Miracle-dz/UniFAR-FTUs huggingface dataset:
Transgene-mediated skeletal phenotypic variation in zebrafish

When considering relationships between genotype and phenotype we frequently ignore the fact that the genome of a typical animal, notably including that of a fish and a human, harbors a huge amount of foreign DNA. Some of it, including the DNA of “autonomous” transposable elements, can spontaneously mobilize to occupy new chromosomal sites and take on new functions, presenting a challenge to the host organism and also possibly introducing new fuel for evolutionary change. Transposable elements are useful for introducing transgenes, integrating them into host genomes with high efficiency. Transgenesis has become very widespread in biological research, and in our society at large. This year the governments of both Canada and the United States have approved the first use of ‘genetically engineered’ animals in food production, Atlantic salmon, Salmo salar. With the recent advent of amazing gene-editing technology, there is no doubt that the transgene industry will grow explosively in the coming years. The biology of transgenes needs to be included in our understanding of the genome. It is in this spirit that we have investigated an unexpected and novel phenotypic effect of the chromosomally integrated transgene fli1a-F-hsp70l:Gal4VP16. We examine larval fras1 mutant zebrafish (Danio rerio). Gal4VP16 is a potent transcriptional activator, and already well known for toxicity and mediating unusual transcriptional effects. In the presence of the transgene, phenotypes in the neural crest-derived craniofacial skeleton, notably fusions and shape changes associated with loss of function fras1 mutations, are made more severe, as we quantify by scoring phenotypic penetrance, the fraction of mutants expressing the trait. A very interesting feature is that the enhancements are highly specific for fras1 mutant phenotypes – occurring in the apparent absence of more wide-spread changes. Except for the features due to the fras1 mutation, the transgene-bearing larvae appear generally healthy and to be developing normally. The transgene behaves as a genetic partial dominant: A single copy is sufficient for the enhancements, yet, for some traits, two copies may exert a stronger effect. We made new strains bearing independent insertions of the fli1a-F-hsp70l:Gal4VP16 transgene in new locations in the genome, and observed increased severities of the same phenotypes as observed for the original insertion. This finding suggests that sequences within the transgene, e.g. Gal4VP16, are responsible for the enhancements, rather than effect on neighboring host sequences (such as an insertional mutation). The specificity, and biological action underlying the traits, are subjects of considerable interest for further investigation, as we discuss. Our findings show that work with transgenes needs to be undertaken with caution and attention to detail.
Some risk factors behavior of dysphonia in teachers at Camagüey Municipality

An analytic observation, longitudinal, and retrospective non paired case control study was performed, in teachers of different teaching levels of Camagüey municipality, from January to December 2004, with the objective to determine the behavior of some risk factors of occupational chronic functional dysphonia. The universe was constituted by 2776 teachers stratified by each level of teaching, to which was applied a phoniatric exam and an epidemiological survey. Classified as risk factors: the smoking habit, the personnel pathological antecedent of laryngitis, to give continuous classes during the morning and more than 35h classes to the week, as well as the lack of discipline of the students and to be a teacher of the primary level of teaching. It was emphasized that the 100% of the polled teachers were not carried out the pre-employment medical checkup neither periodic medical checkups and they did not receive training for the correct use of the voice. DeSC: VOICE DISORDERS; RISK FACTORS _______________________________________________________________
Assessment of cutting time on nutrient values, in vitro fermentation and methane production among three ryegrass cultivars

