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University of Ruhuna is a thriving modern Sri Lankan university with strengths in both research and teaching. Library system of University of Ruhuna provides an enormous contribution to the university in order to provide access to scholarly information through journals (online and printed), books, e-repositories and other means. Library network of the university spend substantial amount of money for subscribing to printed and electronic journals annually. Access to paid scholarly literature is limited depending on the subscription type to the database or journal. There is a renewed trend of searching for open-access (OA) knowledge which break the price boundaries and provide better access to the current knowledge among academic community. Open access repositories provide searching and downloading of scholarly information materials for free of charge. Spending extra time on sorting and filtering of OA-materials by information seekers out of the search results obtained has been a major demerit of using OA knowledge. Finding and searching on different open access repositories separately is also been a difficult and time consuming task. A unified interface for searching on different OA repositories worldwide can facilitates readers by reducing the searching time and effort of different scholarly materials and OA repositories in the world. Harvester System of University of Ruhuna (HaSURu) deployed in order to fulfil the gap of a unified interface that can connect number of OA archives together and search over the internet for OA information. HaSURu keeps OA information of OAIregistered open-access archives worldwide. OAI is an organization that promotes the better dissemination of knowledge among researchers. There are 1944 OA repositories worldwide has registered under OAI as data providers. Present study aimed at acquiring all the OA repository information from OAI and provide access through a unified interface using OAI-PMH driven metadata harvester. This paper discusses the process of installing and customizing PKP OHS Harvester2 as OA information finder carried out at University of Ruhuna. All the Information seekers of Sri Lanka will find this new service as a better source of access to OA repositories worldwide for their future research work. [ABSTRACT FROM AUTHOR]

The host–guest interactions between cucurbit[7]uril and a series of novel cationic bis(4,5-dihydro-1H-imidazol-2-yl)arene and 1-(4,5-dihydro-1H-imidazol-2-yl)- and 1,3-bis(4,5-dihydro-1H-imidazol-2-yl)-adamantane guests have been investigated in aqueous solution using UV–vis and NMR spectroscopy, and electrospray mass spectrometry. With the exception of the 1,3-bis(4,5-dihydro-1H-imidazol-2-yl)adamantane (which binds externally to the CB[7]), these guests form very stable inclusion complexes with slow exchange on the 1H NMR timescale. The direction and magnitude of the complexation-induced shifts (CIS) in the proton resonances of the guests are indicative of the residence of the hydrophobic core of the guest within the CB[7] cavity and the charged 4,5-dihydro-1H-imidazol-2-yl units outside the cavity adjacent to the carbonyl-lined portals of the host. The CIS values and the inclusion stability constants have been correlated with the nature of the guest core and with the distance between the charges on the terminal 4,5-dihydro-1H-imidazol-2-yl rings. [ABSTRACT FROM AUTHOR]

BACKGROUND The duration and effectiveness of immunity from infection with and vaccination deagainst severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are relevant to pandemic policy interventions, including the timing of vaccine boosters. METHODS We investigated the duration and effectiveness of immunity in a prospective cohort of asymptomatic health care workers in the United Kingdom who underwent routine polymerase-chain-reaction (PCR) testing. Vaccine effectiveness (310 months after the first dose of vaccine) and infection-acquired immunity were assessed by comparing the time to PCR-confirmed infection in vaccinated persons with that in unvaccinated persons, stratified according to previous infection status. We used a Cox regression model with adjustment for previous SARS-CoV-2 infection status, vaccine type and dosing interval, demographic characteristics, and workplace exposure to SARS-CoV-2. RESULTS Of 35,768 participants, 27% (9488) had a previous SARS-CoV-2 infection. Vaccine coverage was high: 9796 ofthe participants had received two doses (78°6 had received BNT162b2 vaccine [Pfizer-BioNTech] with a long interval between doses, 9% BNT162b2 vaccine with a short interval between doses, and 8°6 ChAdOxl 11(oV-19 vaccine [AstraZeneca]). Between December 7, 2020, and September 21, 2021, a total of 2747 primary infections and 210 reinfections were observed. Among previously uninfected participants who received long-interval BNT162b2 vaccine, adjusted vaccine effectiveness decreased from 8596 (95% confidence interval [CI], 72 to 92) 14 to 73 days after the second dose to 51% (95% CI, 22 to 69) at a median of 201 days (interquartile range, 197 to 205) after the second dose; this effectiveness did not differ significantly between the long-interval and short-interval BNT162b2 vaccine recipients. At 14 to 73 days after the second dose, adjusted vaccine effectiveness among ChAdOxl nCoV-19 vaccine recipients was 58°/0 (95% CI, 23 to 77) - considerably lower than that among BNT162b2 vaccine recipients. Infection-acquired immunity waned after 1 year in unvaccinated participants but remained consistently higher than 90°/oin those who were subsequently vaccinated, even in persons infected more than 18 months previously. CONCLUSIONS Two doses of BNT162b2 vaccine were associated with high short-term protection against SARS-CoV-2 infection; this protection waned considerably after 6 months. Infection-acquired immunity boosted with vaccination remained high more than 1 year after infection. [ABSTRACT FROM AUTHOR]

