Biological Literature Research Articles

Living with observational data in biological anthropology.

The establishment of cause and effect relationships is a fundamental objective of scientific research. Many lines of evidence can be used to make cause-effect inferences. When statistical data are involved, alternative explanations for the statistical relationship need to be ruled out. These include chance (apparent patterns due to random factors), confounding effects (a relationship between two variables because they are each associated with an unmeasured third variable), and sampling bias (effects due to preexisting properties of compared groups). The gold standard for managing these issues is a controlled randomized experiment. In disciplines such as biological anthropology, where controlled experiments are not possible for many research questions, causal inferences are made from observational data. Methods that statisticians recommend for this difficult objective have not been widely adopted in the biological anthropology literature. Issues involved in using statistics to make valid causal inferences from observational data are discussed.

Research Output of Biological Science during 1901 1945 A Scientometric Analysis

A scientometric evaluation of India’s scientific productions in the field of biological science during 1901-1947 has been performed. The growth rate, authorship pattern, collaboration trend, and prolific researchers (male and female) of biological science literature is investigated. From the result it is found that the mean relative growth rate and duplication time is 0.615 and 1.007 respectively for the period 1901-1945. The calculated results follow the spirit of the ‘Price Law’ i.e. the coefficient of determination of the exponential plot is greater than that of the linear plot. About 75 per cent papers are single-authored and the degree of collaboration is 0.249. The Collaborative author index (CAI) for single author shows decreasing trend while for two author and more than two author shows increasing trend. The data set derived from this study follows Lotka’s law of author productivity. The productivity of ten most productive researchers together contributed 15 per cent publication share. It is also found that the productivity of women researchers together contributed 0.62 per cent publication share in biological science research.

The effects of statins on benign prostatic hyperplasia and the lower urinary tract symptoms: A Meta-analysis.

The aim of this meta-analysis was to understand the relationship between statin with benign prostatic hyperplasia (BPH) and lower urinary tract symptoms (LUTS). A systematic literature search was conducted using PubMed, Embase, Cochrane Library, Chinese Medical and Biological Literature Database, China HowNet, Vip, and Wanfang. We calculated pooled odds ratios (OR) and 95% CI and standardized mean difference (SMD). Using Stata 12.0 and Review 5.3 for meta-analysis. This meta-analysis included 11 articles and 49,128 participants. Results show statins could not reduce the incidence of BPH [OR = 0.77 (0.57, 1.03, P = .08]. For patients over 60 years old, statins could reduce the incidence of BPH [OR = 0.35 (0.22, 0.55), P < .0001]. Statins can slow down the progression of LUTS in BPH [SMD = -0.32 (-0.54, -0.10), P = .004], but there is no significant correlation between them in patients taking drugs for less than 1 year. Statins have no significant effect on the incidence of BPH, but statins can reduce the risk of BPH for patients over 60 years old. For patients with hyperlipidemia, the duration of medication is more than 1 year, which can slow down the progression of LUTS. However, more high-quality and large sample size studies are needed to further improve and verify.

Locating uncertainty in stochastic evolutionary models: divergence time estimation

Philosophers of biology have worked extensively on how we ought best to interpret the probabilities which arise throughout evolutionary theory. In spite of this substantial work, however, much of the debate has remained persistently intractable. I offer the example of Bayesian models of divergence time estimation (the determination of when two evolutionary lineages split) as a case study in how we might bring further resources from the biological literature to bear on these debates. These models offer us an example in which a number of different sources of uncertainty are combined to produce an estimate for a complex, unobservable quantity. These models have been carefully analyzed in recent biological work, which has determined the relationship between these sources of uncertainty (their relative importance and their disappearance in the limit of increasing data), both quantitatively and qualitatively. I suggest here that this case shows us the limitations of univocal analyses of probability in evolution, as well as the simple dichotomy between “subjective” and “objective” probabilities, and I conclude by gesturing toward ways in which we might introduce more sophisticated interpretive taxonomies of probability (modeled on some recent work in the philosophy of physics) as a path toward advancing debates on probability in the life sciences.

