bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying Coevolving Partners from Paralogous Gene Families
Authors: Yeang Chen-Hsiang
Published: November 2017

Many methods have been developed to detect coevolution from aligned sequences. However, all the existing methods require a one-to-one mapping of candidate coevolving partners (nucleotides, amino acids) a priori. When two families of sequences have distinct duplication and loss histories, finding the one-to-one mapping of coevolving partners can be computationally involved. We propose an algorithm to identify the coevolving partners from two families of sequences with distinct phylogenetic trees. The algorithm maps each gene tree to a reference species tree, and builds a joint state of sequence composition and assignments of coevolving partners for each species tree node. By applying dynamic programming on the joint states, the optimal assignments can be identified. Time complexity is quadratic to the size of the species tree, and space complexity is exponential to the maximum number of gene tree nodes mapped to the same species tree node. Analysis on both simulated data and Pfam protein domain sequences demonstrates that the paralog coevolution algorithm picks up the coevolving partners with 60%–88% accuracy. This algorithm extends phylogeny-based coevolutionary models and make them applicable to a wide range of problems such as predicting protein-protein, protein-DNA and DNA-RNA interactions of two distinct families of sequences.
Assessing the Evolution of Gene Expression Using Microarray Data
Authors: Woody Owen Z. , Doxey Andrew C. , McConkey Brendan J.
Published: November 2017

Classical studies of the evolution of gene function have predominantly focused on mutations within protein coding regions. With the advent of microarrays, however, it has become possible to evaluate the transcriptional activity of a gene as an additional characteristic of function. Recent studies have revealed an equally important role for gene regulation in the retention and evolution of duplicate genes. Here we review approaches to assessing the evolution of gene expression using microarray data, and discuss potential influences on expression divergence. Currently, there are no established standards on how best to identify and quantify instances of expression divergence. There have also been few efforts to date that incorporate suspected influences into mathematical models of expression divergence. Such developments will be crucial to a comprehensive understanding of the role gene duplications and expression evolution play in the emergence of complex traits and functional diversity. An integrative approach to gene family evolution, including both orthologous and paralogous genes, has the potential to bring strong predictive power both to the functional annotation of extant proteins and to the inference of functional characteristics of ancestral gene family members.
Maximum Gene-Support Tree
Authors: Shan Yunfeng , Li Xiu-Qing
Published: November 2017

Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced as well as plants that have the fossil-supported true phylogenetic trees available. In this study, we generated single gene trees of seven yeast species as well as single gene trees of nine baculovirus species using all the orthologous genes among the species compared. Homologous genes among seven known plants were used for validation of the finding. Four algorithms—maximum parsimony (MP), minimum evolution (ME), maximum likelihood (ML), and neighbor-joining (NJ)—were used. Trees were reconstructed before and after weighting the DNA and protein sequence lengths among genes. Rarely a gene can always generate the “true tree” by all the four algorithms. However, the most frequent gene tree, termed “maximum gene-support tree” (MGS tree, or WMGS tree for the weighted one), in yeasts, baculoviruses, or plants was consistently found to be the “true tree” among the species. The results provide insights into the overall degree of divergence of orthologous genes of the genomes analyzed and suggest the following: 1) The true tree relationship among the species studied is still maintained by the largest group of orthologous genes; 2) There are usually more orthologous genes with higher similarities between genetically closer species than between genetically more distant ones; and 3) The maximum gene-support tree reflects the phylogenetic relationship among species in comparison.
Electrostatic and Functional Analysis of the Seven-Bladed WD β-Propellers
Authors: Valeyev Najl V , Downing A. Kristina , Sondek John , Deane Charlotte
Published: November 2017

β-propeller domains composed of WD repeats are highly ubiquitous and typically used as multi-site docking platforms to coordinate and integrate the activities of groups of proteins. Here, we have used extensive homology modelling of the WD40–repeat family of seven-bladed β-propellers coupled with subsequent structural classification and clustering of these models to define subfamilies of β-propellers with common structural, and probable, functional characteristics. We show that it is possible to assign seven-bladed WD β-propeller proteins into functionally different groups based on the information gained from homology modelling. We examine general structural diversity within the WD40-repeat family of seven-bladed β-propellers and demonstrate that seven-bladed β-propellers composed of WD-repeats are structurally distinct from other seven-bladed β-propellers. We further provide some insights into the multifunctional diversity of the seven-bladed WD β-propeller surfaces. This report once again reinforces the importance of structural data and the usefulness of homology models in functional classification.
Exploring the Evolutionary History of the Differentially Expressed Genes between Human Populations: Action of Recent Positive Selection
Authors: Zhang Wei , Dolan M. Eileen
Published: November 2017