Objectives: Bivalent original/BA.4-5 and monovalent XBB.1.5 mRNA boosters were offered to UK healthcare workers (HCWs) in the autumn of 2023. We aimed to estimate booster vaccine effectiveness (VE) and post-infection immunity among the SIREN HCW cohort over the subsequent 6-month period of XBB.1.5 and JN.1 variant circulation., Methods: Between October 2023 to March 2024, 2867 SIREN study participants tested fortnightly for SARS-CoV-2 and completed symptoms questionnaires. We used multi-state models, adjusted for vaccination, prior infection, and demographic covariates, to estimate protection against mild/asymptomatic and moderate SARS-CoV-2 infection., Results: Half of the participants (1422) received a booster during October 2023 (280 bivalent, 1142 monovalent), and 536 (19%) had a PCR-confirmed infection over the study period. Bivalent booster VE was 15.1% (-55.4 to 53.6%) at 0-2 months and 4.2% (-46.4 to 37.3%) at 2-4 months post-vaccination. Monovalent booster VE was 44.2% (95% CI 21.7 to 60.3%) at 0-2 months, and 24.1% (-0.7 to 42.9%) at 2-4 months. VE was greater against moderate infection than against mild/asymptomatic infection, but neither booster showed evidence of protection after 4 months. Controlling for vaccination, compared to an infection >2 years prior, infection within the past 6 months was associated with 58.6% (30.3 to 75.4%) increased protection against moderate infection and 38.5% (5.8 to 59.8%) increased protection against mild/asymptomatic infection., Conclusions: Monovalent XBB.1.5 boosters provided short-term protection against SARS-CoV-2 infection, particularly against moderate symptoms. Vaccine formulations that target the circulating variant may be suitable for inclusion in seasonal vaccination campaigns among HCWs., Competing Interests: Declaration of Competing Interest All authors have completed the ICJME uniform disclosure form at: https://www.icmje.org/disclosure-of-interest/ and declare: CSB and SH report grant funding from the NIHR HPRU; CSB reports participation in an ad-hoc one-off market research advisory on a variety of infection topics; no financial relationships with any organisations that might have an interest in the submitted work in the previous three years; no other relationships or activities that could appear to have influenced the submitted work., (Crown Copyright © 2024. Published by Elsevier Ltd. All rights reserved.)

Since June 2020, the SARS-CoV-2 Immunity and Reinfection Evaluation (SIREN) study has conducted routine PCR testing in UK healthcare workers and sequenced PCR-positive samples. SIREN detected increases in infections and reinfections and delected Omicron subvariant waves emergence contemporaneous with national surveillance. SIREN's sentinel surveillance methods can be used for variant surveillance.

Objectives: To investigate serological differences between SARS-CoV-2 reinfection cases and contemporary controls, to identify antibody correlates of protection against reinfection., Methods: We performed a case-control study, comparing reinfection cases with singly infected individuals pre-vaccination, matched by gender, age, region and timing of first infection. Serum samples were tested for anti-SARS-CoV-2 spike (anti-S), anti-SARS-CoV-2 nucleocapsid (anti-N), live virus microneutralisation (LV-N) and pseudovirus microneutralisation (PV-N). Results were analysed using fixed effect linear regression and fitted into conditional logistic regression models., Results: We identified 23 cases and 92 controls. First infections occurred before November 2020; reinfections occurred before February 2021, pre-vaccination. Anti-S levels, LV-N and PV-N titres were significantly lower among cases; no difference was found for anti-N levels. Increasing anti-S levels were associated with reduced risk of reinfection (OR 0·63, CI 0·47-0·85), but no association for anti-N levels (OR 0·88, CI 0·73-1·05). Titres >40 were correlated with protection against reinfection for LV-N Wuhan (OR 0·02, CI 0·001-0·31) and LV-N Alpha (OR 0·07, CI 0·009-0·62). For PV-N, titres >100 were associated with protection against Wuhan (OR 0·14, CI 0·03-0·64) and Alpha (0·06, CI 0·008-0·40)., Conclusions: Before vaccination, protection against SARS-CoV-2 reinfection was directly correlated with anti-S levels, PV-N and LV-N titres, but not with anti-N levels. Detectable LV-N titres were sufficient for protection, whilst PV-N titres >100 were required for a protective effect., Trial Registration Number: ISRCTN11041050., Competing Interests: Declaration of Competing Interest All authors declare no competing interests., (Copyright © 2022. Published by Elsevier Ltd.)

