Mitochondrial DNA (mtDNA) profiles can be classified into phylogenetic clusters (haplogroups), which is of great relevance for evolutionary, forensic and medical genetics. With the extensive growth ...of the underlying phylogenetic tree summarizing the published mtDNA sequences, the manual process of haplogroup classification would be too time-consuming. The previously published classification tool HaploGrep provided an automatic way to address this issue. Here, we present the completely updated version HaploGrep 2 offering several advanced features, including a generic rule-based system for immediate quality control (QC). This allows detecting artificial recombinants and missing variants as well as annotating rare and phantom mutations. Furthermore, the handling of high-throughput data in form of VCF files is now directly supported. For data output, several graphical reports are generated in real time, such as a multiple sequence alignment format, a VCF format and extended haplogroup QC reports, all viewable directly within the application. In addition, HaploGrep 2 generates a publication-ready phylogenetic tree of all input samples encoded relative to the revised Cambridge Reference Sequence. Finally, new distance measures and optimizations of the algorithm increase accuracy and speed-up the application. HaploGrep 2 can be accessed freely and without any registration at http://haplogrep.uibk.ac.at.
There is currently no calibration available for the whole human mtDNA genome, incorporating both coding and control regions. Furthermore, as several authors have pointed out recently, linear ...molecular clocks that incorporate selectable characters are in any case problematic. We here confirm a modest effect of purifying selection on the mtDNA coding region and propose an improved molecular clock for dating human mtDNA, based on a worldwide phylogeny of > 2000 complete mtDNA genomes and calibrating against recent evidence for the divergence time of humans and chimpanzees. We focus on a time-dependent mutation rate based on the entire mtDNA genome and supported by a neutral clock based on synonymous mutations alone. We show that the corrected rate is further corroborated by archaeological dating for the settlement of the Canary Islands and Remote Oceania and also, given certain phylogeographic assumptions, by the timing of the first modern human settlement of Europe and resettlement after the Last Glacial Maximum. The corrected rate yields an age of modern human expansion in the Americas at ∼15 kya that—unlike the uncorrected clock—matches the archaeological evidence, but continues to indicate an out-of-Africa dispersal at around 55–70 kya, 5–20 ky before any clear archaeological record, suggesting the need for archaeological research efforts focusing on this time window. We also present improved rates for the mtDNA control region, and the first comprehensive estimates of positional mutation rates for human mtDNA, which are essential for defining mutation models in phylogenetic analyses.
Multiple viruses are often detected in children with respiratory infection but the significance of co-infection in pathogenesis, severity and outcome is unclear.
To correlate the presence of viral ...co-infection with clinical phenotype in children admitted with acute respiratory infections (ARI).
We collected detailed clinical information on severity for children admitted with ARI as part of a Spanish prospective multicenter study (GENDRES network) between 2011-2013. A nested polymerase chain reaction (PCR) approach was used to detect respiratory viruses in respiratory secretions. Findings were compared to an independent cohort collected in the UK.
204 children were recruited in the main cohort and 97 in the replication cohort. The number of detected viruses did not correlate with any markers of severity. However, bacterial superinfection was associated with increased severity (OR: 4.356; P-value = 0.005), PICU admission (OR: 3.342; P-value = 0.006), higher clinical score (1.988; P-value = 0.002) respiratory support requirement (OR: 7.484; P-value < 0.001) and longer hospital length of stay (OR: 1.468; P-value < 0.001). In addition, pneumococcal vaccination was found to be a protective factor in terms of degree of respiratory distress (OR: 2.917; P-value = 0.035), PICU admission (OR: 0.301; P-value = 0.011), lower clinical score (-1.499; P-value = 0.021) respiratory support requirement (OR: 0.324; P-value = 0.016) and oxygen necessity (OR: 0.328; P-value = 0.001). All these findings were replicated in the UK cohort.
The presence of more than one virus in hospitalized children with ARI is very frequent but it does not seem to have a major clinical impact in terms of severity. However bacterial superinfection increases the severity of the disease course. On the contrary, pneumococcal vaccination plays a protective role.
