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Trajectory analysis
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T Cell responses to whole SARS Coronavirus in humans
Effective vaccines should confer long-term protection against future outbreaks of severe acute respiratory syndrome (SARS) caused by a novel zoonotic coronavirus (SARS-CoV) with unknown animal reservoirs. We conducted a cohort study examining multiple parameters of immune responses to SARS-CoV infection, aiming to identify the immune correlates of protection. We used a matrix of overlapping peptides spanning whole SARS-CoV proteome to determine T cell responses from 128 SARS convalescent samples by ex vivo IFN-γ ELISPOT assays. Approximately 50% of convalescent SARS patients were positive for T cell responses, and 90% possessed strongly neutralizing Abs. Fifty-five novel T cell epitopes were identified, with spike protein dominating total T cell responses. CD8+ T cell responses were more frequent and of a greater magnitude than CD4+ T cell responses (p < 0.001).
Polychromatic cytometry analysis indicated that the virus-specific T cells from the severe group tended to be a central memory phenotype (CD27+/CD45RO+) with a significantly higher frequency of polyfunctional CD4+ T cells producing IFN-γ, TNF-α, and IL-2, and CD8+ T cells producing IFN-γ, TNF-α, and CD107a (degranulation), as compared with the mild-moderate group. Strong T cell responses correlated significantly (p < 0.05) with higher neutralizing Ab. The serum cytokine profile during acute infection indicated a significant elevation of innate immune responses. Increased Th2 cytokines were observed in patients with fatal infection. Our study provides a roadmap for the immunogenicity of SARS-CoV and types of immune responses that may be responsible for the virus clearance, and should serve as a benchmark for SARS-CoV vaccine design and evaluation
Trichoglottis quadriga Atthan., C. Bandara, Peiris & Kumar 2023, sp. nov.
<i>Trichoglottis quadriga</i> Atthan., C.Bandara, Peiris & Kumar <i>sp. nov</i>. (Figs. 1–3) <p> <b>TYPE:</b> SRI LANKA. Sabaragamuwa Province, Ratnapura District, Samanala Nature Reserve, Mukkuwatte –Sri Pada Trail, 1145 m a.s.l., 23 March 2022, <i>AKAG 15.2022</i> (holotype-PDA!); <i>AKAG 16.2022</i> (topotype PDA!-spirit).</p> <p> <b>Diagnosis:</b> <i>Trichoglottis quadriga</i> is morphologically very similar to a Vietnamese endemic, <i>T. canhii</i>, but it can be easily distinguished from the latter in having leaf apex bi-lobed with acute lobules (vs. leaf apex bi-lobed with rounded lobules); 4-flowered racemes (vs. 5–12-flowered racemes); longer terete spur, more than half the length of the pedicel and ovary, 3.2 mm long, 1.2 mm wide, with bi-lobed apex (vs. shorter, broadly conical spur, less than half of length of pedicel and ovary, 1.4–1.8 mm long, 1.2–1.5 mm wide, with round apex); larger labellum (5.5 mm long and 3.5 mm wide) (vs. shorter labellum, 3.8–4.0 mm long, 1.8–2.0 mm wide), with longer side lobes; rostellum strongly beaked with the beak arching upwards (vs. rostellum feebly beaked); lobes of pollinia less than half the length of the caudicle and viscidium (vs. lobes of pollinia more than half the length of stipe and viscidium).