Though debates exist on the early human evolutionary models such as the “Out of Africa” theory, which hypothesizes that modern humans migrated from Africa to Europe about 50,000 to 100,000 years ago, Africans and Europeans were geographically separated with minimal gene flow for tens of thousands of years. The variations between the current European and African populations, therefore, should have evolved during this timeframe. To gain more insights into the evolutionary history of human phenotypes including gene expression, it is critical to tell how recent positive selection has played a role in the variations observed in the current populations. Using the list of differentially expressed genes we previously identified between the HapMap samples derived from individuals of African (from Ibadan, Nigeria) and European (from Utah, USA) ancestry, we searched for evidence of selection among these differential genes. We found that 27 differentially expressed genes (out of 356 tested) between these two European and African populations have been under recent positive selection. Our findings suggest that the variation between these two populations appears to be affected primarily by neutral genetic drift and/or stabilizing selection and to a lesser degree by positive selection. Further annotation enrichment analyses showed that these 27 genes under selection were overrepresented in certain Gene Ontology biological processes, molecular functions and cellular components such as transcription, lipid binding and lysosome. Our results can provide unique insights into the evolutionary history of the variation in the gene expression phenotype between these two human populations.
Testing the Accuracy of Eukaryotic Phylogenetic Profiles for Prediction of Biological Function
Authors: Singh Saurav , Wall Dennis P.
Published: November 2017

A phylogenetic profile captures the pattern of gene gain and loss throughout evolutionary time. Proteins that interact directly or indirectly within the cell to perform a biological function will often co-evolve, and this co-evolution should be well reflected within their phylogenetic profiles. Thus similar phylogenetic profiles are commonly used for grouping proteins into functional groups. However, it remains unclear how the size and content of the phylogenetic profile impacts the ability to predict function, particularly in Eukaryotes. Here we developed a straightforward approach to address this question by constructing a complete set of phylogenetic profiles for 31 fully sequenced Eukaryotes. Using Gene Ontology as our gold standard, we compared the accuracy of functional predictions made by a comprehensive array of permutations on the complete set of genomes. Our permutations showed that phylogenetic profiles containing between 25 and 31 Eukaryotic genomes performed equally well and significantly better than all other permuted genome sets, with one exception: we uncovered a core of group of 18 genomes that achieved statistically identical accuracy. This core group contained genomes from each branch of the eukaryotic phylogeny, but also contained several groups of closely related organisms, suggesting that a balance between phylogenetic breadth and depth may improve our ability to use Eukaryotic specific phylogenetic profiles for functional annotations.
Inconsistent Distances in Substitution Matrices can be Avoided by Properly Handling Hydrophobic Residues
Authors: Baussand J. , Carbone A.
Published: November 2017

The adequacy of substitution matrices to model evolutionary relationships between amino acid sequences can be numerically evaluated by checking the mathematical property of triangle inequality for all triplets of residues. By converting substitution scores into distances, one can verify that a direct path between two amino acids is shorter than a path passing through a third amino acid in the amino acid space modeled by the matrix. If the triangle inequality is not verified, the intuition is that the evolutionary signal is not well modeled by the matrix, that the space is locally inconsistent and that the matrix construction was probably based on insufficient biological data. Previous analysis on several substitution matrices revealed that the number of triplets violating the triangle inequality increases with sequence divergence. Here, we compare matrices which are dedicated to the alignment of highly divergent proteins. The triangle inequality is tested on several classical substitution matrices as well as in a pair of “complementary” substitution matrices recording the evolutionary pressures inside and outside hydrophobic blocks in protein sequences. The analysis proves the crucial role of hydrophobic residues in substitution matrices dedicated to the alignment of distantly related proteins.
Article Commentary: Environmental Health: Threats and their Interactions
Authors: Holdstock Douglas
Published: November 2017

Improvements in the provision of an acceptable standard of health care, particularly in the developing world, will be undermined by three ongoing processes: ongoing armed conflicts; the threat of global warming due to rising levels of greenhouse gases, particularly carbon dioxide emitted by developed countries; and by rapidly rising populations. The key features of these three threats are summarised, and it is shown that interactions between them increase both the likelihood of their occurrence and the probable harm that they will cause. Some of the interactions are described, with ways of providing health care taking into account the threats and their interactions, and the paradox is emphasised that better health care in the developing world will further increase population growth followed by increased greenhouse gas emissions. Improved education for women and free and unlimited access to modern methods of contraception are vital.
Parks, Recreation, and Public Health Collaborative
Authors: Kruger Judy
Published: November 2017

The primary goal of many park and recreation agencies is to provide resources and programs that improve quality of life for the community. Increasing physical activity is one aspect of this agenda. Promoting physical activity is a public health goal; however, increasing population-level physical activity will require access to places for physical activity (e.g. parks). Practitioners and policy makers need more information to document the roles that parks and recreation facilities play to promote physical activity and contribute to public health. A working group of approximately 20 professionals experienced in data collection came together to discuss the needs for better surveillance and measurement instruments in the fields of parks, recreation, and public health. The working group made two major recommendations: (1) the need for collaborative research and data sharing, and (2) the need for surveillance measures to demonstrate the amount of health-related physical activity acquired in the park setting.
Comparability of Weighed Dietary Records and a Self-Administered Diet History Questionnaire for Estimating Monetary Cost of Dietary Energy
Authors: Murakami Kentaro , Sasaki Satoshi , Takahashi Yoshiko , Okubo Hitomi , Hirota Naoko , Notsu Akiko , Fukui Mitsuru , Date Chigusa
Published: November 2017