Objective The 3×3 factorial arrangement was used to investigate if either high water-soluble carbohydrates (WSC) cultivars or suitable time of day that the grass cut could improve nutrient values and in vitro fermentation characteristics. Methods The 3 cultivars were mowed at 3 diurnal time points and included a benchmark WSC ryegrass cultivar ‘Premium’, and 2 high WSC cultivars AberAvon and AberMagic, which contained, on average, 157, 173, and 193 g/kg dry matter (DM) of WSC, and 36.0, 36.5, and 34.1 g/kg DM of N during 7th regrowth stage, respectively. The fermentation jars were run at 39°C with gas production recorded and sampled at 2, 5, 8, 11, 14, 17, 22, 28, 36, and 48 h. The rumen liquid was collected from 3 rumen fistulated cows grazing on ryegrass pasture. Results High WSC cultivars had significantly greater WSC content, in vitro DM digestibility (IVDMD) and total gas production (TGP), and lower lag time than Premium cultivar. Methane production for AberMagic cultivar containing lower N concentration was marginally lower than that for AberAvon and Premium cultivars. Grass cut at Noon or PM contained greater WSC concentration, IVDMD and TGP, and lower N and neutral detergent fiber (NDF) contents, but CH4 production was also increased, compared to grass cut in AM. Meanwhile, the effects of diurnal cutting time were influenced by cultivars, such as in vitro CH4 production for AberMagic was not affected by cutting time. The IVDMD and gas production per unit of DM incubated were positively related to WSC concentration, WSC/N and WSC/NDF, respectively, and negatively related to N and NDF concentrations. Conclusion These results imply either grass cut in Noon or PM or high WSC cultivars could improve nutrient values, IVDMD and in vitro TGP, and that AberMagic cultivar has a slightly lower CH4 production compared to AberAvon and Premium. Further study is necessary to determine whether the increase of CH4 production response incurred by shifting from AM cutting to Noon and/or PM cutting could be compensated for by high daily gain from increased WSC concentration and DM digestibility.
Noninvasive ultrasound techniques for assessment of early atherosclerosis

Currently, the only way to predict the development of atherosclerosis is to assess risk factors for the disease. Problematically, some risk factors for atherosclerosis remain unidentified, some patients at risk will not develop atherosclerosis, and evaluation of preventative therapy is based on reduction of risk factors, not on documented cessation of the disease process. The goal of this work was to advance the assessment of early atherosclerosis by improving three noninvasive ultrasound measures of arterial health: vasoreactivity, intima-media thickness (IMT), and distensibility. Vasoreactivity was assessed by measuring brachial artery diameter and flow velocity continuously before, during, and after a 5-minute occlusion of the forearm vasculature. Arterial diameter was measured from end-diastolic B-mode images using edge detection and a new model-based diameter estimation algorithm, which reduced measurement variance by a factor of 5 over the subjective caliper-based method. Variability of the time series of diameter estimates was additionally reduced by acquiring images in the skew plane (i.e., a plane rotated about 10 degrees off-axis of the artery), and by.conducting edge-detection in consistent locations over time. Multiple parameters of vasoreactivity were extracted from the time-series measurements. Measurement of IMT in the distal common carotid artery was based on automated border detection from B-mode images. The standard deviation of individual IMT measurements compared favorably with other techniques. Arterial distensibility measurements were based on digitization and storage of radio-frequency ultrasound, followed by off-line echo tracking, which allowed detection of tracking errors. Several pilot studies were conducted with this measurement system. Whereas subjects with familial hypercholesterolemia (FH) are known to have abnormal flow-mediated dilation (FMD), we demonstrated nearly normal FMD and reduced progression of carotid IMT in FH subjects treated chronically with Heparin-induced Extracorporeal LDL Precipitation (HELP). Evidence of the individual specificity of our vasoreactivity measurements was demonstrated by consistent deviations from normality in certain HELP subjects. In a study of the effects of acute increase in plasma homocysteine on vasoreactivity, we demonstrated acute but temporary inhibition of FMD in a subject who was later shown to have fasting hyperhomocysteinemia, and a delay in the time course of FMD in normal subjects. Finally, we demonstrated reduced FMD and abnormal arterial constriction during distal vascular occlusion in smokers who refrained from smoking, but acute normalization of vasoreactivity immediately after smoking. We conclude that measurement of vasoreactivity, IMT, and distensibility with our system provides insight to arterial health and may lead to noninvasive assessment of early atherosclerosis and of therapeutic efficacy in individual subjects. Thesis Supervisor: Robert S. Lees Title: Professor of Health Sciences and Technology
Normative data for an expanded set of stimuli for testing high-level influences on object perception: OMEFA-II

