical loading.

Networking and Dynamic Switches in Biological Condensates

Cellular liquid-liquid phase separation (LLPS) plays a key role in the dynamics and function of RNA-protein condensates like stress granules. In this issue ofCell, Yang et al., Guillén-Boixet et al., and Sanders et al. use a combination of experiment and modeling to provide an exciting mechanistic insight into the relationship between stress granules and LLPS, for example, in the context of protein disorder, switchable interactions, graph theory, and multiple interacting dense phases.

Modeling the impact of host resistance on structured tick population dynamics

For a variety of tick species, the resistance, behavioural and immunological response of hosts has been reported in the biological literature but its impact on tick population dynamics has not been mathematically formulated and analyzed using dynamical models reflecting the full biological stages of ticks. Here we develop and simulate a delay differential equation model, with a particular focus on resistance resulting in grooming behaviour. We calculate the basic reproduction number using the spectral analysis of delay differential equations with positive feedback, and establish the existence and uniqueness of a positive equilibrium when the basic reproduction number exceeds unit. We also conduct numerical and sensitivity analysis about the dependence of this positive equilibrium on the the parameter relevant to grooming behaviour. We numerically obtain the relationship between grooming behaviour and equilibrium value at different stages.

Biomarkers of abnormally invasive placenta

IntroductionAbnormally invasive placenta (AIP, aka placenta accreta spectrum; PAS) is an increasingly common pregnancy pathology, which, despite significant morbidity risk to the mother, is often undiagnosed prior to delivery. We tested several potential biomarkers in plasma from PAS mothers to determine whether any were sufficiently robust for a formal, diagnostic accuracy study. MethodsWe examined hyperglycosylated hCG (h-hCG), decorin and IL-8, based on biological plausibility and literature indications that they might be altered in PAS. These analytes were assayed by ELISA in maternal plasma from five groups, comprising (1) normal term controls, (2) placenta previa controls, and cases of (3) placenta increta/percreta without placenta previa, (4) placenta previa increta/percreta and (5) placenta previa accreta. ResultsThere were no differences in h-hCG, ß-hCG or the h-hCG/ß-hCG ratio between the groups. Mean decorin levels were increased in previa controls (Group 2) compared to the other groups, but there was substantial overlap between the individual values. While an initial multiplex assay showed a greater value for IL-8 in the placenta previa increta/percreta group (Group 4) compared to placenta previa controls (Group 2), the subsequent validation ELISA for IL-8 showed no differences between the groups. DiscussionWe conclude that the absence of differences and the extent of overlap between cases and controls does not justify further assessment of these biomarkers.

Communicating the consensus on climate change to college biology majors: The importance of preaching to the choir.

College and university biology majors who are not climate change deniers may yet be unaware of the degree of scientific consensus on climate change and unprepared to communicate about climate science to others. This study reports on a population of climate change accepting biology majors at a large, private research university in the American northeast. Our students tended to greatly underestimate the degree of scientific consensus around climate change, to be only moderately worried about climate change, and to be unconfident in their ability to communicate about the state of the scientific consensus around climate change. After an introduction to the scholarly literature that substantiates and quantifies the scientific consensus on climate change in the context of a course on biological research literature, our students showed significant increases in their estimates of the consensus on climate change, and their estimates were more accurate. Additionally, they became more worried about climate change as well as more confident in their ability to communicate about the scientific consensus to others. These results are in line with the Gateway Belief Model, which positions perception of scientific agreement on climate change as an important driver of acceptance and motivation toward action.

Safety and Efficacy in Relapsed or Refractory Classic Hodgkin's Lymphoma Treated with PD-1 Inhibitors: A Meta-Analysis of 9 Prospective Clinical Trials.

