200 research outputs found
Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing
No full textThe traditionally accepted relationships among basal jawed vertebrates have been challenged by some molecular phylogenetic analyses based on mitochondrial sequences. Those studies split extant gnathostomes into two monophyletic groups: tetrapods and piscine branch, including Chondrichthyes, Actinopterygii and sarcopterygian fishes. Lungfish and bichir are found in a basal position on the piscine branch. Based on transcriptomes of an armored bichir (Polypterus delhezi) and an African lungfish (Protopterus sp.) we generated, expressed sequences and whole genome sequences available from public databases, we obtained 111 genes to reconstruct the phylogenetic tree of basal jawed vertebrates and estimated their times of divergence. Our phylogenomic study supports the traditional relationship. We found that gnathostomes are divided into Chondrichthyes and the Osteichthyes, both with 100% support values (posterior probabilities and bootstrap values). Chimaeras were found to have a basal position among cartilaginous fishes with a 100% support value. Osteichthyes were divided into Actinopterygii and Sarcopterygii with 100% support value. Lungfish and tetrapods form a monophyletic group with 100% posterior probability. Bichir and two teleost species form a monophyletic group with 100% support value. The previous tree, based on mitochondrial data, was significantly rejected by an approximately unbiased test (AU test, p=0). The time of divergence between lungfish and tetrapods was estimated to be 391.8 Ma and the divergence of bichir from pufferfish and medaka was estimated to be 330.6 Ma. These estimates closely match the fossil record. In conclusion, our phylogenomic study successfully resolved the relationship of basal jawed vertebrates based on transtriptomes, EST and whole genome sequences.The traditionally accepted relationships among basal jawed vertebrates have been challenged by some molecular phylogenetic analyses based on mitochondrial sequences. Those studies split extant gnathostomes into two monophyletic groups: tetrapods and piscine branch, including Chondrichthyes, Actinopterygii and sarcopterygian fishes. Lungfish and bichir are found in a basal position on the piscine branch. Based on transcriptomes of an armored bichir (Polypterus delhezi) and an African lungfish (Protopterus sp.) we generated, expressed sequences and whole genome sequences available from public databases, we obtained 111 genes to reconstruct the phylogenetic tree of basal jawed vertebrates and estimated their times of divergence. Our phylogenomic study supports the traditional relationship. We found that gnathostomes are divided into Chondrichthyes and the Osteichthyes, both with 100% support values (posterior probabilities and bootstrap values). Chimaeras were found to have a basal position among cartilaginous fishes with a 100% support value. Osteichthyes were divided into Actinopterygii and Sarcopterygii with 100% support value. Lungfish and tetrapods form a monophyletic group with 100% posterior probability. Bichir and two teleost species form a monophyletic group with 100% support value. The previous tree, based on mitochondrial data, was significantly rejected by an approximately unbiased test (AU test, p=0). The time of divergence between lungfish and tetrapods was estimated to be 391.8 Ma and the divergence of bichir from pufferfish and medaka was estimated to be 330.6 Ma. These estimates closely match the fossil record. In conclusion, our phylogenomic study successfully resolved the relationship of basal jawed vertebrates based on transtriptomes, EST and whole genome sequences
Evaluation of medication administration errors in geriatric patient in medical wards in two government hospitals of Kabul, Afghanistan / Jawed Ahmad Oneeb Abdul Mohammad
No full textEvaluation of Medication Administration Errors (MAEs) among geriatric inpatients in the local setting requires more extensive investigation and time. There are not enough academic sources on the epidemiology of MAEs and patients' outcomes among geriatric inpatients. Hence, a prospective study was conducted to determine the prevalence, contributing factors, and effects of MAEs on patients' outcomes in geriatrics. This study was carried out in two government hospitals of Kabul city, Afghanistan. In Ibn Sina Emergency hospital, total number of observations was 456, and MAEs were calculated for 204 cases (44.7%). The most common type of MAEs was the wrong time (67.6%) followed by missed dose (15.7%), wrong concentration (5.0%), with 8 errors (3.9%) caused patient harm but did not need interventions. Multivariate analysis of variables indicates that the route of administration (adjusted OR: 4.26; 95% CI: 2.42 - 7.5; p = 0.000), type of medication (adjusted OR: 0.35; 95% CI: 0.17 - 0.74; p = 0.006), and number of nurses serving medicine (adjusted OR: 0.45; 95% CI: 0.29 - 0.71; p = 0.000) were significantly associated with MAEs. Medication administration errors were not significantly associated with total number of patients in the ward, medication administration time, medication supply system, and day of observations. In Ali Abad Teaching, hospital 414 cases of medication administration were supervised, among those 164 cases (39.6%) were with erroneous administration. Wrong time error (61%) was the most frequent type of error, followed by missed dose (25.6%), compliance error (7.3%), with 8 errors (4.88%), which were reached to the patients and caused harm, but did not require interventions. Result of multivariate analysis shows that route of administration (adjusted OR: 6.82; 95 % CI: 4.11 - 11.31; p = 0.000) medication supply system (adjusted OR: 3.03; 95% CI: 1.76 - 5.2; p = 0.000) number of nurses serving medicine (adjusted OR: 0.37; 95% CI: 0.17 - 0.84; p = 0.016) and time of administration (adjusted OR: 4.17; 95% CI: 2.06 - 8.49; p = 0.000) were significantly associated with MAEs. The total number of patients in the ward, type of medication and day of observations were not significantly associated with MAEs. Based on the result of the Chi square test, number of medications was significantly associated with the number of errors in both hospitals (p < 0.05). The medication distribution system should be always updated, and all healthcare professionals should work together as an allied team to reduce incidences of MAEs. Thus, the unwanted consequences of MAEs will be prevented in patients and society