An increasing number of studies have estimated monetary diet cost using various dietary assessment methods, based on databases on retail food prices, for investigating its association with dietary intake and health outcomes. However, information regarding the comparability of monetary diet cost across dietary assessment methods is absolutely lacking. This study compared monetary cost of dietary energy estimated from weighed dietary records (DRs) with that estimated from a self-administered diet history questionnaire (DHQ). The subjects were 92 Japanese women aged 31-69 years and 92 Japanese men aged 32-76 years. The DHQ (assessing diet during the preceding month) and 4-day DRs (one weekend day and three weekdays) were completed in each season over a 1-year period (DHQs1-4 and DRs1-4, respectively). An additional DHQ was completed at one year after completing DHQ1 (DHQ5). Monetary cost of dietary energy (Japanese yen/4184 kJ) was calculated using food intake information derived from each dietary assessment method, based on retail food prices. Pearson correlation between the mean of DRs1-4 and mean of DHQs1-4 was 0.64 for women and 0.69 for men. Pearson correlation between the mean of DRs1-4 and DHQ1 was 0.60 for women and 0.52 for men, while intraclass correlation between DHQ1 and DHQ5 was 0.64 for women and 0.51 for men. These data indicate reasonable comparability of monetary cost of dietary energy across DR and a DHQ as well as usefulness of a single administration of the DHQ for estimating monetary cost of dietary energy.
Article Commentary: Environmental Sanitation Crisis: More than just a health issue
Authors: Harvey Peter A.
Published: November 2017

The global environmental sanitation crisis cannot be denied: well over a century after the sanitary revolution in 19th century Europe, 40% of the world's population still lacks access to improved sanitation. Important lessons from the past must be applied today if the crisis is to be averted. Sanitation has suffered from a lack of prioritization for as long as it has remained the poor relation to water supply. The International Year of Sanitation 2008 provides an opportunity to separate the two and give sanitation the emphasis it requires. The economic argument for sanitation must be articulated and non-health incentives for improved sanitation exploited. Environmental sanitation results in a multitude of socio-economic benefits and can contribute positively to all the Millennium Development Goals. Community-led bottom-up approaches, rather than supply-led or technology-driven approaches, are most effective in increasing and sustaining access to sanitation but need to be implemented at scale. Targeted strategies for urban and school sanitation are also required. Evidence-based advocacy can help develop the political will that is now needed to ensure sufficient public sector investment, leadership, legislation and regulation to ensure that the fundamental human right of access to sanitation is realized.
Economic Evaluation of Environmental Health Interventions to Support Decision Making
Authors: Hutton Guy
Published: November 2017

Environmental burden of disease represents one quarter of overall disease burden, hence necessitating greater attention from decision makers both inside and outside the health sector. Economic evaluation techniques such as cost-effectiveness analysis and cost-benefit analysis provide key information to health decision makers on the efficiency of environmental health interventions, assisting them in choosing interventions which give the greatest social return on limited public budgets and private resources. The aim of this article is to review economic evaluation studies in three environmental health areas–-water, sanitation, hygiene (WSH), vector control, and air pollution–-and to critically examine the policy relevance and scientific quality of the studies for selecting and funding public programmers. A keyword search of Medline from 1990-2008 revealed 32 studies, and gathering of articles from other sources revealed a further 18 studies, giving a total of 50 economic evaluation studies (13 WSH interventions, 16 vector control and 21 air pollution). Overall, the economic evidence base on environmental health interventions remains relatively weak–-too few studies per intervention, of variable scientific quality and from diverse locations which limits generalisability of findings. Importantly, there still exists a disconnect between economic research, decision making and programmer implementation. This can be explained by the lack of translation of research findings into accessible documentation for policy makers and limited relevance of research findings, and the often low importance of economic evidence in budgeting decisions. These findings underline the importance of involving policy makers in the defining of research agendas and commissioning of research, and improving the awareness of researchers of the policy environment into which their research feeds.
Patterns of Pesticide Use and Associated Factors among the Commercial Farmers of Chitwan, Nepal
Authors: Khanal Gayatri , Singh Amarjeet
Published: November 2017

Farmers in developing countries are exposed to pesticide hazards due to unsafe handling. This study was conducted to identify the prevailing practices of pesticide use and factors affecting the handling of pesticides among the farmers of Chitwan, Nepal. A cross-sectional study was conducted among 125 farmers. None of the farmers completely followed all the protective measures. About 59% disposed the empty pesticide containers to a nearby water source and 62% preferred house ceilings as a storage place. Males (aOR = 3.99, CI = 1.63-9.78) and older farmers (aOR = 6.18, CI = 2.59-14.72) were more likely to smoke or chew tobacco during the process of spray. Males (aOR = 2.42, CI = 1.03-5.67), literate farmers (aOR = 3.56, CI = 1.51-8.33), and farmers aware of color coding (aOR = 2.67, CI = 1.13-5.67) were more likely to read the labels on pesticide bottles. In spite of an extensive use of pesticides, the farmers were not following proper and safe handling practices, exposing them and the community to a potential pesticide hazard.
Public Health Consequences on Vulnerable Populations from Acute Chemical Releases
Authors: Ruckart Perri Zeitz , Orr Maureen F.
Published: November 2017