Bayesian modeling of plant drought resistance pathway

BackgroundPlants are sessile organisms and are unable to relocate to favorable locations under extreme environmental conditions. Hence they have no choice but to acclimate and eventually adapt to the severe conditions to ensure their survival. As traditional methods of bolstering plant defense against stressful conditions come to their biological limit, we require newer methods that can allow us to strengthen plants’ internal defense mechanism. These factors motivated us to look into the genetic networks of plants. The WRKY transcription factors are well known for their role in plant defense against biotic stresses, but recent studies have shed light on their activities against abiotic stresses such as drought. We modeled this network of WRKY transcription factors using Bayesian networks and applied inference algorithm to find the best regulators of drought response. Biologically intervening (activating/inhibiting) these regulators can bolster the defense response of plants against droughts.ResultWe used real world data from the NCBI GEO database and synthetic data generated from dependencies in the Bayesian network to learn the network parameters. These parameters were estimated using both a Bayesian and a frequentist approach. The two sets of parameters were used in a utility-based inference algorithm to determine the best regulator of plant drought response in the WRKY transcription factor network.ConclusionOur analysis revealed that activating the transcription factor WRKY18 had the highest likelihood of inducing drought response among all the other elements of the WRKY transcription factor network. Our observation was also supported by biological literature, as WRKY18 is known to regulate drought responsive genes positively. We also found that activating the protein complex WRKY60-60 had the second highest likelihood of inducing drought defense response. Consistent with the existing biological literature, we also found the transcription factor WRKY40 and the protein complex WRKY40-40 to suppress drought response.

Computational modeling of epithelial wound healing: Short and long term chemo-mechanical mechanisms

During the lifetime of all living multicellular organisms, wounds in their tissues are frequently observed. The capability of closing those gaps is fundamental for a healthy development. If done deficiently, many diseases may occur from simple inflammation to tumor formation. The wound healing process in epithelial tissue occurs in three different stages. The first one is the assembly of a supra-cellular actomyosin cable and its migration towards the wound edge, triggered by biochemical processes in which calcium plays a distinctive role. How this process is orchestrated following damage remains unclear. Later, after its positioning, the cable contracts driving the tissue towards the gap and reducing the wound area. Finally, cell migration towards the interior of the wound ends up sealing the tissue. In this work, we make use of a mechanical continuum model for the first two stages in order to developed and 2D finite element simulations within a monolithically fully implicit implementation. The model for the actomyosin cable formation involves the coupling of transient calcium ions transport, with actin fibers and myosin motors recruitment and non-linear mechanical response of the tissue. The contraction stage, the active deformation of the previously formed actomyosin cable is taken into account. The relative motion of the myosin motors over the actin filaments is modeled so there exists an active tissue contraction in the direction of those fibers. Upon implementation, the model is capable of performing a wide range of biophysical situations reported experimentally, as we demonstrate in our numerical results. We have been able to rationalize through computational mechanics the firing of calcium in the wound right after damage infliction as well as the consequent formation of actin ring, reproducing nicely what has been reported in biological literature. Thereafter, the numerical model of acto-myosin contraction, fully integrated with the non-linear mechanics of the problem, correlates with the mechanics of wound closure at the actin-ring contraction stage. More importantly, the approach is the first of its kind in the modeling of epithelial and embryonic cell layers, where a wide number of complex mechanics has been integrated and solved though computational methods in engineering. We believe that the simulations will help to unravel new insights in open questions of developmental biology.

Bitcoin for the biological literature.

Scientific publishing is increasingly adopting the technology underlying cryptocurrencies. Scientific publishing is increasingly adopting the technology underlying cryptocurrencies.

PPICurator: A Tool for Extracting Comprehensive Protein-Protein Interaction Information.

Protein-protein interaction extraction through biological literature curation is widely employed for proteome analysis. There is a strong need for a tool that can assist researchers in extracting comprehensive PPI information through literature curation, which is critical in research on protein, for example, construction of protein interaction network, identification of protein signaling pathway, and discovery of meaningful protein interaction. However, most of current tools can only extract PPI relations. None of them are capable of extracting other important PPI information, such as interaction directions, effects, and functional annotations. To address these issues, this paper proposes PPICurator, a novel tool for extracting comprehensive PPI information with a variety of logic and syntax features based on a new support vector machine classifier. PPICurator provides a friendly web-based user interface. It is a platform that automates the extraction of comprehensive PPI information through literature, including PPI relations, as well as their confidential scores, interaction directions, effects, and functional annotations. Thus, PPICurator is more comprehensive than state-of-the-art tools. Moreover, it outperforms state-of-the-art tools in the accuracy of PPI relation extraction measured by F-score and recall on the widely used open datasets. PPICurator is available at https://ppicurator.hupo.org.cn.

Computational elucidation of the binding mechanisms of curcumin analogues as bacterial RecA inhibitors.