To protect biodiversity we must understand its structure and composition including the bacteria and microparasites associated with wildlife, which may pose risks to human health. However, acquiring ...this knowledge often presents challenges, particularly in areas of high biodiversity where there are many undescribed and poorly studied species and funding resources can be limited. A solution to fill this knowledge gap is sampling roadkill (animals that die on roads as a result of collisions with circulating vehicles). These specimens can help characterize local wildlife and their associated parasites with fewer ethical and logistical challenges compared to traditional specimen collection. Here we test this approach by analyzing 817 tissue samples obtained from 590 roadkill vertebrate specimens (Amphibia, Reptilia, Aves and Mammalia) collected in roads within the Tropical Andes of Ecuador. First, we tested if the quantity and quality of recovered DNA varied across roadkill specimens collected at different times since death, exploring if decomposition affected the potential to identify vertebrate species and associated microorganisms. Second, we compared DNA stability across taxa and tissues to identify potential limitations and offer recommendations for future work. Finally, we illustrate how these samples can aid in taxonomic identification and parasite detection. Our study shows that sampling roadkill can help study biodiversity. DNA was recovered and amplified (allowing species identification and parasite detection) from roadkill even 120 hours after death, although risk of degradation increased overtime. DNA was extracted from all vertebrate classes but in smaller quantities and with lower quality from amphibians. We recommend sampling liver if possible as it produced the highest amounts of DNA (muscle produced the lowest). Additional testing of this approach in areas with different environmental and traffic conditions is needed, but our results show that sampling roadkill specimens can help detect and potentially monitor biodiversity and could be a valuable approach to create biobanks and preserve genetic data.
Evaporative cooling has a major role to play in fighting climate change and in achieving a low‐carbon economy. As it helps to reduce energy demand for air conditioning, it is gaining attention in ...terms of improving energy efficiency in buildings. Evaporative cooling from wetted media can enhance water–air contact, thereby improving heat and mass transfer further and avoiding aerosols. Wetted media are commonly called evaporative cooling pads and are widely used in greenhouses, intensive livestock farming, and industrial facilities. However, a deep understanding of evaporative cooling pad performance can enhance their application to indoor occupied spaces such as residential or commercial cooling, or in hybrid air conditioning systems. Most studies analyze pad performance mainly in terms of pressure drop and saturation effectiveness. However, some studies propose alternative cooling efficiency parameters and others provide insights into key aspects such as power requirements and the coefficient of performance, water consumption, risk of water entrainment, material decay, and air quality, as well as the effect of water temperature and salinity, solar radiation, or wind speed. Existing results on these less studied performance issues are reviewed, and we identify the gaps in the literature in addition to highlighting the main challenges encountered, in an effort to guide future researchers in the field and enhance the application of direct evaporative cooling.
This article is categorized under:
Energy Efficiency > Systems and Infrastructure
Energy Systems Analysis > Systems and Infrastructure
Direct evaporative cooling from wetted media can be fiber, rigid media, and fill pads. Performance is studied through saturation effectiveness, pressure drop, power requirements (coefficient of performance), and so on. This is mainly influenced by pad characteristics and supply air, but also by supply water, solar radiation, and wind speed.
Vaccine hesitancy is among the top 10 threats to global health, according to the World Health Organization (WHO). In this exploration, we delve into ChatGPT capacity to generate opinions on vaccine ...hesitancy by interrogating this AI chatbot for the 50 most prevalent counterfait messages, false and true contraindications, and myths circulating on the internet regarding vaccine safety. Our results indicate that, while the present version of ChatGPT's default responses may be incomplete, they are generally satisfactory. Although ChatGPT cannot substitute an expert or the scientific evidence itself, this form of AI has the potential to guide users toward information that aligns well with scientific evidence.
El objetivo de está investigación trata en demostrar el desempeño académico en la asignatura de física e inducir la motivación por el aprendizaje mediante la gamificación en estudiantes de tercer ...semestre del Colegio de Bachilleres del Estado de Zacatecas, plantel Ignacio Zaragoza, la metodología empleada es de corte cuantitativa y de tipo descriptiva, la muestra es no probabilística por conveniencia y corresponde a 50 estudiantes de los grupos A y E, se desarrolló un cuestionario a escala Likert con cinco posibles respuestas que permitió conocer las percepciones sobre el uso de la gamificación como estrategia educativa. Los resultados obtenidos demuestran que la integración de esta técnica de aprendizaje es fructífera, conceden habilidades y motivaciones en la manera de llevar a cabo diversas actividades para lograr conocimientos y mejores resultados en su trayectoria escolar. Se concluye que la utilización de herramientas tecnológicas y juegos típicos fortalecieron el proceso de enseñanza aprendizaje de manera innovadora, interactiva y colaborativa, además mejoró el desempeño académico, favoreciendo los lineamientos de la Nueva Escuela Mexicana mediante la inclusión de políticas educativas que contemplen mejores enseñanzas mediante el uso de recursos tecnológicos.
