Barley has one of the largest and most complex genomes of all economically important food crops. The rise of new short read sequencing technologies such as Illumina/Solexa permits such large genomes ...to be effectively sampled at relatively low cost. Based on the corresponding sequence reads a Mathematically Defined Repeat (MDR) index can be generated to map repetitive regions in genomic sequences.
We have generated 574 Mbp of Illumina/Solexa sequences from barley total genomic DNA, representing about 10% of a genome equivalent. From these sequences we generated an MDR index which was then used to identify and mark repetitive regions in the barley genome. Comparison of the MDR plots with expert repeat annotation drawing on the information already available for known repetitive elements revealed a significant correspondence between the two methods. MDR-based annotation allowed for the identification of dozens of novel repeat sequences, though, which were not recognised by hand-annotation. The MDR data was also used to identify gene-containing regions by masking of repetitive sequences in eight de-novo sequenced bacterial artificial chromosome (BAC) clones. For half of the identified candidate gene islands indeed gene sequences could be identified. MDR data were only of limited use, when mapped on genomic sequences from the closely related species Triticum monococcum as only a fraction of the repetitive sequences was recognised.
An MDR index for barley, which was obtained by whole-genome Illumina/Solexa sequencing, proved as efficient in repeat identification as manual expert annotation. Circumventing the labour-intensive step of producing a specific repeat library for expert annotation, an MDR index provides an elegant and efficient resource for the identification of repetitive and low-copy (i.e. potentially gene-containing sequences) regions in uncharacterised genomic sequences. The restriction that a particular MDR index can not be used across species is outweighed by the low costs of Illumina/Solexa sequencing which makes any chosen genome accessible for whole-genome sequence sampling.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Enhancing the quality of life (QOL) of people living with HIV and AIDS (PLWHA) has become a significant global health goal, as combination antiretroviral therapy has helped to transform HIV/AIDS from ...a fatal illness to chronic disease. In this study, we aim to comprehensively describe the growth of research publications and the development of research landscapes regarding interventions to improve QOL among PLWH, as well as to characterize interdisciplinary topics and emerging interests of the research community. English articles and reviews published from 1991 to 2018 concerning interventions to improve QOL among PLWHA were retrieved from the Web of Science. Collaboration among organizations sharing coauthorships and co-occurrence network of authors' keywords was illustrated through network graphs. Latent Dirichlet Allocation was used for classifying papers into corresponding topics. A total of 2304 publications were included in the study. The USA continues to lead in research productivity, followed by South Africa, China, and India. Emerging research themes were found to be the application of multilevel interventions and long-term care, rehabilitation, along with topics relating to mental health issues, behavioral therapy and social supports for patients receiving treatments, and application of e-health approaches in designing and implementing interventions. There has been, however, a modest appearance of topics covering local, cultural, and environmental contexts of interventions. The findings of the study suggest expanding the coverage of psychosocial, behavioral, and contextualized interventions, increasing the involvement of family and community, improving the effectiveness of technology-based and e-health interventions, and developing strategies for lifelong treatment of HIV/AIDS.
Monitoring populations is critical for understanding how they respond to anthropogenic disturbance and for management of protected areas. The use of passive acoustic monitoring can improve monitoring ...efforts as it allows for collection of data on vocal animals at spatial and temporal scales that are difficult using only human observers. In this study, we used a multiseason occupancy model to monitor occurrence, apparent extinction, and colonization probabilities of a northern yellow-cheeked gibbon, Nomascus annamensis population with acoustic data collected from mobile smartphones in Dakrong Nature Reserve, Vietnam. Forty-five sites were randomly selected for repeated surveys in 2019 and 2022. At each site, a mobile smartphone was attached to a tree and recorded sounds for 4.2 days and 3.89 days on average, in 2019 and 2022, respectively. We manually annotated spectrograms for the presence of gibbon calls, and we detected gibbons at 24 and 12 recording posts in 2019 and 2022, respectively. Estimated local apparent extinction from occupancy models was high with 67% of occupied sites in 2019 becoming unoccupied in 2022. Apparent colonization was low with ~25% of unoccupied sites in 2019 becoming occupied in 2022. As a result, the apparent occurrence probability declined from 0.58 in 2019 to 0.30 in 2022. If the absence of calls indicates that cells are unoccupied this would mean an alarming decline of the gibbon population in the nature reserve. We suggest that in the areas with high hunting pressure, monitoring intervals should be shortened to at least yearly. In addition, urgent actions, such as patrolling, or gun confiscation, should be implemented to conserve the gibbon populations in Dakrong Nature Reserve and other protected areas with the same management context.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
The aim of this study was to identify factors associated with high Framingham Risk Score (FRS) in medicated patients with major depressive disorder (MDD).