We present normative data for bipartite displays used to investigate high-level contributions to object perception in general and to figure-ground perception in particular. In these vertically-elongated displays, two equal-area regions of different luminance abut a central, articulated, vertical border. In Intact displays, a portion of a mono-oriented well-known (“familiar”) object is sketched along one side of the border; henceforth the “critical side. ” The other side is the “complementary side. ” We measured inter-subject agreement among 32 participants regarding objects depicted on the critical and complementary sides of the borders of Intact displays and two other types of displays: upright and inverted Part-Rearranged displays. The parts on the critical side of the border are the same in upright Intact and Part-Rearranged displays but spatially rearranged into a new configuration in the latter. Inter-subject agreement is taken to index the extent to which a side activates traces of previously seen objects near the central border. We report normative data for 288 regions near the central borders of 144 displays (48/type) and a thorough description of the image features. This set of stimuli is larger than an older “Object Memory Effects on Figure Assignment” (OMEFA) set. This new OMEFA-II set of high-resolution displays is available online (https://osf.io/j9kz2/).
Socio-demographic determinants associated with iron deficiency anemia in pregnancy in rural population of central India

Worldwide Iron deficiency anemia (IDA) affects 25% of the population and in India it affects 80% of pregnant women. A prospective observational study was conducted to know the relationship between IDA and socio-demographic determinants in pregnancy. Pregnant women with singleton pregnancy with gestational age more than 20 weeks and IDA (Hb <10 gm %) were selected and studied for socio-economic and demographic parameters.15. 02% rural women had severe anemia IDA as compare to women who did not show IDA. 60% anemic women belonged to the age group of 20-25 years and 20% illiterate women had severe anemia. Multigravida women were at more risk for IDA of which. 13.84% were severely anemic out of whom 65% were vegetarian. 19% were married before age of 20 years of which 26.31% had severe IDA. This study emphasize that demographic parmeters have a major role to play in development of IDA and that improvement in socioeconomic condition , educational status and living conditions can prevent IDA.
New deletion alleles for Caenorhabditis elegans Hedgehog pathway-related genes wrt-6 and wrt-10

Figure 1: Deletion alleles for wrt-6 and wrt-10. A. wrt-6(aus41). B. wrt-10(aus36) and wrt-10(aus37). Description We have generated new putative null alleles of two members of the C. elegans Hedgehog-related pathway: wrt-6 and wrt10. The warthog (wrt) family member wrt-6 encodes a predicted secreted signalling molecule that contains an N-terminal Wart domain and a C-terminal autoprocessing domain (Hint or Hog domain) (Bürglin 1996; Aspöck et al. 1999; Bürglin, 2008). wrt-10 encodes another member of this Wrt family that contains the Wart domain but lacks the Hog domain (Bürglin 1996; Aspöck et al. 1999). To generate deletion alleles, we used CRISPR-Cas9 to target the first exon of wrt-6 or wrt-10 (wrt-6 sgRNA: 5′GATGCTGTTACACCTCGTGT-3′, wrt-10 sgRNA: 5′-GCGGATTCCATTCATGATGG-3′). We isolated the wrt-6 (aus41) allele that contains a 49 bp out-of-frame deletion, predicted to cause a premature stop codon after 7 amino acids (Figure 1A). We also generated two wrt-10 deletion alleles: aus36 and aus37. The aus36 allele contains a 5 bp deletion, predicted to cause a premature stop codon after 33 amino acids (Figure 1B). The aus37 allele contains a 2 bp deletion, predicted to cause a premature stop codon after 34 amino acids (Figure 1B). As all these alleles are predicted to cause premature stop codons in the first exon of each gene, they are likely to represent molecular nulls. We found that these alleles are viable and have no obvious gross morphological phenotype. Therefore, in-depth phenotypic examination is required to dissect their functional role. To conclude, we have isolated specific deletion alleles for wrt-6 and wrt-10 and will therefore help reveal new insights into the functions of Hedgehog-related signaling in C. elegans. 10/15/2019 Open Access
Knowledge about Hepatitis B and Vaccination Status among Healthcare Workers in a Tertiary Care Teaching Hospital, Mysuru. -