A pathogen inactivation step during collection or processing of clinical samples has the potential to reduce infectious risks associated with diagnostic procedures. It is essential that these inactivation methods are demonstrated to be effective, particularly for non-traditional inactivation reagents or for commercial products where the chemical composition is undisclosed. This study assessed inactivation effectiveness of twenty-four next-generation (guanidine-free) nucleic acid extraction lysis buffers and twelve rapid antigen test buffers against SARS-CoV-2, the causative agent of COVID-19. These data have significant safety implications for SARS-CoV-2 diagnostic testing and support the design and evidence-based risk assessment of these procedures., (© 2021. The Author(s).)

Down syndrome in humans is caused by trisomy of chromosome 21. DSCR4 (Down syndrome critical region 4) is a de novo-originated protein-coding gene present only in human chromosome 21 and its homologous chromosomes in apes. Despite being located in a medically critical genomic region and an abundance of evidence indicating its functionality, the roles of DSCR4 in human cells are unknown. We used a bioinformatic approach to infer the biological importance and cellular roles of this gene. Our analysis indicates that DSCR4 is likely involved in the regulation of interconnected biological pathways related to cell migration, coagulation and the immune system. We also showed that these predicted biological functions are consistent with tissue-specific expression of DSCR4 in migratory immune system leukocyte cells and neural crest cells (NCCs) that shape facial morphology in the human embryo. The immune system and NCCs are known to be affected in Down syndrome individuals, who suffer from DSCR4 misregulation, which further supports our findings. Providing evidence for the critical roles of DSCR4 in human cells, our findings establish the basis for further experimental investigations that will be necessary to confirm the roles of DSCR4 in the etiology of Down syndrome.

Legends to Figures 4 and 5 (p. 7) should be exchanged. Below are the correct legends to Figure 4 and Figure 5. Fig. 4. Interconnection of DSCR4 overexpression-mediated perturbed pathways. KEGG analysis of DSCR4 overexpression-mediated DEGs shows enrichment for the tightly interconnected pathways of the coagulation cascade and the complement cascade (highlighted in red) and further confirm the connection of these cascades with cell adhesion, migration and proliferation (red circle). Fig. 5. Expression profile of DSCR4 across human cell lines and tissues. According to Roadmap Epigenomics Project data, DSCR4 and DSCR8, which share a bidirectional promoter, are highly expressed only in K562 cells, a type of leukemia cell. Analysis of transcriptome data provided by Prescott et al. (2015) showed that DSCR4 and DSCR8 also display high expression in human and chimpanzee neural crest cells, which are critical migratory cells involved in facial morphogenesis in the embryo. (1) Data from Prescott et al. (2015). (2) Samples also include esophagus, lung, spleen and fetal large intestine. (3) Samples also include brain germinal matrix, hippocampus, fetal small intestine, stomach, left ventricle, small intestine, sigmoid colon, HEPG2 cells and HMEC cells. The PDF file for DOI: https://doi.org/10.1266/ggs.20-00012 has been replaced with the corrected version as of June 17, 2021.

The COVID-19 pandemic has necessitated a multifaceted rapid response by the scientific community, bringing researchers, health officials, and industry together to address the ongoing public health emergency. To meet this challenge, participants need an informed approach for working safely with the etiological agent, the novel human coronavirus SARS-CoV-2. Work with infectious SARS-CoV-2 is currently restricted to high-containment laboratories, but material can be handled at a lower containment level after inactivation. Given the wide array of inactivation reagents that are being used in laboratories during this pandemic, it is vital that their effectiveness is thoroughly investigated. Here, we evaluated a total of 23 commercial reagents designed for clinical sample transportation, nucleic acid extraction, and virus inactivation for their ability to inactivate SARS-CoV-2, as well as seven other common chemicals, including detergents and fixatives. As part of this study, we have also tested five filtration matrices for their effectiveness at removing the cytotoxic elements of each reagent, permitting accurate determination of levels of infectious virus remaining following treatment. In addition to providing critical data informing inactivation methods and risk assessments for diagnostic and research laboratories working with SARS-CoV-2, these data provide a framework for other laboratories to validate their inactivation processes and to guide similar studies for other pathogens., (© Crown copyright 2020.)