</p> <p> <b>Epiphytic</b> monopodial herb. <b>Roots</b> numerous, terete, 3.0‒ 16.5 cm long, 0.8‒1.2 mm in diameter, flexuose, greenish-grey, glabrous, arising from basal part of the stem. <b>Stem</b> unbranched, stout, rigid, 0.7‒2.0 cm long, 0.4‒0.6 cm in diameter, greenish with silvery white velamen; internodes 3.0‒ 4.5 mm long, rarely branched near base. <b>Leaves</b> 3‒7, almost sessile, distichous, narrowly lanceolate to oblanceolate, margins entire and wavy, 4‒8(‒12) cm long, 0.4‒0.7 cm wide, arching, obliquely bi-lobed at the apex, longer lobule 1 mm long, shorter lobule 0.5 mm long, acute, midrib keeled, extended to a pointed setae in between lobules, ca. 0.2‒0.3 mm long. <b>Inflorescence</b> 4-flowered racemes, 1.1‒ 4.6 cm long, arising from stem through the leaf sheaths on internodes. <b>Peduncle</b> stout, terete, rigid, 1.5‒2.0 cm long, 0.9–1.3 mm in diam, greenish; with 2–3 persistent, triangular sterile bracts, 1.0– 1.2 mm long and wide, appressed to the peduncle. <b>Rachis</b> irregularly angled in cross section, 1.0– 1.5 mm in thick. <b>Pedicel</b> and <b>ovary</b> almost cylindric, slightly swollen in upper half, ca. 5.5‒6.0 mm long, curved, glabrous, green when unfertilized. <b>Flowers</b> widely opened, sepals and petals spreading, 9.0‒ 10 mm across, sepals and petals dull-yellow speckled with brown; lip white and spur pale yellow; column base brown and operculum light dull yellowish to almost whitish; pollinia pale yellowish. <b>Floral bracts</b> persistent, triangular, 0.7 mm long, 1 mm broad, acute, concave, dull greenish to light brown. <b>Dorsal sepal</b> oblanceolate, 9.0 mm long, 1.8 mm wide, narrowly obtuse, obtuse, 3-veined. <b>Petals</b> linear-elliptic to linearoblanceolate, 3.5 mm long, 1.6 mm wide, obtuse, 3-veined. <b>Lateral sepals</b> oblique-falcate, 4.3 mm long, 1.7 mm wide, apex rounded, 3-veined. <b>Labellum</b> 5.5 mm long, 3.5 mm wide (length from the base of column to the apex of median lobe), firmly attached to the column, spurred, elongate disc at the base, 3-lobed in the apical half; disc terete, channeled longitudinally on the upper side with slightly winged and raised margin, channel with dense soft hairs inside, leading to the spur; median lobe glabrous, fleshy, almost hexagonal, 3.2 mm long, 2.2 mm wide, margin crenulate indistinctly forming 5-lobules, lobules obtuse, prominent hollow on the ventral surface at the base; side lobes prominent, thumblike, up to ca. 1 mm long, erect and fleshy. <b>Spur</b> terete, 3.2 mm long, 1.2 mm diameter, apex equally bi-lobed, sparsely hairy on the inner margin with a bifid callus arising from the back wall of spur and ending at the throat, ca. 0.5 mm. <b>Column</b> short, 1.5 mm long, 1.2 mm diameter, stout, erect, broadly cylindrical, foot inconspicuous. <b>Rostellum</b> small, bifid, ca. 1.0 mm long, 0.5 mm wide, greenish-brown, extended into a prominent beak, beak arched upwards. <b>Operculum</b> hemispherical, 2 mm long, 1.2–1.4 mm wide, with a prominent beak oriented in parallel above the beak of the rostellum. <b>Anther</b> terminal, 2 loculed, 1.8 mm long, 2.0 mm wide. <b>Pollinia</b> 4, in 2 pairs, each lobe with 2 unequal sized pollinia tightly appressed to each other into a globular structure, 0.3‒0.4 mm in diameter each; stipe clavate, 1.6–1.8 mm long, with each lobe of pollinia attached on the broader side of the stipe; viscidium ovate, ca. 0.15‒0.20 mm long. <b>Ovary and pedicel</b> clavate, 5.3–5.5 mm long. <b>Capsule</b> fusiform or almost clavate, 2.0– 2.5 cm long, 0.6–0.7 cm diameter, dull green, dotted with dark purple spots and streaks, strongly ribbed.</p> <p> <b>Phenology:</b> Flowering and fruiting observed during November to March.</p> <p> <b>Etymology:</b> The specific epithet ‘quadriga’ in Latin stands for the word ‘team’ in English, and is used here appreciating the teamwork of young botanists and naturalists in Sri Lanka for describing this new species.</p> <p> <b>Vernacular name:</b> Samanala cherub orchid.</p> <p> <b>Distribution:</b> <i>Trichoglottis quadriga</i> is so far known from Mukkuwatte‒Sri Pada trail in Samanala Nature Reserve, Diyawilla, Rassagala, Bambarabotuwa and Pettigala in Sabaragamuwa Province. Endemic to Sri Lanka.