Miracle-dz/UniFAR-FTUs huggingface dataset:
Droplet Digital PCR for the Detection of Plasmodium falciparum DNA in Whole Blood and Serum: A Comparative Analysis with Other Molecular Methods

Background: The estimation of Plasmodium falciparum parasitaemia can vary according to the method used. Recently, droplet digital PCR (ddPCR) has been proposed as a promising approach in the molecular quantitation of Plasmodium, but its ability to predict the actual parasitaemia on clinical samples has not been largely investigated. Moreover, the possibility of applying the ddPCR-sensitive method to serum samples has never been explored. Methods: We used, for the first time, ddPCR on both blood and serum to detect the DNA of P. falciparum in 52 paired samples from 26 patients. ddPCR was compared with loop-mediated isothermal amplification (LAMP) and rtPCR. The correlation between the ddPCR results, microscopy, and clinical parameters was examined. Results: ddPCR and microscopy were found to be strongly correlated (ρ(26) = 0.83111, p < 0.0001) in blood. Samples deviating from the correlation were partially explained by clinical parameters. In serum samples, ddPCR revealed the best performance in detecting P. falciparum DNA, with 77% positive samples among malaria subjects. Conclusion: Absolute quantitation by ddPCR can be a flexible technique for Plasmodium detection, with potential application in the diagnosis of malaria. In particular, ddPCR is a powerful approach for Plasmodium DNA analysis on serum when blood samples are unavailable.
VARIABILIDADE GENÉTICA DE Atherinella brasiliensis (QUOY & GAIMARD, 1825) (ATHERINIFORMES: ATHERINOPSIDAE) AO LONGO DA COSTA BRASILEIRA

vii INTRODUÇÃO. 1 MATERIAL E MÉTODOS. 4 RESULTADOS.7 DISCUSSÃO. 10 REFERÊNCIAS BIBLIOGRÁFICAS. 16 TABELAS.22 FIGURAS.25 ANEXOS.29
CTELS: A Cell-Free System for the Analysis of Translation Termination Rate

Translation termination is the final step in protein biosynthesis when the synthesized polypeptide is released from the ribosome. Understanding this complex process is important for treatment of many human disorders caused by nonsense mutations in important genes. Here, we present a new method for the analysis of translation termination rate in cell-free systems, CTELS (for C-terminally extended luciferase-based system). This approach was based on a continuously measured luciferase activity during in vitro translation reaction of two reporter mRNA, one of which encodes a C-terminally extended luciferase. This extension occupies a ribosomal polypeptide tunnel and lets the completely synthesized enzyme be active before translation termination occurs, i.e., when it is still on the ribosome. In contrast, luciferase molecule without the extension emits light only after its release. Comparing the translation dynamics of these two reporters allows visualization of a delay corresponding to the translation termination event. We demonstrated applicability of this approach for investigating the effects of cis- and trans-acting components, including small molecule inhibitors and read-through inducing sequences, on the translation termination rate. With CTELS, we systematically assessed negative effects of decreased 3′ UTR length, specifically on termination. We also showed that blasticidin S implements its inhibitory effect on eukaryotic translation system, mostly by affecting elongation, and that an excess of eRF1 termination factor (both the wild-type and a non-catalytic AGQ mutant) can interfere with elongation. Analysis of read-through mechanics with CTELS revealed a transient stalling event at a “leaky” stop codon context, which likely defines the basis of nonsense suppression.
Runx2 silencing promotes adipogenesis via down‐regulation of DLK1 in chondrogenic differentiating MSCs

For cartilage regeneration, stem cells are a promising cell source; however, even the advances made in the differentiation of stem cells into precursor‐differentiated cartilage cells have not been successful with respect to reprograming these cells to achieve complete differentiation and fully functioning cells until now. Previous findings suggest that Runx2 plays a major role in chondrocyte differentiation and maturation. Although targeting Runx2 has enhanced some chondrocyte properties, the adipogenic lineage shift has eventually occurred in these cells. The present study mainly aimed to reveal the mechanism of this adipogenesis.
Validation of FRIEND and ACSM Equations for Cardiorespiratory Fitness: Comparison to Direct Measurement in CAD Patients