Background: Hepatitis B is a major infectious disease of mankind. It is the most common cause of chronic hepatitis, liver cirrhosis and hepato-cellular carcinoma worldwide. Health professionals are at the most risk. Vaccination against Hepatitis B can prevent this deadly disease. Objectives: This study was conducted to assess the knowledge and status of Hepatitis B vaccination among technicians, nurses and group D workers. Materials and Methods: A cross-sectional study was conducted among 150 members and the data was analyzed by cross tabulation and Chi square tests. Results: The Knowledge regarding hepatitis b among group D workers was found to be low with a mean score of 2.66. The attitude and practices to prevent transmission of Hepatitis B infection was low among group D workers when compared to nurses and technicians in the hospital. Conclusions: The, Knowledge, Practices and vaccination status among group D workers was poor when compared to technicians and nurses. A considerable amount of improvement in practice is required among health care workers to prevent hepatitis B infection.
Implications of using different metrics for niche analysis in ecological communities

: Explaining the mechanisms driving niche partitioning among species is of great importance in ecology. Unlike the fundamental niche, a species’ realised niche can only be measured in situ , as a result of biotic and abiotic interactions defining its size. Following current methodology, the realised niche of a species is often influenced by the rare and divergent individuals of the community sampled. In this study, using fish on coral and temperate reefs as an example, behavioural empirical data were collected to estimate realised niche sizes and niche overlaps. Niche measurements were made using the total area of the convex hull (TA), but as an alternative, a metric not as strongly influenced by sample size, standard ellipse area (SEA), was also used. A comprehensive description is given, and context-dependent pros and cons of using both metrics are discussed. Additionally, an alternative sample size correction was presented for both metrics. The analyses re vealed large differences in the sizes of realised niches and their overlaps between species depending on the measurement metric used. Regardless of the species, niche size and overlap were always larger for TA than SEA. Increasing sample size re duced niche size variability for both TA and SEA, but the variation was always smaller for SEA than TA. We successfully adapted the SEA metric for analysis of behavioural niche components and demonstrated that measuring niche sizes using the 2 metrics, each with their own strengths and weaknesses, can pro-duce contradictory results, the ecological conse-quences of which are likely to be important. Two fish species from the temperate reef community stud- ied, East Atlantic peacock wrasse Symphodus tinca (fore -ground) and common two-banded seabream Diplodus vul- garis (background).
Spatial distribution patterns of benthic macroinvertebrate functional feeding groups by stream size and gradient in Republic of Korea

Abstract Benthic macroinvertebrate functional feeding groups (FFGs) are influenced by the availability of food sources, which can be affected by stream size and gradient. We investigated the spatial distribution patterns of FFGs by stream size (stream order, catchment area and stream width) and gradient (altitude and slope). In addition, we attempted stream classification based on the distribution patterns of FFGs. To achieve these goals, a total of 996 sampling sites of national scale located in the Republic of Korea were investigated from 2008 to 2016. Among the five physical variables, stream width and slope showed linear relationships with the indicator values of FFGs. These two physical variables had larger influences on the distribution of FFGs compared to other variables. Geology (the type of rocks) showed little influences on the distribution of benthic macroinvertebrate communities. We classified streams focusing on catchment (stream size) area and altitude (stream gradient) because they are constants that do not change with disturbances. The FFGs and benthic macroinvertebrate assemblages were distinctly changed by stream types, indicating that the stream classification criterion adequately represented changes in physical variables in biotic terms. In addition, the distribution of FFGs and biotic assemblages showed that benthic macroinvertebrates in the Republic of Korea were more influenced by the altitude (stream gradient) than the catchment area (stream size). In overall, this study found that the stream size and gradient markedly influence the distribution of FFGs in national regions of the Republic of Korea. Further research is needed focusing on the level of microhabitats and other parameters to identify the promising variables that influence biotic distribution.
A dual role for shape skeletons in human vision: perceptual organization and object recognition

