Plasma DNA fragmentomics is an emerging area of research covering plasma DNA sizes, end points, and nucleosome footprints. In the present study, we found a significant increase in the diversity of ...plasma DNA end motifs in patients with hepatocellular carcinoma (HCC). Compared with patients without HCC, patients with HCC showed a preferential pattern of 4-mer end motifs. In particular, the abundance of plasma DNA motif CCCA was much lower in patients with HCC than in subjects without HCC. The aberrant end motifs were also observed in patients with other cancer types, including colorectal cancer, lung cancer, nasopharyngeal carcinoma, and head and neck squamous cell carcinoma. We further observed that the profile of plasma DNA end motifs originating from the same organ, such as the liver, placenta, and hematopoietic cells, generally clustered together. The profile of end motifs may therefore serve as a class of biomarkers for liquid biopsy in oncology, noninvasive prenatal testing, and transplantation monitoring. SIGNIFICANCE: Plasma DNA molecules originating from the liver, HCC and other cancers, placenta, and hematopoietic cells each harbor a set of characteristic plasma DNA end motifs. Such markers carry tissue-of-origin information and represent a new class of biomarkers in the nascent field of fragmentomics.
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Massively parallel sequencing of DNA molecules in the plasma of pregnant women has been shown to allow accurate and noninvasive prenatal detection of fetal trisomy 21. However, whether the sequencing ...approach is as accurate for the noninvasive prenatal diagnosis of trisomy 13 and 18 is unclear due to the lack of data from a large sample set. We studied 392 pregnancies, among which 25 involved a trisomy 13 fetus and 37 involved a trisomy 18 fetus, by massively parallel sequencing. By using our previously reported standard z-score approach, we demonstrated that this approach could identify 36.0% and 73.0% of trisomy 13 and 18 at specificities of 92.4% and 97.2%, respectively. We aimed to improve the detection of trisomy 13 and 18 by using a non-repeat-masked reference human genome instead of a repeat-masked one to increase the number of aligned sequence reads for each sample. We then applied a bioinformatics approach to correct GC content bias in the sequencing data. With these measures, we detected all (25 out of 25) trisomy 13 fetuses at a specificity of 98.9% (261 out of 264 non-trisomy 13 cases), and 91.9% (34 out of 37) of the trisomy 18 fetuses at 98.0% specificity (247 out of 252 non-trisomy 18 cases). These data indicate that with appropriate bioinformatics analysis, noninvasive prenatal diagnosis of trisomy 13 and trisomy 18 by maternal plasma DNA sequencing is achievable.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Objectives To validate the clinical efficacy and practical feasibility of massively parallel maternal plasma DNA sequencing to screen for fetal trisomy 21 among high risk pregnancies clinically ...indicated for amniocentesis or chorionic villus sampling.Design Diagnostic accuracy validated against full karyotyping, using prospectively collected or archived maternal plasma samples.Setting Prenatal diagnostic units in Hong Kong, United Kingdom, and the Netherlands.Participants 753 pregnant women at high risk for fetal trisomy 21 who underwent definitive diagnosis by full karyotyping, of whom 86 had a fetus with trisomy 21. Intervention Multiplexed massively parallel sequencing of DNA molecules in maternal plasma according to two protocols with different levels of sample throughput: 2-plex and 8-plex sequencing. Main outcome measures Proportion of DNA molecules that originated from chromosome 21. A trisomy 21 fetus was diagnosed when the z score for the proportion of chromosome 21 DNA molecules was >3. Diagnostic sensitivity, specificity, positive predictive value, and negative predictive value were calculated for trisomy 21 detection.Results Results were available from 753 pregnancies with the 8-plex sequencing protocol and from 314 pregnancies with the 2-plex protocol. The performance of the 2-plex protocol was superior to that of the 8-plex protocol. With the 2-plex protocol, trisomy 21 fetuses were detected at 100% sensitivity and 97.9% specificity, which resulted in a positive predictive value of 96.6% and negative predictive value of 100%. The 8-plex protocol detected 79.1% of the trisomy 21 fetuses and 98.9% specificity, giving a positive predictive value of 91.9% and negative predictive value of 96.9%.Conclusion Multiplexed maternal plasma DNA sequencing analysis could be used to rule out fetal trisomy 21 among high risk pregnancies. If referrals for amniocentesis or chorionic villus sampling were based on the sequencing test results, about 98% of the invasive diagnostic procedures could be avoided.
This qualitative study aims to investigate how the COVID-19 pandemic has affected South Asians in Hong Kong. A total of 34 South Asian adults completed the interview. Data were analysed thematically ...and three broad themes emerged: the impact of the pandemic on daily life, discrimination experienced, coping with challenges. The impacts of COVID-19 have spanned across from individual, family, community, to societal domains. Future research using a longitudinal approach and the inclusion of those with quarantine or infection experiences would yield a more comprehensive understanding of the experiences of South Asian communities in Hong Kong.
Laboratory diagnosis of SARS Chan, Paul K S; To, Wing-Kin; Ng, King-Cheung ...