The regression equation of the American College of Sports Medicine (ACSM) was a preferred method for estimating maximal oxygen consumption (VO2max). Recently, a more precise equation from the fitness registry and the importance of exercise national database (FRIEND) for healthy people was developed. This study compared VO2max estimated by the ACSM and FRIEND equations to VO2max directly measured in coronary artery disease (CAD) patients. Overall, 293 CAD patients who participated in cardiac rehabilitation between June 2015 and December 2018 were analyzed. Directly measured VO2max values were compared to the ACSM and FRIEND equations. The directly measured VO2max was significantly different from the estimated VO2max by ACSM equation (24.16 vs. 28.7 mL/kg/min, p < 0.001), which was overestimated by 20% in men and 16% in women. However, there was no statistically significant difference between the directly measured VO2max and the estimated VO2max by the FRIEND equation. (24.16 vs. 24.15 mL/kg/min, p = 0.986). In CAD patients, the estimated VO2max from the ACSM equation was significantly higher than the directly measured VO2max. In addition, estimated cardiorespiratory fitness (CRF) by the FRIEND equation showed similar results with directly measured CRF. As a result, the FRIEND equation can predict CRF more accurately than the ACSM.
Genome-wide Association Study for Alcohol-related Cirrhosis Identifies Risk Loci in MARC1 and HNRNPUL1.

BACKGROUND & AIMS Little is known about genetic factors that affect development of alcohol-related cirrhosis. We performed a genome-wide association study (GWAS) of samples from the United Kingdom Biobank (UKB) to identify polymorphisms associated with risk of alcohol-related liver disease. METHODS We performed a GWAS of 35,839 participants in the UKB with high intake of alcohol against markers of hepatic fibrosis (FIB-4, APRI and Forns index scores) and hepatocellular injury (levels of aminotransferases). Loci identified in the discovery analysis were tested for their association with alcohol-related cirrhosis in 3 separate European cohorts (phase 1 validation cohort; n=2545). Variants associated with alcohol-related cirrhosis in the validation at a false-discovery rate of less than 20% were then directly genotyped in 2 additional European validation cohorts (phase 2 validation, n=2068). RESULTS In the GWAS of the discovery cohort, we identified 50 independent risk loci with genome-wide significance (P<5 x 10-8). Nine of these loci were significantly associated with alcohol-related cirrhosis in the phase 1 validation cohort; 6 of these 9 loci were significantly associated with alcohol-related cirrhosis in phase 2 validation cohort, at a false discovery rate below 5%. The loci included variants in the mitochondrial amidoxime reducing component 1 gene (MARC1) and the heterogeneous nuclear ribonucleoprotein U like 1 gene (HNRNPUL1). After we adjusted for age, sex, body mass index, and type-2 diabetes in the phase 2 validation cohort, the minor A allele of MARC1:rs2642438 was associated with reduced risk of alcohol-related cirrhosis (adjusted odds ratio, 0.76; P=.0027); conversely the minor C allele of HNRNPUL1:rs15052 was associated with an increased risk of alcohol-related cirrhosis (adjusted odds ratio, 1.30; P=.020). CONCLUSIONS In a GWAS of samples from the UKB, we identified and validated (in 5 European cohorts) single-nucleotide polymorphisms that affect risk of alcohol-related cirrhosis in opposite directions: the minor A allele in MARC1:rs2642438 decreases risk whereas the minor C allele in HNRNPUL1:rs15052 increases risk.
High-Speed Atomic Force Microscopy Reveals the Structural Dynamics of the Amyloid-β and Amylin Aggregation Pathways