Background Classic Hodgkin's lymphoma (cHL) is characterized by the unique biology in which rare Hodgkin-Reed-Sternberg cells propagate an immunosuppressive microenvironment. Checkpoint inhibitors that target the interaction of PD-1 immune checkpoint receptors have demonstrated remarkable activities in various cancers, such as cHL. This study aims to evaluate the safety and efficacy of PD-1 inhibitors in treating relapsed or refractory cHL (rrHL). Methods We searched PubMed, MEDLINE, Embase, Cochrane Central Register of Controlled Trials, China National Knowledge Infrastructure, Wanfang, Chinese Biological Medical Literature, and s of Conference proceedings of annual meetings without any language restrictions to limit language bias (up to January 2019) for prospective clinical trials that evaluate PD-1 inhibitors in treating relapsed or refractory cHL. Results A total of 9 prospective clinical trials with 731 patients were included in the meta-analysis. The pooled risks of all-grade and grade ≥3 adverse events (AEs) were 0.86 (95% CI: 0.66–0.98) and 0.21 (95% CI: 0.17–0.24), respectively. The pooled response, complete response, partial response, and stable disease rates were 0.74 (95% CI: 0.70–0.79), 0.24 (95% CI: 0.18–0.34), 0.48 (95% CI: 0.41–0.55), and 0.15 (95% CI: 0.12–0.17), respectively. The pooled 6-month progression-free survival and 1-year overall survival rates were 0.76 (95% CI: 0.72–0.79) and 0.93 (95% CI: 0.90–0.96), correspondingly. Conclusions Our meta-analysis suggested that anti-PD1 monoclonal antibodies improve the outcomes of response and survival rates with tolerable AEs in cHL. However, evidence of immune checkpoint inhibitors for patients with cHL remained insufficient. Well-designed randomized controlled trials or at least nonrandomized trials with a control group should be conducted to confirm the findings of this meta-analysis.

Cell Line Classification Using Electric Cell-Substrate Impedance Sensing (ECIS).

We present new methods for cell line classification using multivariate time series bioimpedance data obtained from electric cell-substrate impedance sensing (ECIS) technology. The ECIS technology, which monitors the attachment and spreading of mammalian cells in real time through the collection of electrical impedance data, has historically been used to study one cell line at a time. However, we show that if applied to data from multiple cell lines, ECIS can be used to classify unknown or potentially mislabeled cells, factors which have previously been associated with the reproducibility crisis in the biological literature. We assess a range of approaches to this new problem, testing different classification methods and deriving a dictionary of 29 features to characterize ECIS data. Most notably, our analysis enriches the current field by making use of simultaneous multi-frequency ECIS data, where previous studies have focused on only one frequency; using classification methods to distinguish multiple cell lines, rather than simple statistical tests that compare only two cell lines; and assessing a range of features derived from ECIS data based on their classification performance. In classification tests on fifteen mammalian cell lines, we obtain very high out-of-sample predictive accuracy. These preliminary findings provide a baseline for future large-scale studies in this field.

Competence-Oriented Technology of Young Sprint Athletes Training

This research is triggered by the need to expand the educational content at children’s sport schools, applying a competence-based approach, and also by the lack of attempts to implement it in sprint athletes training. The research aims to explain, develop and test, within pilot searching efforts, the efficiency of competenceoriented technology for training 12–14-year-old sprinters. This technology is based on the theory of stage-by-stage creation of benchmark basis for activities. To solve the above tasks, we used the following research methods: comparative and systemic analysis of psychological and pedagogical, medical and biological literature; studying practical experience; observational methods (observation and selfobservation); psychological, pedagogical and sociological methods (polls, testing, expert estimates); experimental methods (a teaching experiment). The expert evaluation of competence-building efficiency was conducted with the qualimetric method. The structure and content of 5 sprint athlete competences were identified. A high level of competence-building was achieved with athletes in the experimental group. There, numeric indicators of general athletes’ capabilities – determining warm-up structure and content, performing motor development exercises correctly, maintaining a healthy lifestyle – were 85.1%, 86.2% and 89.5% respectively. The level of special competences – capability to perform motor actions according to rules of the sprint running technique, capability to psyche up for competitions – was slightly lower, reaching 71.9% and 73.3% respectively. Taking into account the relatively short period of competence-oriented training (3 months), we believe that the above performance indicators can be considered positive.