Emerging infectious diseases,
05/2004, Letnik:
10, Številka:
5
Journal Article
Recenzirano
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The virologic test results of 415 patients with severe acute respiratory syndrome (SARS) were examined. The peak detection rate for SARS-associated coronavirus occurred at week 2 after illness onset ...for respiratory specimens, at weeks 2 to 3 for stool or rectal swab specimens, and at week 4 for urine specimens. The latest stool sample that was positive by reverse transcription-polymerase chain reaction (RT-PCR) was collected on day 75 while the patient was receiving intensive care. Tracheal aspirate and stool samples had a higher diagnostic yield (RT-PCR average positive rate for first 2 weeks: 66.7% and 56.5%, respectively). Pooled throat and nasal swabs, rectal swab, nasal swab, throat swab, and nasopharyngeal aspirate specimens provided a moderate yield (29.7%-40.0%), whereas throat washing and urine specimens showed a lower yield (17.3% and 4.5%). The collection procedures for stool and pooled nasal and throat swab specimens were the least likely to transmit infection, and the combination gave the highest yield for coronavirus detection by RT-PCR. Positive virologic test results in patient groups were associated with mechanical ventilation or death (p < 0.001), suggesting a correlation between viral load and disease severity.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, ODKLJ, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Many consequences of cerebrovascular disease are identifiable by magnetic resonance imaging (MRI), but variation in methods limits multicenter studies and pooling of data. The European Union Joint ...Program on Neurodegenerative Diseases (EU JPND) funded the HARmoNizing Brain Imaging MEthodS for VaScular Contributions to Neurodegeneration (HARNESS) initiative, with a focus on cerebral small vessel disease.
Surveys, teleconferences, and an in-person workshop were used to identify gaps in knowledge and to develop tools for harmonizing imaging and analysis.
A framework for neuroimaging biomarker development was developed based on validating repeatability and reproducibility, biological principles, and feasibility of implementation. The status of current MRI biomarkers was reviewed. A website was created at www.harness-neuroimaging.org with acquisition protocols, a software database, rating scales and case report forms, and a deidentified MRI repository.
The HARNESS initiative provides resources to reduce variability in measurement in MRI studies of cerebral small vessel disease.
The Internet is being exploited as a medium for illegal wildlife trade, and protected wildlife can now be sold and bought across social media and e-commerce platforms. This article is a 13-mo study ...on the online trade of Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES)-listed chelonians on a localized Hong Kong website. During this period, more than 400 posts were collected, with more than 300 posts selling CITES-listed chelonians. Based on our findings, we give 2 general recommendations in enforcing the online illegal wildlife trade: 1) increase knowledge of CITES regulations on pet trade forums and 2) introduce digital solutions to monitor pet trade forums.
Human-wildlife interactions in urban Asia Wierucka, Kaja; Hatten, Chloe ER; Murphy, Derek ...
Global ecology and conservation,
October 2023, 2023-10-00, 2023-10-01, Letnik:
46
Journal Article
Recenzirano
Odprti dostop
While urban areas may not seem conducive to human-wildlife interactions (HWI), rapid land use transformations can result in frequent encounters with wildlife in the context of changing habitats, as ...well as encounters with species that thrive in urban settings. In Asia, the processes of rapid land-use change can bring into sharp relief the juxtaposition of biodiversity hotspots with urban space. This provides an interesting context to study human-wildlife interactions, and also gives considerable scope for input into sustainable urban design worldwide. We conducted a structured review of published literature on HWI across urban southern and eastern Asia. Within the extracted literature, we investigated the framing of the interactions, as HWI have been predominantly perceived through the lens of dualistic antagonism and framed by paradigms of conflict, however there is also substantial discourse emphasizing interspecific coexistence. Invertebrates, mammals and birds occurred most commonly in the abstracts included in our review, with examples of conflict and coexistence common among all three taxonomic groups. Very few studies mentioned amphibians, reptiles and fish. Within each taxonomic group excluding amphibians, at least 50 % of interactions with humans were framed as conflicts. Humans were presented as causing conflict or negative impact on animals in the majority of studies on amphibians, birds, fish and insects, while mammals and lizards were more often considered to negatively impact humans. Our study illustrates the variety and complexity of human-wildlife interactions in Asia that need to be taken into account when planning sustainable urban designs.
In this study we examined the relationship between teacher and student intrinsic motivation in project-based learning. The participants were 126 Hong Kong secondary school teachers and their 631 ...students who completed evaluation questionnaires after a semester-long project-based learning program. Both teachers and students were asked to indicate their motivation in the program, and students were also asked to report the instructional support they received from their teachers. The results of hierarchical linear modeling analyses showed that teacher intrinsic motivation predicted student intrinsic motivation directly as well as indirectly through the mediation of instructional support. When teachers reported higher intrinsic motivation in the program, their students tended to perceive receiving more support from them and to report higher intrinsic motivation in the learning experience.
We evaluated an indirect immunofluorescence assay based on virus-infected cells for detecting anti-severe acute respiratory syndrome-associated coronavirus (SARS-CoV) immunoglobulin (Ig) G antibody. ...All confirmed SARS cases demonstrated seroconversion or fourfold rise in IgG antibody titer; no control was positive. Sensitivity and specificity of this assay were both 100%. Immunofluorescence assay can ascertain the status of SARS-CoV infection.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, ODKLJ, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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