Individual Alzheimer’s disease (AD) patients have been shown to have structurally distinct amyloid-β (Aβ) aggregates, including fibrils, in their brain. These findings suggest the possibility of a relationship between AD progression and Aβ fibril structures. Thus, the characterization of the structural dynamics of Aβ could aid the development of novel therapeutic strategies and diagnosis. Protein structure and dynamics have typically been studied separately. Most of the commonly used biophysical approaches are limited in providing substantial details regarding the combination of both structure and dynamics. On the other hand, high-speed atomic force microscopy (HS-AFM), which simultaneously visualizes an individual protein structure and its dynamics in liquid in real time, can uniquely link the structure and the kinetic details, and it can also unveil novel insights. Although amyloidogenic proteins generate heterogeneously aggregated species, including transient unstable states during the aggregation process, HS-AFM elucidated the structural dynamics of individual aggregates in real time in liquid without purification and isolation. Here, we review and discuss the HS-AFM imaging of amyloid aggregation and strategies to optimize the experiments showing findings from Aβ and amylin, which is associated with type II diabetes, shares some common biological features with Aβ, and is reported to be involved in AD.
ThedivIVAMinicell Locus ofBacillus subtilis

TheBacillus subtilis divIVA1mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate minicells. This study reports the cloning and sequence analysis of 2.4 kb of theB. subtilischromosome including thedivIVAlocus. Three open reading frames were identified:orf, whose function is unknown;divIVA; and isoleucyl tRNA synthetase (ileS). We identified the point mutation in the divIVA1 mutant allele. Inactivation of divIVA produces a minicell phenotype, whereas overproduction of DivIVA results in afilamentation phenotype. Mutants with mutations at both of the minicell loci ofB. subtilis, divIVA and divIVB, possess a minicell phenotype identical to that of the DivIVB 2 mutant. The DivIVA 2 mutants, but not the DivIVB 2 mutants, show a decrease in sporulation efficiency and a delay in the kinetics of endospore formation. The data support a model in whichdivIVAencodes the topological specificity subunit of the minCD system. The model suggests that DivIVA acts as a pilot protein, directing minCD to the polar septation sites. DivIVA also appears to be the interface between a sporulation component and MinCD, freeing up the polar septation sites for use during the asymmetric septation event of the sporulation process. Bacillus subtilis is a gram-positive rod-shaped endosporeforming soil bacterium. Like other rod-shaped bacteria, this bacterium replicates by a process in which the cell doubles its mass by doubling its length and then divides into two daughter cells. The division process is highly regulated both temporally and spatially. Temporal regulation ensures that chromosomal replication and segregation precede cytokinesis and spatial regulation results in the division septum forming at the central site of the cell, equidistant from the cell poles. The cellular architecture which defines a septation site remains one of the most significant unanswered questions left in procaryotic biology. It is known that bacterial cell division can occur at sites otherthanthecellmidpoint.Minicell-producingdivisionshave
SPERM MEDIATED GENE TRANSFER (SMGT) -A NOVEL APPROACH TO PRODUCE TRANGENIC ANIMALS

Animal Genetics Division, Indian veterinary Research Institute, Bareilly, UP. , India ISSN: 0976-3031 RESEARCH ARTICLE SPERM MEDIATED GENE TRANSFER (SMGT) A NOVEL APPROACH TO PRODUCE TRANGENIC ANIMALS Pramod Kumar R1. *, Anju Rajan R2. and Abhijit Mitra1 1Animal Genetics Division, Indian veterinary Research Institute, Bareilly, UP. , India 2Department of Poultry science, College of Veterinary and animal sciences, Thrissur, Kerala, India
A pragmatic approach to the comparison of wrist-based cutpoints of physical activity intensity for the MotionWatch8 accelerometer in children