Data from a large, multi-state surveillance system on acute chemical releases were analyzed to describe the type of events that are potentially affecting vulnerable populations (children, elderly and hospitalized patients) in order to better prevent and plan for these types of incidents in the future. During 2003-2005, there were 231 events where vulnerable populations were within ¼ mile of the event and the area of impact was greater than 200 feet from the facility/point of release. Most events occurred on a weekday during times when day care centers or schools were likely to be in session. Equipment failure and human error caused a majority of the releases. Agencies involved in preparing for and responding to chemical emergencies should work with hospitals, nursing homes, day care centers, and schools to develop policies and procedures for initiating appropriate protective measures and managing the medical needs of patients. Chemical emergency response drills should involve the entire community to protect those that may be more susceptible to harm.
Mortality in the Bedouin Population and Proximity to a Regional Industrial Complex
Authors: Karakis Isabella , Bolotin Arkady , Kordysh Ella , Belmaker Ilana , Sarov Batia
Published: November 2017

Background

The study was initiated by public concern about exposure to an industrial park (IP) emission. The study examined whether mortality in the Bedouin population in the southern part of Israel is associated with the residential distance to the IP.

Material and Methods

Ecological study during 1995-2001 included the entire Bedouin population. Mortality data was obtained from the Central Bureau of Statistics. As an indirect measurement of exposure we used residential distance to the IP (with 20 km radius as a cut-of-point) based on residents’ complaints about odor related to the IP. Differences in mortality rates by distance were assessed by the Mantel-Haenszel relative risk (M-H RR) within the 95% CI. The country Arab population served as a reference for calculation of the age-adjusted standardized mortality ratio (SMR).

Results

Increased mortality rates due to symptoms/ill-defined conditions and non-external causes were observed in the Bedouin population of both sexes, residing up to 20 km from the IP, compared to those living in more remote areas. Corresponding M-H RR (plus 95% CI) were 1.66 (1.17-2.36), 1.24 (1.06-1.44) in females, and 1.55 (1.15-2.10), 1.32 (1.15-1.52) in males.

Conclusions

The study results suggest an association between residential proximity to the regional IP and increased mortality rates in the Negev Bedouin population. These findings have been accepted by the authorities as an issue for community health protection.
Article Commentary: Indicators to Measure Success of Smoke-free Policies
Authors: Niskar Amanda
Published: November 2017

The health consequences of involuntary exposure to tobacco smoke are well documented. The past decade provides several examples of successful smoke-free policies that are directly related to improving public health. The objective of this communication is to identify indicators that demonstrate the success of smoke-free policies. Indicators are identified from smoke-free policy evaluations conducted by countries such as the United States, New Zealand, and Israel. Indicators were identified that demonstrate the success of smoke-free policies in the areas of compliance, indoor air quality, bio-monitoring, medical tests, and health behaviors. As smoke-free policies continue to be implemented, indicator evaluation activities should be considered from the start.
Eco-psychiatry and Environmental Conservation: Study from Sundarban Delta, India
Authors: Chowdhury Arabinda N. , Mondal Ranajit , Brahma Arabinda , Biswas Mrinal K.
Published: November 2017

Aims

This study attempts to examine the extent and impact of human-animal conflicts visa-vis psychosocial stressors and mental health of affected people in two villages adjacent to Sundarban Reserve Forest (SRF) in the Gosaba Block, West Bengal, India.

Methods

Door to door household survey for incidents of human-animal conflicts, Focus Group Discussions, In-depth Interviews, Case studies, Community Mental health clinics and participatory observation.

Results

A total of 3084 households covering a population of 16,999 were surveyed. 32.8% people live on forest-based occupation. During the last 15 years 111 persons (male 83, female 28) became victims of animal attacks, viz, Tiger (82%), Crocodile (10.8%) and Shark (7.2%) of which 73.9% died. In 94.5% cases the conflict took place in and around the SRF during livelihood activities. Tracking of 66 widows, resulted from these conflicts, showed that majority of them (51.%) are either disabled or in a very poor health condition, 40.9% are in extreme economic stress and only 10.6% remarried. 1 widow committed suicide and 3 attempted suicide. A total of 178 persons (male 82, female 96) attended the community mental health clinics. Maximum cases were Major Depressive Disorder (14.6%), followed by Somatoform Pain Disorder (14.0%), Post Traumatic Stress Disorder-animal attack related (9.6%) and Adjustment Disorder (9%). 11.2% cases had history of deliberate self-harm attempt, of which 55% used pesticides.