Antimicrobial resistance (AMR) presents as a serious threat to global public health, which urgently demands action to develop alternative antimicrobial strategies with minimized selective pressure. The bacterial SOS response regulator RecA has emerged as a promising target in the exploration of new classes of antibiotic adjuvants, as RecA has been implicated in bacterial mutagenesis and thus AMR development through its critical roles in error-prone DNA repair. The natural product curcumin has been reported to be an effective RecA inhibitor in several Gram-negative bacteria, but details on the underlying mechanisms are wanting. In order to bridge the gap in how curcumin operates as a RecA inhibitor, we used computational approaches to model interactions between RecA protein and curcumin analogues. We first identified potential binding sites on E. coli RecA protein and classified them into four major binding pockets based on biological literature and computational findings from multiple in silico calculations. In docking analysis, curcumin–thalidomide hybrids were predicted to be superior binders of RecA compared with bis-(arylmethylidene)acetone curcumin analogues, which was further confirmed by MMGBSA calculations. Overall, this work provides mechanistic insights into bacterial RecA protein as a target for curcumin-like compounds and offers a theoretical basis for rational design and development of future antibiotic adjuvants.

Mathematical models of gene expression

In this paper we analyze the equilibrium properties of a large class of stochastic processes describing the fundamental biological process within bacterial cells, the production process of proteins. Stochastic models classically used in this context to describe the time evolution of the numbers of mRNAs and proteins are presented and discussed. An extension of these models, which includes elongation phases of mRNAs and proteins, is introduced. A convergence result to equilibrium for the process associated to the number of proteins and mRNAs is proved and a representation of this equilibrium as a functional of a Poisson process in an extended state space is obtained. Explicit expressions for the first two moments of the number of mRNAs and proteins at equilibrium are derived, generalizing some classical formulas. Approximations used in the biological literature for the equilibrium distribution of the number of proteins are discussed and investigated in the light of these results. Several convergence results for the distribution of the number of proteins at equilibrium are in particular obtained under different scaling assumptions.

&lt;p&gt;&lt;strong&gt;“Palaeoentomology”: A modern journal for a science dealing with the past&lt;/strong&gt;&lt;/p&gt;

Palaeoentomology started in the late XVIIIth century, shortly after the 10th edition of Linnaeus’ Systema Naturae (the foundation of modern taxonomy), when papers on the curiosities of insects entombed in fossil resins were published. The beginning of XIXth century (with the growing interest in geological sciences and prehistoric life) witnessed the first attempts to study and describe insects from sedimentary rocks. This discipline then developed during the XIXth and beginning of the XXth centuries; and resulted in some major works and reviews (summarizing the knowledge on fossil insects and other terrestrial arthropods) published in the geological and biological literature. The XXth century was a period of relatively slow but constant development in palaeoentomology, during which the famous “Treatise on invertebrate paleontology: Arthropoda 4. Superclass Hexapoda” (cataloguing the knowledge on fossil insects) was published (Carpenter, 1992). At the beginning of XXIst century, palaeoentomology grew significantly and exponentially; and two major manuals (“History of insects” and “Evolution of the insects”) were published (Rasnitsyn &amp; Quicke, 2002; Grimaldi &amp; Engel, 2005, respectively). These manuals helped to encourage more students and researchers to work on fossil insects and other terrestrial arthropods.

Evolutionary design of regulatory control. I. A robust control theory analysis of tradeoffs

The evolutionary design of regulatory control balances various tradeoffs in performance. Fast reaction to environmental change tends to favor plastic responsiveness at the expense of greater sensitivity to perturbations that degrade homeostatic control. Greater homeostatic stability against unpredictable disturbances tends to reduce performance in tracking environmental change. This article applies the classic principles of engineering control theory to the evolutionary design of regulatory systems. The engineering theory clarifies the conceptual aspects of evolutionary tradeoffs and provides analytic methods for developing specific predictions. On the conceptual side, this article clarifies the meanings of integral control, feedback, and design, concepts that have been discussed in a confusing way within the biological literature. On the analytic side, this article presents extensive methods and examples to study error-correcting feedback, which is perhaps the single greatest principle of design in both human-engineered and naturally designed systems. The broad framework and associated software code provide a comprehensive how-to guide for making models that focus on functional aspects of regulatory control and for making comparative predictions about regulatory design in response to various kinds of environmental challenge. The second article in this series analyzes how alternative regulatory designs influence the relative levels of genetic variability, stochasticity of trait expression, and heritability of disease.

Reporting of thermography parameters in biology: a systematic review of thermal imaging literature.