Background A variety of wearable monitors are available for objectively assessing physical activity but there is a lack of established values for the activity intensity of MotionWatch8 (MW8) and a similar lack of studies on comparability across devices. Our study aimed to establish activity intensity cutpoints for the MW8 accelerometer in children, which are necessary to determine whether they are meeting physical activity guidelines. Methods Children (n = 39, ages 9–13 years) were asked to wear two different accelerometers (MW8 and ActiGraph) simultaneously on the same dominant wrist as they performed different activities designed to mimic activities of variable intensity that a child might perform in a free-living environment. Linear regression and receiver operating characteristic (ROC) curves were performed to assess sensitivity and specificity of the identified MW8 intensity cutpoints compared to established ActiGraph cutpoints. Results Mean values for each activity were positively correlated using the MW8 and ActiGraph monitors (r = 0.85, p<0.001). The optimal cutpoints for differentiating sedentary from light physical activity, light from moderate, and moderate from vigorous activity were ≤32 counts, ≥ 371.5 counts, and ≥ 859.5 counts per 30 seconds, respectively. Conclusions Our study demonstrated the ability of MW8 to discriminate different intensity activities and provided the first cutoff values for researchers using the MW8 to measure physical activity patterns among children.
Automated generation of gene summaries at the Alliance of Genome Resources

Abstract Short paragraphs that describe gene function, referred to as gene summaries, are valued by users of biological knowledgebases for the ease with which they convey key aspects of gene function. Manual curation of gene summaries, while desirable, is difficult for knowledgebases to sustain. We developed an algorithm that uses curated, structured gene data at the Alliance of Genome Resources (Alliance; www.alliancegenome.org) to automatically generate gene summaries that simulate natural language. The gene data used for this purpose include curated associations (annotations) to ontology terms from the Gene Ontology, Disease Ontology, model organism knowledgebase (MOK)-specific anatomy ontologies and Alliance orthology data. The method uses sentence templates for each data category included in the gene summary in order to build a natural language sentence from the list of terms associated with each gene. To improve readability of the summaries when numerous gene annotations are present, we developed a new algorithm that traverses ontology graphs in order to group terms by their common ancestors. The algorithm optimizes the coverage of the initial set of terms and limits the length of the final summary, using measures of information content of each ontology term as a criterion for inclusion in the summary. The automated gene summaries are generated with each Alliance release, ensuring that they reflect current data at the Alliance. Our method effectively leverages category-specific curation efforts of the Alliance member databases to create modular, structured and standardized gene summaries for seven member species of the Alliance. These automatically generated gene summaries make cross-species gene function comparisons tenable and increase discoverability of potential models of human disease. In addition to being displayed on Alliance gene pages, these summaries are also included on several MOK gene pages.
Fiber-Optic Based Smart Textiles for Real-Time Monitoring of Breathing Rate

Wearable light textiles are gaining widespread interest in application for measurement and monitoring of biophysical parameters. Fiber optic sensors, in particular Bragg Grating (FBG) sensors, can be a competitive method for monitoring of respiratory behavior for chest and abdomen regions since the sensors are able to convert physical movement into wavelength shift. This study aims to show the performance of elastic belts with integrated optical fibers during the breathing activities done by two volunteers. Additionally, the work aims to determine how the positions of the volunteers affect the breathing pattern detected by optical fibers. As a reference, commercial mobile application for sensing vibration is used. The obtained results show that the FBGs are able to detect chest and abdomen movements during breathing and consequently reconstruct the breathing pattern. The accuracy of the results varies for two volunteers but remains consistent.
A Revision of the Neotropical Genus Cryptocanthon Balthasar (Coleoptera: Scarabaeidae: Scarabaeinae)