Relationship between mercury concentration and size of long-jawed orb weaver spiders
No full textMethylmercury (MeHg) is an environmental contaminant that poses a serious threat to humans and wildlife. There are approximately 9 million water bodies in the United States alone that have all been contaminated with MeHg. Since there are so many water bodies, it is difficult to know the level of contamination for each, and whether or not they pose a threat to humans and/or wildlife. Ecologists use biosentinels, or a species that reflects the MeHg contamination of the aquatic ecosystem, in order to determine the level of contamination. In the present study, the author proposed the long-jawed orb weaver spider (Tetragnatha sp.) as a potential biosentinel for MeHg contamination of water bodies. The author collected spiders from 15 ponds in September and October of 2013, where she found a positive correlation between MeHg concentration and size of long-jawed orb weaver spiders. The author then found a positive relationship between MeHg concentration of the spiders and the overall MeHg contamination of the aquatic ecosystem, thus suggesting the long-jawed orb weaver spider is an effective biosentinel. This study proposes that long-jawed orb weaver spiders could be used as an efficient bioseninel to determine MeHg contamination in many of the 9 million water bodies across the United States
Dynamics of a flexible helical filament rotating in a viscous fluid near a rigid boundary
No full textWe study the effect of a no-slip rigid boundary on the dynamics of a flexible helical filament rotating in a viscous fluid, at low Reynolds number conditions (Stokes limit). This system is taken as a reduced model for the propulsion of uniflagellar bacteria, whose locomotion is known to be modified near solid boundaries. Specifically, we focus on how the propulsive force generated by the filament, as well as its buckling onset, are modified by the presence of a wall. We tackle this problem through numerical simulations that couple the elasticity of the filament, the hydrodynamic loading, and the wall effect. Each of these three ingredients is respectively modeled by the discrete elastic rods method (for a geometrically nonlinear description of the filament), Lighthill's slender body theory (for a nonlocal fluid force model), and the method of images (to emulate the boundary). The simulations are systematically validated by precision experiments on a rescaled macroscopic apparatus. We find that the propulsive force increases near the wall, while the critical rotation frequency for the onset of buckling usually decreases. A systematic parametric study is performed to quantify the dependence of the wall effects on the geometric parameters of the helical filament.FLEXLA
Better understanding extrapulmonary tuberculosis: A scoping review of public health impact in Pakistan, Afghanistan, India, and Bangladesh
No full textBACKGROUND AND AIMS: South Asian countries, including Pakistan, Afghanistan, India, and Bangladesh, have a high prevalence of pulmonary and extra-pulmonary tuberculosis (EPTB). This prevalence is influenced by various risk factors such as ethnicity, nutrition, socioeconomic disparities, high out-of-pocket healthcare expenses, and specific Mycobacterium Tuberculosis (TB) lineages. The COVID-19 pandemic has likely hindered access to healthcare and led to under-reporting of EPTB cases nationally and internationally. This rapid review aimed to summarize the literature on the prevalence and disease outcomes of EPTB in the mentioned countries, compare the situations across countries, and provide recommendations for future action.METHODS: The review utilized PubMed and Google Scholar databases to search for literature on EPTB in South Asian countries. The search string included keywords related to different forms of EPTB and the countries of interest while excluding pulmonary tuberculosis.RESULTS: The results showed that both TB, including drug-resistant TB, and EPTB are prevalent and burdensome in South Asia. In Pakistan, pleural TB was the most commonly reported form of EPTB, followed by lymph node TB, abdominal TB, osteoarticular TB, Central Nervous System TB, and miliary TB. In India, lymph node TB(LNTB) was more common among EPTB cases. Bangladesh reported a high prevalence of EPTB involving lymph node, pleura, and abdomen, while Afghanistan had a higher prevalence of forms such as LNTB and tuberculous meningitis.CONCLUSION: In conclusion, the prevalence of EPTB in Pakistan, Afghanistan, India, and Bangladesh is alarmingly high and negatively impacts population health. Effective measures are needed for treatment and management of this condition, along with addressing current and future challenges. Strengthening the evidence base through surveillance and research is crucial to understand the patterns and significant factors related to EPTB, requiring investment in these areas.</p
Untangling the Mechanics and Topology in the Frictional Response of Long Overhand Elastic Knots