Background: The 'cannot intubate cannot oxygenate' (CICO) emergency requires urgent front of neck airway (FONA) access to prevent death. In cases reported to the 4th National Audit Project, the most successful FONA was a surgical technique, almost all of which were performed by surgeons. Subsequently, UK guidelines adopted surgical cricothyroidotomy as the preferred emergency surgical FONA technique. Despite regular skills-based training, anaesthetists may still be unwilling to perform an emergency surgical FONA. Consultant anaesthetists, head and neck surgeons, and general surgeons were compared in a high-fidelity simulated emergency. We hypothesised that head and neck surgeons would successfully execute emergency surgical FONA faster than anaesthetists and general surgeons., Methods: We recruited 15 consultants from each specialty (total of 45) at a single tertiary care hospital in the UK. All agreed to participate in an in situ high-fidelity simulation of an 'anaesthetic emergency'. Participants were not told in advance that this would be a CICO scenario., Results: There were no significant differences in total time to successful ventilation between anaesthetists, head and neck surgeons and general surgeons (median 86 vs 98 vs 126 s, respectively, P=0.078). Anaesthetists completed the emergency surgical FONA procedure significantly faster than general surgeons (median 50 vs 86 s, P=0.018). Despite this strong performance, qualitative data suggested some anaesthetists still believed 'surgeons' best placed to perform emergency surgical FONA in a genuine CICO situation., Conclusion: Anaesthetists regularly trained in emergency surgical FONA function at levels comparable with head and neck surgeons and should feel empowered to lead this procedure in the event of a CICO emergency., (Copyright © 2019 British Journal of Anaesthesia. Published by Elsevier Ltd. All rights reserved.)

Conserved non-coding sequences (CNSs) of Eukaryotes are known to be significantly enriched in regulatory sequences. CNSs of diverse lineages follow different patterns in abundance, sequence composition, and location. Here, we report a thorough analysis of CNSs in diverse groups of Eukaryotes with respect to GC content heterogeneity. We examined 24 fungi, 19 invertebrates, and 12 non-mammalian vertebrates so as to find lineage specific features of CNSs. We found that fungi and invertebrate CNSs are predominantly GC rich as in plants we previously observed, whereas vertebrate CNSs are GC poor. This result suggests that the CNS GC content transition occurred from the ancestral GC rich state of Eukaryotes to GC poor in the vertebrate lineage due to the enrollment of GC poor transcription factor binding sites that are lineage specific. CNS GC content is closely linked with the nucleosome occupancy that determines the location and structural architecture of DNAs., (© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Family Hominidae, which includes humans and great apes, is recognized for unique complex social behavior and intellectual abilities. Despite the increasing genome data, however, the genomic origin of its phenotypic uniqueness has remained elusive. Clade-specific genes and highly conserved noncoding sequences (HCNSs) are among the high-potential evolutionary candidates involved in driving clade-specific characters and phenotypes. On this premise, we analyzed whole genome sequences along with gene orthology data retrieved from major DNA databases to find Hominidae-specific (HS) genes and HCNSs. We discovered that Down syndrome critical region 4 (DSCR4) is the only experimentally verified gene uniquely present in Hominidae. DSCR4 has no structural homology to any known protein and was inferred to have emerged in several steps through LTR/ERV1, LTR/ERVL retrotransposition, and transversion. Using the genomic distance as neutral evolution threshold, we identified 1,658 HS HCNSs. Polymorphism coverage and derived allele frequency analysis of HS HCNSs showed that these HCNSs are under purifying selection, indicating that they may harbor important functions. They are overrepresented in promoters/untranslated regions, in close proximity of genes involved in sensory perception of sound and developmental process, and also showed a significantly lower nucleosome occupancy probability. Interestingly, many ancestral sequences of the HS HCNSs showed very high evolutionary rates. This suggests that new functions emerged through some kind of positive selection, and then purifying selection started to operate to keep these functions., (© The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Cynomolgus macaques (Macaca fascicularis) were introduced to the island of Mauritius by humans around the 16th century. The unique demographic history of the Mauritian cynomolgus macaques provides the opportunity to not only examine the genetic background of well-established nonhuman primates for biomedical research but also understand the effect of an extreme population bottleneck on the pattern of polymorphisms in genomes. We sequenced the whole genomes of six Mauritian cynomolgus macaques and obtained an average of 20-fold coverage of the genome sequences for each individual. The overall level of nucleotide diversity was 23% smaller than that of the Malaysian cynomolgus macaques, and a reduction of low-frequency polymorphisms was observed. In addition, we also confirmed that the Mauritian cynomolgus macaques were genetically closer to a representative of the Malaysian population than to a representative of the Indochinese population. Excess of nonsynonymous polymorphisms in low frequency, which has been observed in many other species, was not very strong in the Mauritian samples, and the proportion of heterozygous nonsynonymous polymorphisms relative to synonymous polymorphisms is higher within individuals in Mauritian than Malaysian cynomolgus macaques. Those patterns indicate that the extreme population bottleneck made purifying selection overwhelmed by the power of genetic drift in the population. Finally, we estimated the number of founding individuals by using the genome-wide site frequency spectrum of the six samples. Assuming a simple demographic scenario with a single bottleneck followed by exponential growth, the estimated number of founders (∼20 individuals) is largely consistent with previous estimates., (© The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Many studies on conserved noncoding sequences (CNSs) have found that CNSs are enriched significantly in regulatory sequence elements. We conducted whole-genome analysis on plant CNSs to identify lineage-specific CNSs in eudicots, monocots, angiosperms,and vascular plants based on the premise that lineage-specific CNSs define lineage-specific characters and functions in groups of organisms. We identified 27 eudicot, 204 monocot, 6,536 grass, 19 angiosperm, and 2 vascular plant lineage-specific CNSs(lengths range from 16 to 1,517 bp) that presumably originated in their respective common ancestors. A stronger constraint on the CNSs located in the untranslated regions was observed. The CNSs were often flanked by genes involved in transcription regulation. A drop of A+T content near the border of CNSs was observed and CNS regions showed a higher nucleosome occupancy probability. These CNSs are candidate regulatory elements, which are expected to define lineage-specific features of various plant groups.