Abstract The Neotropical genus Cryptocanthon Balthasar (Scarabaeinae: Canthonini) is revised. Diagnoses, descriptions and a key to the 35 species are presented, including 22 new species: C. bochilae, C. howdeni, C. montebello, C. ocosingo and C. rayonensis from Mexico; C. osaensis and C. solisi from Costa Rica; C. denticulum and C. lobipygus from Panama; C. escobari, C. foveatus, C. medinae and C. pumilus from Colombia; C. andersoni, C. gilli and C. punctatus from Venezuela; C. galbao from French Guiana; C. curticrinus, C. genieri, C. napoensis, C. otonga and C. urguensis from Ecuador. All of the known species of Cryptocanthon are inhabitants of wet forest litter. A phylogenetic hypothesis and biogeographical discussion are included. Based on the phylogenetic analysis, four species groups were established: a northern South America relict species group, an Amazonian-Guianan lowland species group, a middle American species group, and a northern Andean species group. The diversity and level of endemicity of Cryptocanthon is consistent with other small-sized scarab beetles.
Infant Care Practices among Resettled Refugee Mothers from East and Central Africa

Refugees often parent under extreme circumstances. Parenting practices have implications for child outcomes, and parenting in the context of refugee resettlement is likely to be dynamic as parents negotiate a new culture. This study examined African origin mothers’ infant care values and practices related to feeding, carrying, and daily activities following resettlement in the Southeastern region of the U.S. Ten African origin mothers were asked about their infant care practices through semi-structured interviews. Results indicated that mothers valued breastfeeding but often chose to use formula as a supplement or instead of breastfeeding. In addition, participants valued carrying their infants close to the body but used equipment such as strollers. Mothers expressed that perceptions of American culture and rules, social support, interactions with community agencies, and the need to engage in formal employment were factors that influenced their infant care practices.
At the limits: habitat suitability modelling of northern 17‐year periodical cicada extinctions (Hemiptera: Magicicada spp.)

Aim Adult periodical cicadas emerge as temporally isolated, synchronized multispecies communities (‘broods’) that are for the most part geographically contiguous and that fit together in jigsaw-puzzle-like fashion. Some year-classes of 17-year cicadas have become extinct within historical times. We investigate two general causes for these extinctions – anthropogenic habitat destruction and post-glacial climate change. Location Periodical cicadas are confined to the eastern United States, east of the Great Plains. We document the locations of known periodical cicada extinctions in two broods of 17-year cicadas in Connecticut, Rhode Island, and upstate New York, USA. Methods Using additional distributional records of 17-year cicadas, we develop habitat suitability models for all 17-year periodical cicadas, using data layers that reflect both ecological and anthropogenic factors. Results Climatological data layers related specifically to annual mean temperature and temperature during the warmest months make the greatest contributions to our models, and data layers most specifically related to deforestation and habitat fragmentation tend to make much smaller contributions. Two well-documented extinct populations of periodical cicadas occurred in locations where these models predict relatively low habitat suitability for 17-year cicadas. Main conclusions Our results and other circumstantial evidence discount the importance of anthropogenic habitat destruction in explaining these particular extinctions.
Diffuse domain method for needle insertion simulations

We present a new strategy for needle insertion simulations without the necessity of meshing. A diffuse domain approach on a regular grid is applied to overcome the need for an explicit representation of organ boundaries. A phase field function captures the transition of tissue parameters and boundary conditions are imposed implicitly. Uncertainties of a volume segmentation are translated in the width of the phase field, an approach that is novel and overcomes the problem of defining an accurate segmentation boundary. We perform a convergence analysis of the diffuse elastic equation for decreasing phase field width, compare our results to deformation fields received from conforming mesh simulations and analyze the diffuse linear elastic equation for different widths of material interfaces. Then, the approach is applied to computed tomography data of a patient with liver tumors. A three‐class U‐Net is used to automatically generate tissue probability maps serving as phase field functions for the transition of elastic parameters between different tissues. The needle tissue interaction forces are approximated by the absolute gradient of a phase field function, which eliminates the need for explicit boundary parameterization and collision detection at the needle‐tissue interface. The results show that the deformation field of the diffuse domain approach is comparable to the deformation of a conforming mesh simulation. Uncertainties of tissue boundaries are included in the model and the simulation can be directly performed on the automatically generated voxel‐based probability maps. Thus, it is possible to perform easily implementable patient‐specific elastomechanical simulations directly on voxel data.