We examined 61 medicated patients with MDD ...(mean age 37.77 ± 7.67, 90.2% women) and 43 non-depressed controls (mean age 38.26 ± 9.20, 90.7% women). We administered the Hamilton Depression Rating Scale (HAM-D) and measured systolic blood pressure (SBP), diastolic BP (DBP), mean arterial BP (MAP), pulse wave velocity (PWV), intima-media thickness (IMT), interleukin-6 (IL-6) and triglycerides.
We found that medicated patients with MDD had significantly higher levels of HAM-D score (
< 0.01), SBP (
= 0.015), MAP (
= 0.037), IL-6 level (
= 0.007), as compared with controls. Medicated patients who remained moderately to severely depressed showed significantly higher SBP (
= 0.049), DBP (
= 0.009), MAP (
= 0.024), IL-6 level (
= 0.019), left PWV (
= 0.004) and average PWV (
= 0.026) than those with mild depression. Multivariate regression showed that the interaction effect between HAM-D score and triglyceride level (
= 0.018) was significantly associated with FRS in medicated patients with MDD.
This study highlights that the interaction effect of the severity of depression and the triglyceride level, was a modifiable factor positively associated with high FRS.
Epigenetic mechanisms are involved in regulation of crucial cellular processes in eukaryotic organisms. Data on the epigenetic features of plant telomeres and their epigenetic regulation were ...published mostly for Arabidopsis thaliana, in which the presence of interstitial telomeric repeats (ITRs) may interfere with genuine telomeres in most analyses. Here, we studied the epigenetic landscape and transcription of telomeres and ITRs in Nicotiana tabacum with long telomeres and no detectable ITRs, and in Ballantinia antipoda with large blocks of pericentromeric ITRs and relatively short telomeres. Chromatin of genuine telomeres displayed heterochromatic as well as euchromatic marks, while ITRs were just heterochromatic. Methylated cytosines were present at telomeres and ITRs, but showed a bias with more methylation toward distal telomere positions and different blocks of B. antipoda ITRs methylated to different levels. Telomeric transcripts TERRA (G-rich) and ARRET (C-rich) were identified in both plants and their levels varied among tissues with a maximum in blossoms. Plants with substantially different proportions of internally and terminally located telomeric repeats are instrumental in clarifying the chromatin status of telomeric repeats at distinct chromosome locations.
All 18 species of gibbons are considered threatened with extinction and listed on the IUCN Red List of Threatened Species. Because gibbons (Hylobatidae) are one of the most threatened primate ...families, a great need exists to determine and monitor their status effectively. To meet this need, we employed distance sampling methods to estimate the density and number of gibbon groups. We focused on southern yellow‐cheeked crested gibbon in the Nam Cat Tien sector of Cat Tien National Park, Vietnam, from July to October, 2016. We used an auditory point count method at 48 listening posts to detect gibbon groups. We estimated our detection probability of calling groups of gibbons within 1,200 m of a listening post was 0.63 (95% CI: 0.54–0.74). In addition, we estimated the daily calling probability of a gibbon group to be 0.46 (95% CI: 0.33–0.59) and interpreted this as the probability that a group was available to be detected. We adjusted our group density and abundance estimates by both detection and availability probabilities. Ultimately we estimated 325 (95% CI: 232–455) gibbon groups in the Nam Cat Tien sector. Our results suggest that Cat Tien National Park contains one of the largest populations of southern yellow‐cheeked crested gibbon in Vietnam. Our methods are one way of avoiding underestimation of gibbon group density and abundance by incorporating uncertainty in gibbon group availability and detection.