Infrared (IR) thermography, where temperature measurements are made with IR cameras, has proven to be a very useful and widely used tool in biological science. Several thermography parameters are critical to the proper operation of thermal cameras and the accuracy of measurements, and these must usually be provided to the camera. Failure to account for these parameters may lead to less accurate measurements. Furthermore, the failure to provide information of parameter choices in reports may compromise appraisal of accuracy and replicate studies. In this review, we investigate how well biologists report thermography parameters. This is done through a systematic review of biological thermography literature that included articles published between years 2007 and 2017. We found that in primary biological thermography papers, which make some kind of quantitative temperature measurement, 48% fail to report values used for emissivity (an object's capacity to emit thermal radiation relative to a black body radiator), which is the minimum level of reporting that should take place. This finding highlights the need for life scientists to take into account and report key parameter information when carrying out thermography, in the future.

Elusive Fungus?

This article explores how attraction, a companion term to elusiveness, reveals insights into multispecies worlds by showing how different organisms such as the matsutake mushroom interpret the world and interact with each other, whether or not humans are involved. Building on scholarly interest in the ‘animal turn’ (explorations of the human-animal relationship), this article moves beyond human-centered scholarship by using, but also modifying, the concept of umwelt introduced by the Baltic German biologist Jakob von Uexküll. Employing a critical social scientific reading of the biological literature that analyzes its findings, as well as challenges its animal-centric models of agency and behavior, I argue that this perspective helps us better understand ourselves as humans in a world that is much more than human.

Communication Model–Task Pairing in Artificial Swarm Design

Unraveling the nature of the communication model that governs which two individuals in a swarm interact with each other is an important line of inquiry in the collective behavior sciences. A number of models have been proposed in the biological swarm literature, with the leading models being the metric, topological, and visual models. The hypothesis evaluated in this letter is whether the choice of a communication model impacts the performance of a tasked artificial swarm. The biological models are used to design coordination algorithms for a simulated swarm, which are evaluated over a range of six swarm robotics tasks. Each task has an associated set of performance metrics that are used to evaluate how the communication models fare against each other. The general findings demonstrate that the communication model significantly affects the swarm's performance for individual tasks, and this result implies that the communication model–task pairing is an important consideration when designing artificial swarms. Further analysis of each tasks’ performance metrics reveals instances in which pairwise considerations of model and one of the various experimental factors become relevant. The reported research demonstrates that the artificial swarm's task performance can be increased through the careful selection of a communication model.

Global prevalence of molar incisor hypomineralisation.

Data sourcesPubMed, Web of Science, ScienceDirect, Chinese Biological Medical Literature Database, Chinese Wanfang Database, Chinese National Knowledge Infrastructure and reference lists of key publications. Language restrictions were placed with inclusion of English and Chinese texts only. No date restrictions were applied.Study selectionOriginal population-based studies that described the diagnostic criteria of MIH and provided prevalence data or sufficient information that could be used to calculate MIH prevalence.Data extraction and synthesisTwo reviewers independently extracted the data. Meta-regression was done using a random effects model for parameters of age, gender and region. Heterogeneity was assessed using I2 statistic.ResultsSeventy studies were included that encompassed a total of 89,520 people and 10,823 cases of MIH. The pooled global prevalence of MIH was 14.2% (95% CI 12.6-15.8), with South America having the highest prevalence (18%; 95% CI 13.8-22.2) and Africa the lowest (10.9%; 95% CI 4.2-17.6). There was no significant difference between male and female participants. Prevalence of MIH amongst children ten years of age or younger (15.1%, 95% CI 12.1-18.2) was higher than older children (12.1%, 95% CI 8.0-16.3).ConclusionsThis meta-analysis showed the average global prevalence of MIH as 14.2%. Some geographic regions had higher than average prevalence, which could inform oral health policy in those areas.

Follicular competition in cows: the selection of dominant follicles as a synergistic effect.

The reproductive cycle of mono-ovulatory species such as cows or humans is known to show two or more waves of follicular growth and decline between two successive ovulations. Within each wave, there is one dominant follicle escorted by subordinate follicles of varying number. Under the surge of the luteinizing hormone a growing dominant follicle ovulates. Rarely the number of ovulating follicles exceeds one. In the biological literature, the change of hormonal concentrations and individually varying numbers of follicular receptors are made responsible for the selection of exactly one dominant follicle, yet a clear cause has not been identified. In this paper, we suggest a synergistic explanation based on competition, formulated by a parsimoniously defined system of ordinary differential equations (ODEs) that quantifies the time evolution of multiple follicles and their competitive interaction during one wave. Not discriminating between follicles, growth and decline are given by fixed rates. Competition is introduced via a growth-suppressing term, equally supported by all follicles. We prove that the number of dominant follicles is determined exclusively by the ratio of follicular growth and competition. This number turns out to be independent of the number of subordinate follicles. The asymptotic behavior of the corresponding dynamical system is investigated rigorously, where we demonstrate that the [Formula: see text]-limit set only contains fixed points. When also including follicular decline, our ODEs perfectly resemble ultrasound data of bovine follicles. Implications for the involved but not explicitly modeled hormones are discussed.