</p> <p> <b>Habitat and ecology:</b> <i>Trichoglottis quadriga</i> grows in montane and sub-montane forests at 900‒1800 m a.s.l. in Central Highlands of Sri Lanka. The new species is a strict canopy-dweller, growing 6‒15 meters above the ground level epiphytic on medium-sized stumps and branches of lianas and trees of <i>Entada rheedei</i> Sprengel [Fabaceae], <i>Horsfieldia iryaghedhi</i> (Gaertner) Warburg [Myristicaceae], <i>Macaranga peltata</i> (Roxburgh) Müller Argoviensis [Euphorbiaceae], <i>Cullenia ceylanica</i> (Gardner) Wight ex K.Schumann [Malvaceae], <i>Dipterocarpus glandulosus</i> Thwaites and <i>Shorea gardneri</i> (Thwaites) P.S.Ashton [Dipterocarpaceae]. Other Orchidaceae species which sharing the same habitat of this new species are <i>Cylindrolobus lindleyi</i> (Thwaites) Ormerod & C.S.Kumar, <i>Bulbophyllum crassifolium</i> Thwaites ex Trimen, <i>B. elegans</i> Gardner ex Thwaites, <i>Pinalia tricolor</i> (Thwaites) Kuntze and <i>Podochilus sp.</i>.</p> <p> With respect to sharing of habitat by different species in this genus, <i>Trichoglottis tenera</i> is widespread in the tropical montane and sub-montane forests at Nuwara-Eliya and Maturata (Nuwara-Eliya District, Central Province), Laggala (Matale District, Central Province), Rangala and Hunnasgiriya (Kandy District, Central Province), and Namunukula (Badulla District, Uva Province) (Jayaweera 1981) 1200 m a.s.l., while, <i>T. longifolia</i> is distributed in sub-montane forests at Aranayaka, (Kegalle District) and Bambarabotuwa, Kuruwita, Palabaddala, Samanala Nature Reserve and adjacent areas of Sinharaja MAB (Man and the Biosphere Reserve) (Ratnapura District) in Sabaragamuwa Province between 910‒1200 m a.s.l. (Bandara <i>et al.</i> 2022) (Fig. 4). <i>Trichoglottis quadriga</i> and <i>T. longifolia</i> can occur in same habitat but, can be easily identified following the field identification key provided in this manuscript.</p> <p> <b>Conservation status:</b> Based on the distribution data, the EOO and AOO were estimated as ~ 47 km 2 and 20 km 2 respectively. So far no threat is known to this species except for the anthropogenic pressure in the habitats, which is inferred to cause a depletion in the quality of habitat for the species. With 5 sub-populations, comprising less than 50 mature individuals <i>Trichoglottis quadriga</i> can be assessed depending on its extremely small population size as Critically Endangered (CR: D) following IUCN guidelines (IUCN 2022).</p> <p> <b>Additional specimens examined:</b> <i>Trichoglottis tenera</i>: <b>— SRI LANKA. NUWARA ELIYA DISTRICT:</b> Nuwara Eliya, Aug. 1962, <i>Jayaweera 2192</i> (PDA!); Hakgala, Mar. 1889, <i>W. Nock s.n</i>. (PDA!); Punduluoya, Feb. 1973, <i>Cramer 4067</i> (US!- <i>US00506216</i>); along road Kandy to Nuwara Eliya, May 1978, <i>D.D. Soejarto 4876</i> (US!- <i>US00506217</i>, L!- <i>L1529312</i>, P!- <i>P00361712</i>); <b>BADULLA DISTRICT</b>: Namunukula, Mar. 1907, <i>J.M. Silva s.n.</i> (PDA!); <b>LOCALITY UNKNOWN</b>: 1829, <i>Macrae 66</i> (K!- <i>K000895724</i>, holotype); <i>Macrae s.n.</i> (K!- <i>K000974382</i>); <i>Macrae s.n.</i> (K!- <i>K000974383</i>); <i>Thwaites C.P.2983</i> (PDA!); <i>Walker 118</i> (PDA!); 1869, <i>Thwaites C.P.2983</i> (P!- <i>P00361710</i>); 1854, <i>Thwaites C.P.2983</i> (P!- <i>P00361711</i>). <b>INDIA.</b> Grands bois à Neddoubitta, Jan. 1841, <i>L. Claude</i> s.n. (P!- <i>P00361713</i>). <i>Trichoglottis longifolia</i>: <b>— SRI LANKA. KEGALLE DISTRICT:</b> Maligakande, Aranayaka, Apr. 2022, <i>AKAG 29.2022</i> (PDA!-spirit); <b>RATNAPURA DISTRICT:</b> Seethagangula, Kuruwita‒Eratne trail, Samanala Nature Reserve, May 2022, <i>AKAG 30.2022</i> (PDA!).</p>Published as part of <i>Bandara, Champika, Atthanagoda, Anusha Gayan, Peiris, Gayan Prasanga, Jayasundara, Ramitha, Ranasinghe, Bhanuka, Kumara, Udayanga Nuwan, Aberathne, Nimantha, Hettiarachchi, Dushantha, Dissanayake, Malith, Karunathilake, Thimira, Bandara, Niwahal Vimukthi, Fernando, Oshan Dewmith, Wijesundara, Chandra Bandara, Bandara, Nadeesha Lewke & Kumar, Pankaj, 2023, Trichoglottis quadriga (Orchidaceae: Epidendroideae: Vandeae: Aeridinae), a new species from Central Highlands of Sri Lanka, pp. 265-272 in Phytotaxa 609 (4)</i> on pages 266-270, DOI: 10.11646/phytotaxa.609.4.2, <a href="http://zenodo.org/record/8297097">http://zenodo.org/record/8297097</a>