Conclusions

Improvement of quality of life of this deltaic population by appropriate income generation and proper bio-forest management are the key factors to save their life as well as the mangrove environment of the Sundarban region.
Biomonitoring of Human Exposure to Prestige Oil: Effects on DNA and Endocrine Parameters
Authors: Pérez-Cadahfa Beatriz , Méndez Josefina , Pasaro Eduardo , Lafuente Anunciación , Cabaleiro Teresa , Laffon Blanca
Published: November 2017

Since 1960, about 400 tankers spilled more than 377765 tons of oil, with the Prestige accident (Galician coast, NW Spain, November 2002) the most recent. Taking into account the consistent large number of individuals exposed to oil that exists all over the world, it seems surprising the absence in the literature of studies focused on the chronic effects of this exposure on human health. In this work we evaluated the level of DNA damage by means of comet assay, and the potential endocrine alterations (prolactin and cortisol) caused by Prestige oil exposure in a population of 180 individuals, classified in 3 groups according to the tasks performed, and 60 controls. Heavy metals in blood were determined as exposure biomarkers, obtaining significant increases of aluminum, nickel and lead in the exposed groups as compared to controls. Higher levels of genetic damage and endocrine alterations were also observed in the exposed population. DNA damage levels were influenced by age, sex, and the use of protective clothes, and prolactin concentrations by the last two factors. Surprisingly, the use of mask did not seem to protect individuals from genetic or endocrine alterations. Moreover, polymorphisms in genes encoding for the main enzymes involved in the metabolism of oil components were analyzed as susceptibility biomarkers. CYP1A1-3'UTR and EPHX1 codons 113 and 139 variant alleles were related to higher damage levels, while lower DNA damage was observed in GSTM1 and GSTT1 null individuals.
RNAi-Mediated Knockdown Showing Impaired Cell Survival in Drosophila Wing Imaginal Disc
Authors: Umemori Makoto , Habara Okiko , Iwata Tatsunori , Maeda Kousuke , Nishinoue Kana , Okabe Atsushi , Takemura Masahiko , Takahashi Kuniaki , Saigo Kaoru , Ueda Ryu , Adachi-Yamada Takashi
Published: November 2017

The genetically amenable organism Drosophila melanogaster has been estimated to have 14,076 protein coding genes in the genome, according to the flybase release note R5.13 ( http://flybase.bio.indiana.edu/static_pages/docs/release_notes.html ). Recent application of RNA interference (RNAi) to the study of developmental biology in Drosophila has enabled us to carry out a systematic investigation of genes affecting various specific phenotypes. In order to search for genes supporting cell survival, we conducted an immunohistochemical examination in which the RNAi of 2,497 genes was independently induced within the dorsal compartment of the wing imaginal disc. Under these conditions, the activities of a stress-activated protein kinase JNK (c-Jun N-terminal kinase) and apoptosis-executing factor Caspase-3 were monitored. Approximately half of the genes displayed a strong JNK or Caspase-3 activation when their RNAi was induced. Most of the JNK activation accompanied Caspase-3 activation, while the opposite did not hold true. Interestingly, the area activating Caspase-3 was more broadly seen than that activating JNK, suggesting that JNK is crucial for induction of non-autonomous apoptosis in many cases. Furthermore, the RNAi of essential factors commonly regulating transcription and translation snowed a severe and cell-autonomous apoptosis but also elicited another apoptosis at an adjacent area in a non-autonomous way. We also found that the frequency of apoptosis varies depending on the tissues.
A Novel Function of Ethylene
Authors: Amagai Aiko
Published: November 2017

The cellular slime mold, Dictyostelium mucoroides-7 (Dm7) exhibits clear dimorphism; macrocyst formation as a sexual process and sorocap formation as an asexual process. These two life cycles are regulated by two regulators, ethylene and cyclic AMP (cAMP). This is the first report demonstrating a novel function of ethylene at the cellular level. That is, ethylene induces a zygote formed by cell fusion and subsequent nuclear fusion. Recently, the function of ethylene at the molecular level has been clarified as it induces zygote formation through an enhanced expression of a novel gene, zyg1. The signaling pathway for induction or inhibition of zygote formation is now trying to be clarified focusing on the ZYG1 protein.
Hereditary Inclusion Body Myopathy (HIBM2)
Authors: Jay Chris M. , Levonyak Nick , Nemunaitis Gregory , Maples Phillip B. , Nemunaitis John
Published: November 2017

Hereditaiy inclusion body myopathy type 2 (HIBM2) is a myopathy characterized by progressive muscle weakness with early adult onset. The disease is the result of a recessive mutation in the Glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase gene (GNE), which results in reduced enzyme function and sialic acid levels. A majority of individuals with HIBM2 are from Iranian-Jewish or Japanese decent, but isolated cases have been identified world wide. This article reviews the diagnostic criteria for HIBM2. Current research with a highlight on the biology of the disease and the role of GNE in the sialic acid pathway are assessed. Finally, therapeutic investigations and animal models are discussed with a focus on future studies to better understand the pathology of Hereditaiy Inclusion Body Myopathy and move therapeutic agents towards clinical trials.
Trichoderma Biocontrol: Signal Transduction Pathways Involved in Host Sensing and Mycoparasitism
Authors: Zeilinger Susanne , Omann Markus
Published: November 2017

Fungi of the genus Trichoderma are used as biocontrol agents against several plant pathogenic fungi like Rhizoctonia spp., Pythium spp., Botrytis cinerea and Fusarium spp. which cause both soil-borne and leaf- or flower-borne diseases of agricultural plants. Plant disease control by Trichoderma is based on complex interactions between Trichoderma, the plant pathogen and the plant. Until now, two main components of biocontrol have been identified: direct activity of Trichoderma against the plant pathogen by mycoparasitism and induced systemic resistance in plants. As the mycoparasitic interaction is host-specific and not merely a contact response, it is likely that signals from the host fungus are recognised by Trichoderma and provoke transcription of mycoparasitism-related genes.