Combining entity co-occurrence with specialized word embeddings to measure entity relation in Alzheimer\u2019s disease

BackgroundExtracting useful information from biomedical literature plays an important role in the development of modern medicine. In natural language processing, there have been rigorous attempts to find meaningful relationships between entities automatically by co-occurrence-based methods. It has been increasingly important to understand whether relationships exist, and if so how strong, between any two entities extracted from a large number of texts. One of the defining methods is to measure semantic similarity and relatedness between two entities.MethodsWe propose a hybrid ranking method that combines a co-occurrence approach considering both direct and indirect entity pair relationship with specialized word embeddings for measuring the relatedness of two entities.ResultsWe evaluate the proposed ranking method comparatively with other well-known methods such as co-occurrence, Word2Vec, COALS (Correlated Occurrence Analog to Lexical Semantics), and random indexing by calculating top-ranked entities related to Alzheimer’s disease. In addition, we analyze gene, pathway, and gene–phenotype relationships. Overall, the proposed method tends to find more hidden relationships than the other methods.ConclusionOur proposed method is able to select more useful related entities that not only highly co-occur but also have more indirect relations for the target entity. In pathway analysis, our proposed method shows superior performance at identifying (functional) cross clustering and higher-level pathways. Our proposed method, resulting from phenotype analysis, has an advantage in identifying the common genotype relating to phenotypes from biological literature.

Pre-emptive Intervention for Autism Spectrum Disorder: Theoretical Foundations and Clinical Translation.

Autism spectrum disorders (ASD) are an emergent public health problem, placing significant burden upon the individual, family and health system. ASD are polygenetic spectrum disorders of neural connectome development, in which one or more feedback loops amplify small genetic, structural, or functional variations in the very early development of motor and sensory-motor pathways. These perturbations trigger a ‘butterfly effect’ of unpredictable cascades of structural and functional imbalances in the global neuronal workspace, resulting in atypical behaviors, social communication, and cognition long-term. The first 100 days post-term are critically neuroplastic and comprise an injury-sensitive developmental window, characterized by a neural biomarker, the persistence of the cortical subplate, and a behavioral biomarker, the crying diathesis. By the time potential diagnostic signs are identified, from 6 months of age, ASD neuropathy is already entrenched. The International Society for Autism Research Special Interest Group has called for pre-emptive intervention, based upon rigorous theoretical frames, and real world translation and evaluation. This paper responds to that call. It synthesizes heterogenous evidence concerning ASD etiologies from both psychosocial and biological research literatures with complexity science and evolutionary biology, to propose a theoretical framework for pre-emptive intervention. This paper hypothesizes that environmental factors resulting from a mismatch between environment of evolutionary adaptedness and culture initiate or perpetuate early motor and sensory-motor lesions, triggering a butterfly effect of multi-directional cascades of atypical developmental in the complex adaptive system of the parent and ASD-susceptible infant. Chronic sympathetic nervous system/hypothalamic-pituitary-adrenal axis hyperarousal and disrupted parent-infant biobehavioral synchrony are the key biologic and behavioral mechanisms perpetuating these atypical developmental cascades. A clinical translation of this evidence is proposed, for application antenatally and in the first 6 months of life, as pre-emptive intervention for ASD.

Predictive biomarkers of colorectal cancer

Colorectal cancer is one of the top leading causes of cancer mortality worldwide, especially in China. However, most of the current treatments are invasive and can only be applied to very few cancers. The earlier a malignant tumor is diagnosed, the higher the patient's survival rate. In this study, we proposed a computational framework to identify highly-reliable and easierly-detectable biomarkers capable of secreting into blood, urine and saliva by integrating transcriptomics and proteomics data at the system biology level. First, a large number of transcriptome data were processed to identify candidate biomarkers for colorectal cancer. Second, three classified models are constructed to predict biomarkers for colorectal cancer capable of secreting into blood, urine and saliva, which are effective disease diagnosis media to facilitate clinical screening. Then biological functions and molecular mechanisms of the candidate biomarkers of colorectal cancer are inferred utilizing multi-source biological knowledge and literature mining. Furthermore, the classification power of different combinations of candidate biomarkers is verified by machine learning models. In addition, the targeted drugs of the predicted biomarkers are further analyzed to provide assistance for clinical treatment of colorectal cancer. In this paper, our proposed computational model not only provides the effective candidate biomarkers ESM1, CTHRC1, AZGP1 for colorectal cancer capable of secreting into blood, urine and saliva, but also helps to understand the molecular mechanism of colorectal cancer. This computational framework can span the huge gap between transcriptome and proteomics, which can easily be applied to the biomarker research for other types of tumor.