Polyhydroxyalkanoate (PHA) biosynthesis from structurally unrelated carbon sources by a newly characterized Bacillus spp
A newly acquired polyhydroxyalkanoate (PHA) producing Bacillus spp. was identified to be a strain of Bacillus cereus using a range of microbiological and molecular techniques. This strain, named B. cereus SPV, was found to be capable of using a wide range of carbon sources including glucose, fructose, sucrose, various fatty acids and gluconate for the production of PHAs, an advantage for the commercial production of the polymers. The media used for the polymer production was novel in the context of the genus Bacillus. The PHA, once produced, was found to remain at a constant maximal concentration, without any degradation, a great advantage for the commercial production of the PHAs. This particular strain of Bacillus spp. was able to synthesize various PHAs with 3-hydroxybutyrate (3HB), 3-hydroxyvalerate (3HV) and 4-hydroxybutyrate (4HB)-like monomer units from structurally unrelated carbon sources such as fructose, sucrose and gluconate. This is the first report of the incorporation of a 4HB related monomer containing PHA by the genus Bacillus and from structurally unrelated carbon sources. The PHAs isolated had molecular weights ranging between (0.4 and 0.8) × 106 and low polydispersity index values (MW/MN) ranging from 2.6 to 3.4
H5N1 Clade 2.2 Polymorphism Tracing Identifies Influenza Recombination and Potential Vaccine Targets
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997 1. The number of confirmed human cases now exceeds 300 and the associated Case Fatality Rate exceeds 60% 2. The genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases 3.4. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift 5. We traced polymorphism acquisition in Clade 2.2 sequences. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, Clade 2.2 sub-clades in Egypt, Russia and Ghana. These changes are not easily explained by the current theory of “random mutation” through copy error, and are more easily explained by recombination with a common source. This conclusion is supported by additional polymorphisms shared by Clade 2.2 isolates in Egypt, Nigeria and Germany including aggregation of regional polymorphisms from each of these areas into a single Nigerian human hemagglutinin gene
Spillovers from US monetary policy: Role of policy drivers and cyclical conditions
We provide new evidence on the spillover effects from US monetary policy for a large group of emerging market and advanced economies, focusing on the nature of the shocks driving movements in US interest rates. With an SVAR-IV model used to identify monetary policy, demand, and supply shocks, we find that an increase in US interest rates driven by demand shocks engenders a positive spillover to economic activity in the near-term, while an exogenous tightening of monetary policy has a large negative spillover effect, highlighting the importance of the trade channel. Furthermore, spillovers from US monetary policy shocks depend on the state of the business cycle, exerting larger effects when growth is weak outside the US. Finally, tighter US monetary policy affects the left tail of the growth distribution disproportionately: the fat left tail highlights the salience of growth at risk
Epizootiological survey of Trichinella spp. infection in carnivores, rodents and insectivores in Hokkaido, Japan.