In the last few years examination of signalling pathways underlying Trichoderma biocontrol started and it was shown that heterotrimeric G-proteins and mitogen-activated protein (MAP) kinases affected biocontrol-relevant processes such as the production of hydrolytic enzymes and antifungal metabolites and the formation of infection structures. MAPK signalling was also found to be involved in induction of plant systemic resistance in Trichoderma virens and in the hyperosmotic stress response in Trichoderma harzianum. Analyses of the function of components of the cAMP pathway during Trichoderma biocontrol revealed that mycoparasitism-associated coiling and chitinase production as well as secondary metabolism are affected by the internal cAMP level; in addition, a cross talk between regulation of light responses and the cAMP signalling pathway was found in Trichoderma atroviride.
MicroRNAs Regulate Osteogenesis and Chondrogenesis of Mouse Bone Marrow Stromal Cells
Authors: Suomi Salla , Taipaleenmäki Hanna , Seppänen Anne , Ripatti Tommi , Väänänen Kalervo , Hentunen Teuvo , Säämänen Anna-Marja , Laitala-Leinonen Tiina
Published: November 2017

MicroRNAs (miRNAs) are non-coding RNAs that bind to target mRNA leading to translational arrest or mRNA degradation. To study miRNA-mediated regulation of osteogenesis and chondrogenesis, we compared the expression of 35 miRNAs in osteoblasts and chondroblasts derived from mouse marrow stromal cells (MSCs). Differentiation of MSCs resulted in up- or downregulation of several miRNAs, with miR-199a expression being over 10-fold higher in chondroblasts than in undifferentiated MSCs. In addition, miR-124a was strongly upregulated during chondrogenesis while the expression of miR-96 was substantially suppressed. A systems biological analysis of the potential miRNA target genes and their interaction networks was combined with promoter analysis. These studies link the differentially expressed miRNAs to collagen synthesis and hypoxia, key pathways related to bone and cartilage physiology. The global regulatory networks described here suggest for the first time how miRNAs and transcription factors are capable of fine-tuning the osteogenic and chondrogenic differentiation of mouse MSCs.
User’s Guide for the Six Month Old Infant Dummy (CRABI)
Authors:   Dummy Testing and  Equipment Committee
Published: November 2017

The CRABI dummy was developed to evaluate small child restraint systems in automotive crash environments, in all directions of impact, with or without air bag interaction

Basic anthropometry for this test device was taken from the University of Michigan Transportation Research Institute Report 85-23. Weight distribution and scaling methods for the infant were approved by the Society of Automotive (SAE) Infant Dummy Task Group. The dummy weighs 17.2 pounds and has a 26.4 inches standing or 17.3 inches sitting height. The Hybrid Ill-like neck and lumbar spine are laterally notched to reduce lateral stiffness

The shoulders have flesh support for durability and human-like performance in areas where seatbelt webbing may be placed. In addition, rubber elements are used in each joint to improve biofidelity and to give the CRABI infant-like range of motion. The CRABI Six-Month-Old design meets all the SAE Infant Dummy Task Group anthropometry, biomechanical and instrumentation requirements. The instrumentation design incorporates three 6-channel load cells to provide load measurements at the C1, C7 and L5 vertebrae locations. Accelerometers are used to measure head, chest and pelvic acceleration and head angular acceleration. All instrumentation is easily accessed
Evaluation of the Antifungal Effect of Chicory Extracts on Candida Glabrata and Candida Krusei in a Laboratory Environment
Authors: Rahbar Mahdi , Eslami Hosein , Babaei Hossein , Falsafi Parisa , Najar-Karimi Fereshteh , Pourzare-Mehrbani Solmaz
Published: November 2017

Aim

This research has evaluated the extract's antifungal effects on Candida glabrata and Candida krusei in a laboratory environment.

Materials and methods

In this research, to evaluate the antifungal effect and the minimal inhibitory concentration (MIC) determination of chicory extract, the Clinical and Laboratory Standards Institute (CLSI) was used. Candida glabrata and C. krusei funguses were procured from the Tehran Pasteur Institute; they were grown in the relative growing environment according to the required conditions. Also for further assurance about the macrodilution method reality, the agar well diffusion method was used. Finally, the obtained results were analyzed using the Statistical Package for the Social Sciences version 16 software.

Results

The MIC for the chicory extract was 50 μg/mL for C. krusei and 100 μg/mL for C. glabrata. On the contrary, in the evaluation of different concentrations of the chicory extract by the agar well diffusion method, C. krusei's lack of growth in similar concentrations was greater than that of C. glabrata. As a result, the findings related to both the methods of agar well diffusion and MIC prevention concentration maximization proved that C. krusei sensitivity to the chicory extract is more compared with the sensitivity of C. glabrata.

Conclusion

Chicory extract has the benefits of low price, accessibility, and proper taste as compared with nystatin. It also has fewer side effects, and after a clinical test, it could be considered a proper candidate as an antifungal drug against infections caused by C. krusei and C. glabrata.