Shape perception is crucial for object recognition. However, it remains unknown exactly how shape information is represented, and, consequently, used by the visual system. Here, we hypothesized that the visual system represents “shape skeletons” to both (1) perceptually organize contours and component parts into a shape percept, and (2) compare shapes to recognize objects. Using functional magnetic resonance imaging (fMRI) and representational similarity analysis (RSA), we found that a model of skeletal similarity explained significant unique variance in the response profiles of V3 and LO, regions known to be involved in perceptual organization and object recognition, respectively. Moreover, the skeletal model remained predictive in these regions even when controlling for other models of visual similarity that approximate low- to high-level visual features (i.e., Gabor-jet, GIST, HMAX, and AlexNet), and across different surface forms, a manipulation that altered object contours while preserving the underlying skeleton. Together, these findings shed light on the functional roles of shape skeletons in human vision, as well as the computational properties of V3 and LO.
The novel shapeshifting bacterial phylum Saltatorellota

Our current understanding of a free-living bacterium - capable of withstanding a variety of environmental stresses-is represented by the image of a peptidoglycan-armored rigid casket. The making and breaking of peptidoglycan greatly determines cell shape. The cytoplasmic membrane follows this shape, pressed towards the cell wall by turgor pressure. Consequently, bacteria are morphologically static organisms, in contrast to eukaryotic cells that can facilitate shape changes. Here we report the discovery of the novel bacterial phylum Saltatorellota, that challenges this concept of a bacterial cell. Members of this phylum can change their shape, are capable of amoeba-like locomotion and trunk-formation through the creation of extensive pseudopodia-like structures. Two independent Saltatorellota cells can fuse, and they employ various forms of cell division from budding to canonical binary fission. Despite their polymorphisms, members of the Saltatorellota do possess a peptidoglycan cell wall. Their genomes encode flagella and type IV pili as well as a bacterial actin homolog, the ‘saltatorellin’. This protein is most similar to MamK, a dynamic filament-forming protein, that aligns and segregates magnetosome organelles via treadmilling. We found saltatorellin to form filaments in both, E. coli and Magnetospirillum gryphiswaldense, leading to the hypothesis that shapeshifting and pseudopodia formation might be driven by treadmilling of saltatorellin.
Extrafloral nectar as a driver of ant community spatial structure along disturbance and rainfall gradients in Brazilian dry forest

Abstract Although extrafloral nectar (EFN) is a key food resource for arboreal ants, its role in structuring ground-nesting ant communities has received little attention, despite these ants also being frequent EFN-attendants. We investigated the role of EFN as a driver of the spatial structure of ground-nesting ant communities occurring in dry forest in north-eastern Brazil. We examined the effects on this relationship of two global drivers of biodiversity decline, chronic anthropogenic disturbance and climate change (through decreasing rainfall). We mapped EFN-producing plants and ant nests in 20 plots distributed along independent gradients of disturbance and rainfall. We categorized ant species into three types according to their dependence on EFN: heavy users, occasional users and non-users. We found a strong relationship between ant dependence on EFN and nest proximity to EFN-producing plants: heavy-users (mean distance 1.1 m) nested closer to EFN-producing plants than did occasional users (1.7 m), which in turn nested closer to EFN-producing plants than did non-users (2.3 m). Neither disturbance nor rainfall affected the proximity of heavy-user nests to EFN-producing plants. Our study shows for the first time that EFN is a key driver of the spatial structure of entire communities of ground-nesting ants.