No full textWe combine experiments and theory to study the mechanics of overhand knots in slender elastic rods under tension. The equilibrium shape of the knot is governed by an interplay between topology, friction, and bending. We use precision model experiments to quantify the dependence of the mechanical response of the knot as a function of the geometry of the self-contacting region, and for different topologies as measured by their crossing number. An analytical model based on the nonlinear theory of thin elastic rods is then developed to describe how the physical and topological parameters of the knot set the tensile force required for equilibrium. Excellent agreement is found between theory and experiments for overhand knots over a wide range of crossing numbers.National Science Foundation (U.S.) (CMMI-1129894
Coiling of elastic rods on rigid substrates
No full textThesis: S.M., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2014.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (pages 115-120).We investigate the deployment of a thin elastic rod onto a rigid substrate and study the resulting coiling patterns. In our approach, we combine precision model experiments, scaling analyses, and computer simulations towards developing predictive understanding of the coiling process. Both cases of deposition onto static and moving substrates are considered. We construct phase diagrams for the possible coiling patterns, e.g. meandering, stretched coiling, alternating loops, and translated coiling, and characterize them as a function of the geometric and material properties of the rod, as well as the height and relative speeds of deployment. The various modes selected and their characteristic length-scales are found to arise from a complex interplay between gravitational, bending, and twisting energies of the rod, coupled to the geometric nonlinearities intrinsic to their large deformations. We give particular emphasis to the first sinusoidal mode of instability, which we find to be consistent with a Hopf bifurcation, and rationalize the meandering wavelength and amplitude. Throughout, we systematically vary natural curvature of the rod as a control parameter, which has a qualitative and quantitative effect on the pattern formation, above a critical value that we determine. Upon establishing excellent quantitative agreement between experiments and simulations with no fitting parameters, we perform a numerical survey to relate the pattern size to the relevant length-scales arising from material properties and the setup geometry, and quantify the typical strain levels in the rod. The universality conferred by the prominent role of geometry in the deformation modes of the rod suggests using the gained understanding as design guidelines, in the original applications that motivated the study. These include the coiling of carbon nanotubes and the deployment of submarine cables and pipelines onto the seabed.by Mohammad Khalid Jawed.S.M
Ongoing Research in Jawed Fish Immunity: Structural and Functional Studies at the Protein and Cellular Levels
No full textThis eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contac
Coiling of elastic rods on rigid substrates
No full textWe investigate the deployment of a thin elastic rod onto a rigid substrate and study the resulting coiling patterns. In our approach, we combine precision model experiments, scaling analyses, and computer simulations toward developing predictive understanding of the coiling process. Both cases of deposition onto static and moving substrates are considered. We construct phase diagrams for the possible coiling patterns and characterize them as a function of the geometric and material properties of the rod, as well as the height and relative speeds of deployment. The modes selected and their characteristic length scales are found to arise from a complex interplay between gravitational, bending, and twisting energies of the rod, coupled to the geometric nonlinearities intrinsic to the large deformations. We give particular emphasis to the first sinusoidal mode of instability, which we find to be consistent with a Hopf bifurcation, and analyze the meandering wavelength and amplitude. Throughout, we systematically vary natural curvature of the rod as a control parameter, which has a qualitative and quantitative effect on the pattern formation, above a critical value that we determine. The universality conferred by the prominent role of geometry in the deformation modes of the rod suggests using the gained understanding as design guidelines, in the original applications that motivated the study.National Science Foundation (U.S.) (CMMI-1129894
A Geometric Model for the Coiling of an Elastic Rod Deployed Onto a Moving Substrate
No full textWe report results from a systematic numerical investigation of the nonlinear patterns that emerge when a slender elastic rod is deployed onto a moving substrate; a system also known as the elastic sewing machine (ESM). The discrete elastic rods (DER) method is employed to quantitatively characterize the coiling patterns, and a comprehensive classification scheme is introduced based on their Fourier spectrum. Our analysis yields physical insight on both the length scales excited by the ESM, as well as the morphology of the patterns. The coiling process is then rationalized using a reduced geometric model (GM) for the evolution of the position and orientation of the contact point between the rod and the belt, as well as the curvature of the rod near contact. This geometric description reproduces almost all of the coiling patterns of the ESM and allows us to establish a unifying bridge between our elastic problem and the analogous patterns obtained when depositing a viscous thread onto a moving surface; a well-known system known as the fluid-mechanical sewing machine (FMSM).National Science Foundation (U.S.) (CMMI-1129894
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