In order to evaluate the present epidemiological situation of Trichinella infection in wild animals in Hokkaido, Japan, red foxes (Vulpes vulpes), raccoon dogs (Nyctereutes procyonoides) , brown bears (Ursus arctos) , martens (Martes melampus), rodents and insectivores captured in Hokkaido were examined for muscle larvae by the artificial digestion method from 2000 to 2006. Foxes (44/319, 13.8%), raccoon dogs (6/77, 7.8%) and brown bears (4/126, 3.2%) were found to be infected with Trichinella larvae and all other animal species evaluated were negative. Multiplex PCR and DNA sequencing revealed that larvae from a fox captured in Otofuke, in south-eastern Hokkaido, were T. nativa, and larvae from 27 animals including 21 foxes, 2 raccoon dogs and 4 brown bears captured in western Hokkaido were Trichinella T9
Internet usage trends in medical informatics
Technological growth in the 21st century is exponential. Simultaneously, development of the associated risk, uncertainty and user acceptance are scattered. This required appropriate study to establish people accepting controversial technology (PACT). The Internet and services around it, such as World Wide Web, e-mail, instant messaging and social networking are increasingly becoming important in many aspects of our lives.\ud
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Information related to medical and personal health sharing using the Internet is controversial and demand validity, usability and acceptance. Whilst literature suggest, Internet enhances patients and physicians’ positive interactions some studies establish opposite of such interaction in particular the associated risk. In recent years Internet has attracted considerable attention as a means to improve health and health care delivery. However, it is not clear how widespread the use of Internet for health care really is or what impact it has on health care utilisation. Estimated impact of Internet usage varies widely from the locations locally and globally. As a result, an estimate (or predication) of Internet use and their effects in Medical Informatics related decision-making is impractical. This open up research issues on validating and accepting Internet usage when designing and developing appropriate policy and processes activities for Medical Informatics, Health Informatics and/or e-Health related protocols.\ud
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Access and/or availability of data on Internet usage for Medical Informatics related activities are unfeasible. This paper presents a trend analysis of the growth of Internet usage in medical informatics related activities. In order to perform the analysis, data was extracted from ERA (Excellence Research in Australia) ranked “A” and “A*” Journal publications and reports from the authenticated public domain. The study is limited to the analyses of Internet usage trends in United States, Italy, France and Japan. Projected trends and their influence to the field of medical informatics is reviewed and discussed. The study clearly indicates a trend of patients becoming active consumers of health information rather than passive recipients
Inaction and Impunity: Incidents of Religious Violence Targeting Christians, Muslims and Hindus (2015-2019)
45p. The study is based on information provided by the National Christian Evangelical Alliance of Sri Lanka (NCEASL). It was compiled by Media Team of Verité Research. Mahoshadi Peiris was the lead researcher and author of the study. The team comprised of Mihindu Perera and Jonathan Cruse.Ethno-religious violence in Sri Lanka is a chronic and systemic problem that has continued despite successive changes in government. This study examines the key trends of incidents of violence faced by minority Christian, Muslim and Hindu groups in Sri Lanka between 2015 and 2019.
In 2015, the National Christian Evangelical Alliance of Sri Lanka and Verité Research released Silent Suppression: Restrictions on Religious Freedoms of Christians 1994-2004, a 20-year trend analysis report on ethno-religious violence.
This study build on that previous report by analysing 397 incidents of Freedom of Religion or Belief (FoRB) violations against Christians, multiple incidents of anti-Muslim riots, and discrimination against Hindu communities in the Northern and Eastern Provinces.
The findings of the study highlight a concerning trend of increased involvement of state officials as both active and passive actors in violations against minority communities. Moreover, the study finds that religious violence is sustained invariably through the action or inaction of the state
The presence of 5-HT in myenteric varicosities is not due to uptake of 5-HT released from the mucosa during dissection: use of a novel method for quantifying 5-HT immunoreactivity in myenteric ganglia
Author version made available according to Publisher copyright policy. This is the accepted version of the following article:
Keating, D. J., Peiris, H., Kyloh, M., Brookes, S. J. H. and Spencer, N. J. (2013), The presence of 5-HT in myenteric varicosities is not due to uptake of 5-HT released from the mucosa during dissection: use of a novel method for quantifying 5-HT immunoreactivity in myenteric ganglia. Neurogastroenterology & Motility, 25: 849–853,
which has been published in final form at
http://dx.doi.org/10.1111/nmo.12189.
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