Advanced high-strength steels (AHSSs) are designed for meeting strict requirements, especially in the automotive industry, as a means to directly influence the reduction in the carbon footprint. As ...rotary friction welding (RFW) has many important advantages over other welding technologies, it plays an important role in the automotive sector. On the above basis, in this work, combinations of the first (complex phase (CP)), second (TWIP (TW)), and third (quenched and partitioned (Q&P)) generations of similar and dissimilar high-alloyed advanced steels have been joined by the RFW process. Having a specific microstructure, rods of CP/CP, Q&P/Q&P, CP/TW, and Q&P/TW steels were welded by employing a homemade adaptation machine under fixed parameters. Microstructural characterization has allowed us to corroborate the metallic bonding of all the tested advanced steels and to identify the different zones formed after welding. Results indicate that the welding zone widens in the center of the workpiece, and under the current friction action, the intermixing region shows the redistribution of solute elements, mostly in the dissimilarly welded steels. Furthermore, because of their complex chemistry and the different mechanical properties of the used steels, dissimilarly welded steels present the most noticeable differences in hardness. The TWIP steel has the lower hardness values, whilst the CP and Q&P steels have the higher ones. As a direct effect of the viscoplastic behavior of the steels established by the thermomechanical processing, interlayers and oxidation products were identified, as well as some typical RFW defects. The electrochemical response of the welded steels has shown that the compositional and microstructural condition mostly affect the corrosion trend. This means that the dissimilarly welded steels are more susceptible to corrosion, especially at the TWIP-steel interface, which is attributed to the energy that is stored in the distorted microstructure of each steel plate as a consequence of the thermomechanical processing during RFW.
It is now widely agreed that the Native American founders originated from a Beringian source population ~15-18 thousand years ago (kya) and rapidly populated all of the New World, probably mainly ...following the Pacific coastal route. However, details about the migration into the Americas and the routes pursued on the continent still remain unresolved, despite numerous genetic, archaeological, and linguistic investigations. To examine the pioneering peopling phase of the South American continent, we screened literature and mtDNA databases and identified two novel mitochondrial DNA (mtDNA) clades, here named D1g and D1j, within the pan-American haplogroup D1. They both show overall rare occurrences but local high frequencies, and are essentially restricted to populations from the Southern Cone of South America (Chile and Argentina). We selected and completely sequenced 43 D1g and D1j mtDNA genomes applying highest quality standards. Molecular and phylogeographic analyses revealed extensive variation within each of the two clades and possibly distinct dispersal patterns. Their age estimates agree with the dating of the earliest archaeological sites in South America and indicate that the Paleo-Indian spread along the entire longitude of the American double continent might have taken even <2000 yr. This study confirms that major sampling and sequencing efforts are mandatory for uncovering all of the most basal variation in the Native American mtDNA haplogroups and for clarification of Paleo-Indian migrations, by targeting, if possible, both the general mixed population of national states and autochthonous Native American groups, especially in South America.
Respiratory syncytial virus (RSV) is one of the major causes of acute lower respiratory tract infection worldwide. The absence of a commercial vaccine and the limited success of current therapeutic ...strategies against RSV make further research necessary. We used a multi-cohort analysis approach to investigate host transcriptomic biomarkers and shed further light on the molecular mechanism underlying RSV-host interactions. We meta-analyzed seven transcriptome microarray studies from the public Gene Expression Omnibus (GEO) repository containing a total of 922 samples, including RSV, healthy controls, coronaviruses, enteroviruses, influenzas, rhinoviruses, and coinfections, from both adult and pediatric patients. We identified > 1500 genes differentially expressed when comparing the transcriptomes of RSV-infected patients against healthy controls. Functional enrichment analysis showed several pathways significantly altered, including immunologic response mediated by RSV infection, pattern recognition receptors, cell cycle, and olfactory signaling. In addition, we identified a minimal 17-transcript host signature specific for RSV infection by comparing transcriptomic profiles against other respiratory viruses. These multi-genic signatures might help to investigate future drug targets against RSV infection.
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