Clinical significance

The results obtained from this research have shown that chicory extract has antifungal features and is the best choice as an antifungal drug because of its low price, accessibility, and proper taste as compared with nystatin.

How to cite this article

Eslami H, Babaei H, Falsafi P, Rahbar M, Najar-Karimi F, Pourzare-Mehrbani S. Evaluation of the Antifungal Effect of Chicory Extracts on Candida Glabrata and Candida Krusei in a Laboratory Environment. J Contemp Dent Pract 2017;18(11):1014-1020.
Extrusion of Debris from Primary Molar Root Canals following Instrumentation with Traditional and New File Systems
Authors: Thakur Bhagyashree , Pawar Ajinkya M , Kfir Anda , Neelakantan Prasanna
Published: November 2017

Introduction

To assess the amount of debris extruded apically during instrumentation of distal canals of extracted primary molars by three instrument systems [ProTaper Universal (PTU), ProTaper NEXT (PTN), and self-adjusting file (SAF)] compared with conventional stainless steel hand K-files (HF, control).

Materials and methods

Primary mandibular molars (n = 120) with a single distal canal were selected and randomly divided into four groups (n = 30) for root canal instrumentation using group I, HF (to size 0.30/0.02 taper), group II, PTU (to size F3), group III, PTN (to size X3), and group IV, SAF. Debris extruded during instrumentation was collected in preweighed Eppendorf tubes, stored in an incubator at 70°C for 5 days and then weighed. Statistical analysis was performed by one-way analysis of variance (ANOVA), followed by Turkey'spost hoctest (p = 0.05).

Results

All the groups resulted in extrusion of debris. There was statistically significant difference (p < 0.001) in the debris extrusion between the three groups: HF (0.00133 ± 0.00012), PTU (0.00109 ± 0.00005), PTN (0.00052 ± 0.00008), and SAF (0.00026 ± 0.00004).

Conclusion

Instrumentation with SAF resulted in the least debris extrusion when used for shaping root canals of primary molar teeth.

Clinical significance

Debris extrusion in primary teeth poses an adverse effect on the stem cells and may also alter the permanent dental germ. Debris extrusion is rarely reported for primary teeth and it is important for the clinician to know which endodontic instrumentation leads to less extrusion of debris.

How to cite this article

Thakur B, Pawar AM, Kfir A, Neelakantan P. Extrusion of Debris from Primary Molar Root Canals following Instrumentation with Traditional and New File Systems. J Contemp Dent Pract 2017;18(11):1040-1044.
Self-disinfecting Alginate vs Conventional Alginate: Effect on Surface Hardness of Gypsum Cast—An in vitro Study
Authors: Nagpal Ajay , Madhavan Ranjith , George Navia , Thummala Niharika R , Ravi SV
Published: November 2017

Introduction

For the construction of any dental prosthesis, accurate impressions are necessary. Hence, we undertook the present study to evaluate and compare the surface hardness of gypsum casts poured from impressions made using conventional alginate and self-disinfecting alginate.

Materials and methods

A total of 30 impressions of stainless steel die were made, out of which 15 impressions were made with conventional alginate and 15 were made with selfdisinfecting alginate and poured using Type III dental stone. Thirty stone specimens were subjected for hardness testing. Data were analyzed using independent samples t-test to compare the mean surface hardness.

Results

Difference in surface hardness was statistically insignificant (p > 0.05).

Conclusion

Surface hardness of gypsum casts poured using impressions made from self-disinfecting alginate and conventional alginates were comparable.

Clinical significance

Self-disinfecting alginates may be employed in clinical practice as safe and effective materials to overcome the infection control issues without compromising on the properties of the material.

How to cite this article

Madhavan R, George N, Thummala NR, Ravi SV, Nagpal A. Self-disinfecting Alginate vs Conventional Alginate: Effect on Surface Hardness of Gypsum Cast—An in vitro Study. J Contemp Dent Pract 2017;18(11):1061-1064.
Evolution of Nickel–titanium Alloys in Endodontics
Authors: Anil Sukumaran , Neelakantan Prasanna , Nassif Wadih
Published: November 2017

To improve clinical use of nickel–titanium (NiTi) endodontic rotary instruments by better understanding the alloys that compose them. A large number of engine-driven NiTi shaping instruments already exists on the market and newer generations are being introduced regularly. While emphasis is being put on design and technique, manufacturers are more discreet about alloy characteristics that dictate instrument behavior. Along with design and technique, alloy characteristics of endodontic instruments is one of the main variables affecting clinical performance. Modification in NiTi alloys is numerous and may yield improvements, but also drawbacks. Martensitic instruments seem to display better cyclic fatigue properties at the expense of surface hardness, prompting the need for surface treatments. On the contrary, such surface treatments may improve cutting efficiency but are detrimental to the gain in cyclic fatigue resistance. Although the design of the instrument is vital, it should in no way cloud the importance of the properties of the alloy and how they influence the clinical behavior of NiTi instruments.

Clinical significance

Dentists are mostly clinicians rather than engineers. With the advances in instrumentation design and alloys, they have an obligation to deal more intimately with engineering consideration to not only take advantage of their possibilities but also acknowledge their limitations.