Pseudoparasitism by Spalangia cameroni (Hymenoptera: Pteromalidae) of pupae of Ceratitis capitata (Diptera: Tephritidae): Frequency and implications

The effectiveness of natural enemies in controlling pests may be determined by many traits linked to their ability to regulate the density of their prey. In this respect, the phenomenon of pseudoparasitism, in which female parasitoids reject a host after inserting their ovipositor into it, is fairly common among hymenopteran parasitoids. However, in spite of this its effect on hosts is rarely reported in entomological and biological control literature. For this reason, in the present study, the pseudoparasitism by the parasitoid Spalangia cameroni Perkins of the Mediterranean pest Ceratitis capitata (Wiedemann) and its effect on several biological parameters of the host were studied under laboratory conditions. The results indicate that the percentage pseudoparasitism by S. cameroni of medfly in the laboratory is high, even slightly higher than host-feeding, which is commonly used to evaluate the potential of parasitoids as biological control agents. In addition, the adults that emerge from pseudoparasitized medfly pupae have a male-biased sex ratio, low levels of survival and are frequently damaged, which results in small adults and an inability to mate successfully. In conclusion, our results indicate that pseudoparasitism is common and enhances the effectiveness of S. cameroni attacking medfly, which highlights the importance of this phenomenon when selecting parasitoids to be included in a biological control programme.

Meta analysis of effect of tracheostomy timing on prognosis of patients with cervical spinal cord injury

Objective To evaluate the effects of early tracheostomy and late tracheostomy on the prognosis of patients with cervical spinal cord injury, so as to provide evidence based guidance for the timing of tracheostomy. Methods Relevant literatures studying the timing of tracheostomy in patients with cervical spinal cord injury were searched in PubMed, Embase, Medline, Cochrane Library, Chinese Biological Medical Literature database (CBM), China National Knowledge Infrastructure database (CNKI), and VIP journal database with time range from journal establishment to March 2018. The retrieved articles were screened according to the inclusion and exclusion criteria. The article quality was rigorously evaluated according to the Newcastle-Ottawa scale (NOS). Meta analysis was conducted using Review Manager 5.3 software to compare the mechanical ventilation time, ICU stay, incidence of pneumonia, incidence of complications, and mortality between early and late tracheostomy in patients with cervical spinal cord injury. Results A total of eight articles of cohort study including 466 patients were included , with 241 patients in the early tracheostomy group and 225 patients in the late tracheostomy group. The eight articles were all determined as high quality studies according NOS. The results of Meta analysis showed that there were significant differences between the two groups in terms of the total mechanical ventilation time (MD=-12.28, 95%CI -20.09--4.47, P 0.05) and the incidence of post tracheostomy pneumonia (RR=0.80, 95%CI 0.51-1.26, P>0.05). Conclusion Early tracheostomy can shorten the mechanical ventilation time, ICU stay, incidence of complications, and mortality, but it cannot reduce the incidence of pneumonia. Key words: Tracheotomy; Spinal cord injuries; Prognosis; Meta analysis

On the Biogeographical Significance of Protected Forest Areas in Southern Romania

The current study is seeking to highlight the biogeographical significance of the protected areas located in southern Romania, a territory continuously exposed to strong human pressure since early times (e.g., extensive/intensive agricultural use, industrialization, urbanization/suburbanization processes). As a result, the primeval vegetation has been massively transformed and forests have been significantly fragmented and reduced to even smaller surfaces (e.g., Călăraşi County has the smallest forest-covered area in Romania). Under these conditions, the current forest patches have suffered important floristic and faunistic structural changes. Some forest remnants have been assigned protected areas status of biogeographical significance, as they host and preserve valuable southern arboreta species and xerothermal associations, secular and multi-secular arboreta (even some virgin arboreta), relict, endemic or unique species, or having their world biological limit. To stress the biogeographical significance of the forest protected areas, the authors carried out in-depth investigations of the ecosystem structure focusing on the spatial and statistical changes occurring over recent centuries and the key phyto- and zoological elements relied on the cross-referencing the biological, biogeographical, and geographical scientific literature and on the reviewing of the historical data sources. The study provides a comprehensive analysis of the biogeographical elements based on selected indicative taxa (Quercus species) and witness species considered important for southern Romania, which were able to reconstruct the original ecosystems to explain and understand their significance for the preservation of the current ecosystems.