Our estimate of 325 gibbon groups suggests Cat Tien National Park is home to one of the largest gibbon populations in Vietnam. Using distance sampling methods, we estimated detection probability of calling gibbon groups to be 0.63 and detection probability declined at distances >700 m. Detection probability should be taken into account when monitoring and estimating gibbon group density and abundance.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
The C‐value paradox remains incompletely resolved after >40 yr and is exemplified by 2,350‐fold variation in genome sizes of flowering plants. The carnivorous Lentibulariaceae genus Genlisea, ...displaying a 25‐fold range of genome sizes, is a promising subject to study mechanisms and consequences of evolutionary genome size variation. Applying genomic, phylogenetic, and cytogenetic approaches, we uncovered bidirectional genome size evolution within the genus Genlisea. The Genlisea nigrocaulis Steyerm. genome (86 Mbp) has probably shrunk by retroelement silencing and deletion‐biased double‐strand break (DSB) repair, from an ancestral size of 400 to 800 Mbp to become one of the smallest among flowering plants. The G. hispidula Stapf genome has expanded by whole‐genome duplication (WGD) and retrotransposition to 1550 Mbp. Genlisea hispidula became allotetraploid after the split from the G. nigrocaulis clade ∼29 Ma. Genlisea pygmaea A. St.‐Hil. (179 Mbp), a close relative of G. nigrocaulis, proved to be a recent (auto)tetraploid. Our analyses suggest a common ancestor of the genus Genlisea with an intermediate 1C value (400–800 Mbp) and subsequent rapid genome size evolution in opposite directions. Many abundant repeats of the larger genome are absent in the smaller, casting doubt on their functionality for the organism, while recurrent WGD seems to safeguard against the loss of essential elements in the face of genome shrinkage. We cannot identify any consistent differences in habitat or life strategy that correlate with genome size changes, raising the possibility that these changes may be selectively neutral.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
There has been an increase of fertility desire among people living with HIV/AIDS (PLWH) thanks to the advancement of HIV treatment and prevention of mother-to-children transmission programs. However, ...the development of research focusing on this topic over the past three decades is not well documented. We aimed to explore the trend of global publications regarding fertility desires among PLWH and identify their contents through the natural language processing technique. Dataset from 1992 to 2019 was downloaded using the Web of Science Core Collection. Bibliometric indicators such as change in total publications, citations, and countries' collaboration were examined. Main topics of selected publications were determined using the latent Dirichlet allocation. There were 303 articles published during the period 1992-2019, with a rapid increase in the number of publications in the past 5 years. Common themes included determinants of fertility desire, HIV prevention for adolescents, and safer conception for couples affected with HIV. However, publications on HIV care and antenatal care for women with HIV had been still limited. Findings suggested a call for the future support and collaborations for fertility intention, as well as the promotion of HIV care and service for adolescents and pregnant women with HIV, especially in countries with poor resources and a high burden of HIV/AIDS.
In an Internet of Things (IoT), the number of interconnected devices is huge and has been increasing drastically. Their generated data requires powerful aggregated computing resources and consumes ...enormous energy for processing and transmission. Having said that, most IoT devices are very limited and heterogeneous in computing capabilities, causing a big challenge for designing a commonly used interconnect that is both reliable and energy-efficient. Random Linear Network Coding (RLNC) schemes have proven its capability both theoretically and in practical deployment not only to increase throughput and reliability but also to reduce latency and energy consumption. However, it is unclear how different variations of RLNC, in particular, Fulcrum codes aimed for heterogeneous devices perform in heterogeneous IoT settings. In this paper, we conduct a measurement campaign, allowing for a fair comparison among the state of the art RLNC families, with regard to energy consumption, decoding probability, and goodput. The study provides insights and guidelines for applying RLNC schemes to data transmission in heterogeneous IoT networks.
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