How to cite this article

Ounsi HF, Nassif W, Grandini S, Salameh Z, Neelakantan P, Anil S. Evolution of Nickel–titanium Alloys in Endodontics. J Contemp Dent Pract 2017;18(11):1090-1096.
Fluorosis: Environmental Risk Factor for Periodontal Disease?
Authors: Dalvi Priyanka J , Ghosh Saubhik , Joshi Vinayak M , Bhat Kishor , Prakash Vivek H , Vandana Kharidhi L
Published: November 2017

Background

Periodontitis is multifactorial in nature. The effects of fluorosis as an environmental factor are not evaluated and researched to designate it as a risk factor similar to smoking. The primary objectives of this study were to investigate whether there is any association between fluorosis and periodontal disease and to assess salivary oxidative stress in fluorosed and nonfluorosed patients with periodontitis contributing to periodontal disease.

Aim

This is a case—control study with an aim to investigate whether fluorosis acts as a risk factor for periodontal disease and to assess salivary oxidative stress in fluorosed and nonfluorosed patients with periodontitis contributing to periodontal disease.

Materials and methods

About 295 systemically healthy patients were divided into test group (n = 154 fluorosed subjects) and control group (n = 141 nonfluorosed subjects) and assessed for their periodontal status. Clinical parameters recorded were plaque index, gingival bleeding index (GBI), and Jackson's fluorosis index to assess the degree of fluorosis, and community periodontal index was to assess the periodontal status. Biochemical analysis of saliva was done for assessment of malondialdehyde (MDA) levels, superoxide dismutase (SOD) levels, and total antioxidant (TAOC) levels.

Results

The plaque and GBI scores were found similar in fluorosed and nonfluorosed groups. Gingivitis was significantly higher in nonfluorosed than in fluorosed group; in contrast, periodontitis was significantly higher in fluorosed group than in nonfluorosed group. Gingivitis appeared to decline as the fluoride status worsened, while periodontitis showed an increasing gradient from lower fluoride score to higher fluoride score. As the degree of fluorosis increased, periodontitis also increased. The salivary antioxidant levels were found similar in both the groups.

How to cite this article

Dalvi PJ, Vandana KL, Ghosh S, Joshi VM, Bhat K, Prakash VH. Fluorosis: Environmental Risk Factor for Periodontal Disease? J Postgrad Med Edu Res 2017; 51(4):157-161.
Immune Complex-positive Glomerulonephritis in Antineutrophil Cytoplasmic Antibody-positive Patients
Authors: Joshi Kusum , Gupta Parikshaa , Chhabra Seema , Bhagat Priyanka , Bharti Shreekant , Minz Ranjana W
Published: November 2017

Antineutrophil cytoplasmic antibody (ANCA)-positive glomerulonephritis (GN) has traditionally been considered pauci-immune (PI); however, various reports have demonstrated the presence of immune reactants in a subset of these cases. The study was done to evaluate the prevalence of immune deposits in ANCApositive GN by direct immunofluorescence (DIF). Renal biopsies of 35 patients with ANCA-positive GN were retrospectively analyzed for light microscopic and DIF findings to look for the presence of immune reactants and to correlate these with the corresponding histologic features. Twenty-seven cases (77.2%) showed PI-GN while 8 (22.8%) cases showed. 2+ positivity for one or more immune reactants in the mesangium and/or capillary loops and were categorized as ANCA-positive immune complex GN. Of these, seven were positive for perinuclear (P-ANCA) and one for cytoplasmic (C-ANCA). Immunoglobulin M (IgM) was the most frequent immunoglobulin. On light microscopy, these cases exhibited significantly increased mesangial cellularity (p = 0.033) and more number of normal glomeruli as compared with PI cases (p = 0.015).

How to cite this article

Bhagat P, Bharti S, Gupta P, Minz RW, Joshi K, Chhabra S. Immune Complex-positive Glomerulonephritis in Antineutrophil Cytoplasmic Antibody-positive Patients. J Postgrad Med Edu Res 2017;51(4):166-169.
Tendinopathy and Sports: Understanding the Problem and Options of Management-perspectives from Physiotherapy, Sports Medicine, and Orthopedics
Authors: Dhillon Mandeep , Dhillon Himmat S , Dhillon Sidak , Bachhal Vikas
Published: November 2017

Tendinopathies are perhaps the leading cause of sportsrelated overuse injuries necessitating visit to an expert. Increased general public participation in sports and growing intensity of elite level sport had further warranted more attention and research into pathophysiology and management of tendeno pathies. As a result, its management has seen enormous changes in the last few decades. The newer research methodologies applied to diagnostic and therapeutic aspects have generated a plethora of literature, which has helped sports medicine experts. However, these newer modalities have also added to the confusion among many. This review aims to present current understanding of pathophysiology of tendinopathies and evidence of success or failure of several modalities in current use.

How to cite this article

Dhillon HS, Dhillon S, Bachhal V, Dhillon MS. Tendinopathy and Sports: Understanding the Problem and Options of Management-perspectives from Physiotherapy, Sports Medicine, and Orthopedics. J Postgrad Med Edu Res 2017;51(4):175-181.