A catalog of Athericidae (Diptera) from Neotropical and Andean Regions.

A catalog of the Athericidae from Neotropical and Andean Regions is provided. All valid names and synonyms are presented, totaling twenty-seven species and three genera in these Regions. All references known from the taxonomic and biological literature are given, including information about name, author, year of publication, page number, type species, type locality and bibliography. The genus Atherix Meigen is not represented in Neotropical nor Andean Regions.

Armed with information: chemical self-recognition in the octopus

Of the modalities through which self-recognition is believed to be implemented, philosophical literature on the subject is most familiar with vision and interoception. However, they are not the only ones: chemoreception is another modality that biologists have found to be a contributor to self-recognition in numerous species, of which arthropods are notable. This article aims to help address the gap between philosophical and biological literature by presenting the octopus as an example of a creature in which peripheral chemoreceptive processes appear to be a significant component of self-recognition. Building on the findings of Nesher et al. that chemical compounds in octopus skin interfere with the behaviour of its suckers, this article proffers an account of how chemoreception may contribute to self-recognition in octopuses.

A catalog of Anisopodidae (Diptera) from Chile.

A catalog of the Anisopodidae from Chile is provided. All valid names and synonyms are presented, summing up five species in two genera for the country. All references known to us from the taxonomic and biological literature are provided, including information about name, author, year of publication, page number, type species, type locality, distribution, and references. We keep Tonnoirina Amorim Tozoni as a synonym of Sylvicola and Neomesochria Amorim Tozoni as a synonym of Mycetobia.

Maximum diversity weighting for biomarkers with application in HIV-1 vaccine studies.

While studying the association between risk of HIV-1 infection and vaccine-elicited immune responses in preventative HIV-1 vaccine recipients, we encountered a need to combine a collection of biomarkers in an unsupervised fashion with the goal of preserving signal diversity within that collection. Inspired by methods for weighting protein sequences from the biological sequence analysis literature, we propose novel methods for weighting biomarkers, which we call maximum diversity weights. These weights are defined as the weights that maximize measures of signal diversity within a collection of biomarkers. While the optimization problems do not admit analytical solutions, they are convex and hence can be solved efficiently using iterative search algorithms. Through Monte Carlo studies and a real data example from HIV-1 vaccine research, we show that using maximum diversity weights in association studies can lead to an increase in power over other commonly used weights such as uniform weights or principal component-based weights.

Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0

The Systems Biology Graphical Notation (SBGN) is an international community effort that aims to standardise the visualisation of pathways and networks for readers with diverse scientific backgrounds as well as to support an efficient and accurate exchange of biological knowledge between disparate research communities, industry, and other players in systems biology. SBGN comprises the three languages Entity Relationship, Activity Flow, and Process Description (PD) to cover biological and biochemical systems at distinct levels of detail. PD is closest to metabolic and regulatory pathways found in biological literature and textbooks. Its well-defined semantics offer a superior precision in expressing biological knowledge. PD represents mechanistic and temporal dependencies of biological interactions and transformations as a graph. Its different types of nodes include entity pools (e.g. metabolites, proteins, genes and complexes) and processes (e.g. reactions, associations and influences). The edges describe relationships between the nodes (e.g. consumption, production, stimulation and inhibition). This document details Level 1 Version 2.0 of the PD specification, including several improvements, in particular: 1) the addition of the equivalence operator, subunit, and annotation glyphs, 2) modification to the usage of submaps, and 3) updates to clarify the use of various glyphs (i.e. multimer, empty set, and state variable).