Cardiac fibroblasts are the most abundant cell type in the heart, and play a key role in the maintenance and repair of the myocardium following damage such as myocardial infarction by transforming into a cardiac myofibroblast (CMF) phenotype. Repair occurs through controlled proliferation and migration, which are Ca(2+) dependent processes, and often requires the cells to operate within a hypoxic environment. Angiotensin converting enzyme (ACE) inhibitors reduce infarct size through the promotion of bradykinin (BK) stability. Although CMF express BK receptors, their activity under the reduced O(2) conditions that occur following infarct are entirely unexplored. Using Fura-2 microfluorimetry on primary human CMF, we found that hypoxia significantly increased the mobilisation of Ca(2+) from intracellular stores in response to BK whilst capacitative Ca(2+) entry (CCE) remained unchanged. The enhanced store mobilisation was due to a striking increase in CMF intracellular Ca(2+)-store content under hypoxic conditions. However, BK-induced CMF migration or proliferation was not affected following hypoxic exposure, suggesting that Ca(2+) influx rather than mobilisation is of primary importance in CMF migration and proliferation., (Copyright © 2010 Elsevier Inc. All rights reserved.)

Objectives: It is thought that widespread use of 'over-the-counter' azoles may increase the incidence of resistant Candida species such as Candida glabrata. Infections with species other than Candida albicans frequently do not respond to standard azole treatments. Intravaginal nystatin is an option but is no longer available in the UK. In this paper, the authors review the prevalence of non-albicans candida over the past 5 years, and assess the efficacy of amphotericin and flucytosine vaginal cream in the treatment of non-albicans VVC., Methods: Retrospective review of all vaginal yeast isolates collected from women attending a city centre sexual-health clinic between 2004 and 2008. The women prescribed amphotericin and flucytosine vaginal cream were identified through pharmacy records, and their clinical notes reviewed for treatment outcome., Results: Between 2004 and 2008, the number of isolates of all Candida species increased with increasing clinic workload, but the prevalence of non-albicans yeasts remained stable at between 0.87 and 1.06%. Eighteen patients were prescribed amphotericin and flucytosine vaginal cream. At follow-up, all 18 were clear of their initial yeast isolate on culture, but two had persistent symptoms and had positive cultures for C albicans., Conclusions: There is no evidence of any increase in prevalence of non-albicans Candida species such as C glabrata. The authors have treated 18 women who had non-albicans VVC with amphotericin and flucytosine vaginal cream and achieved clearance of the non-albicans species in all of them.