253 research outputs found
Exacum laxiflorum Geethakumary, Deepu, Kissling & Pandurangan A. Habit 2022, comb. et stat. nov.
No full textExacum laxiflorum (Gamble) Geethakumary, Deepu, Kissling & Pandurangan, comb. et stat. nov. Exacum courtallense var. laxiflorum Gamble (1923: 873). Type:— INDIA. Travancore, 1873, Beddome s.n. (lectotype MH [barcode MH00002366], designated by Henry & Swaminathan (1983: 458); isolectotype K [barcode K000759944]). Exacum courtallense var. boneccordense M. Mohanan in M. Mohanan & A.N. Henry (1994: 305, as “ boneccordensis ”). Type:— INDIA. Kerala, Thiruvananthapuram district, Bonacaud, s. d., M. Mohanan 63225 (holotype CAL n.v.; isotype MH n.v.). Herbs, 15–152 cm tall. Stems much branched, terete at the base, sharply 4-angular above, young branches 4-lineolate, internodes 10–95 mm. Leaves opposite, subsessile, narrowly elliptic to lanceolate, 15–88 × 5–20 mm, chartaceous, glabrous, green, base attenuate, petiolate, apex long acuminate, 3–veined (midvein with one secondary vein on each side), tips recurved, veins diverging from the base of the lamina reaching to the apex prominent. Inflorescence terminal or axillary dichasial lax cymes, rarely solitary from terminal axis; peduncles 15–55 mm long; pedicels 6–25 mm long, enlarging in fruit (10–30 mm), bent towards one side. Calyx 5-lobed; tube campanulate, 2–3 mm long; lobes 5–7 mm long acuminate at apex, winged; wings 2–3 mm broad, wings narrowing at the apex, abruptly narrowing to base, accrescent in fruit, with prominent veins. Corolla tube 3-4 mm long, green; lobes 5, broadly obovate-oblong, 8–11 × 5–12 mm, subacute at apex, long persistent in fruit with prominent nerves but eventually deciduous, blue towards purplish. Stamens 5, 6.5–9.5 mm long; filaments ca. 4 mm long, attached at distal portion of the corolla tube; anthers bottle-shaped with long narrow neck, 5–5.5 mm long, slightly curved with the convex back face, base cordate, opening by apical pores that later widen to slits to the base, without papilla. Ovary ellipsoid, ca. 4mm long; style 9–10 mm long, curved, persistent; stigma capitate. Capsule ovoid, 6–9 × 3–4 mm, dehiscing septicidally, 2-valved; style persistent. Seeds many, irregularly rhomboid, angular, with shallowly sunken sides (Fig. 2). Note:—We searched for the type specimens of Exacum courtallense var. boneccordense in both CAL and MH, and we were unable to locate them. However, for this study, specimens collected from the type locality matching the drawing in the protologue were used for logical conclusions. Phenology:—Flowering and fruiting were observed from July to December. Chromosome number:—2n=68 (Mallikarjuna et al. 1987) Distribution and Habitat:—Occurs in the evergreen and semi-evergreen forests of the Southern Western Ghats in Kerala and Tamil Nadu. This species has a wider distribution than E. courtallense and is recorded from many districts in Kerala. Conservation status: —Based on the information from field surveys and herbarium data, the species is known from 13 subpopulations. Some of these subpopulations are under stress due to a decline in the quality of habitat. The species is annual, and it is observed to have undergone a reduction of over 50% over a period of 10 years due to a decline in area of occupancy (AOO) and quality of habitat, as evident by the fact that some subpopulations seen in the past are currently not present. Some subpopulations occur along the trek paths and wall cuttings along the roads, which are subjected to annual clearing, posing a threat to these subpopulations. Based on the available population information, the AOO of the species is not expected to be greater than 500 km 2. Given the species has a low AOO, suffered population decline over the past, and the continuing threat due to the decline in habitat quality, the species is assessed as Endangered [EN A2ac; B2b(ii, iv, v)]. Specimens examined:— INDIA. Kerala, Ernakulam District, Bhoothathankettu, 22September2012, Geethakumary 70936 (TBGT). Idukki District, Kulamavu, 7 July 1984, C.N. Mohanan 82012 (MH); Thiruvananthapuram District, Travancore hills, 26 December 1821, R. H. Beddome s.n. (MH); Travancore, 1873, R. H. Beddome s.n. (MH); Neyyar Dam, K. Rajappan, s.n. (UCT); Forest near Bonaccord, 500 m, 1 October 1973, J. Joseph 44484 (MH); Bonaccord, 600 m, 22 March 1978, M. Mohanan 54736 (MH); ibid., + 575 m, 3 August 1978, M. Mohanan 58523 (MH); ibid., 700 m, 18 May 1991, N. Mohanan 10818 (TBGT); ibid., 30 October 1992, E S Santhoshkumar & M. A. Jabbar 14727 (TBGT); ibid., ± 600 m, Geethakumary 53681 (TBGT); ibid., 11 December 2014, Geethakumary 80885 (TBGT); ibid., + 700m, 11 December 2014, Geethakumary 80885 (TBGT); ibid., 12 August 2011, Geethakumary 67929 (TBGT); ibid., 16 November 2011, Geethakumary 69883 (TBGT); Athirumala, 11 December 2014, Geethakumary 80887 (TBGT); ibid., 1100 m, 12 October 1988, N. Mohanan 4215 (CALI, TBGT); Meenmutty, 500 m, 6 November 1990, N. Mohanan 10147 (TBGT); Chemunji, 900 m, 5 February 1991, N. Mohanan 10325 (TBGT); Karamanayar, 700 m, 30 July 1991, N. Mohanan 10704 (TBGT); Near Karamana River, 660 m, 26 September 1995, C.S. K. & S. A. K. 24359 (TBGT); near Karamanayar, s.d., Geethakumary 63693 (TBGT); Agasthiyamala MPCA, 27 April 1994, N. Mohanan & T. Shaju 2055 (TBGT); Cement cana, 800 m, 14 August 2001, NWFP team 46630 (TBGT); Way to Koviltherimala, 16 November 2011, Geethakumary 69884 (TBGT); ibid., Geethakumary 69886 (TBGT); Chemunji, 16 November 2011, Geethakumary 69888 (TBGT). TAMILNADU: Kanyakumari District, Way to Muthukuzhivayal, ± 1000 m, 31 August 1976, A.N. Henry 48174 (MH); Thovazha hill, s.d., Narayana Iyer s.n. (TBGT); Tirunelveli District, Mahendragiri, 18 September 1916, s.coll. 13249 (MH).Published as part of Geethakumary, M. P., Deepu, S., Kissling, J. & Pandurangan, A. G., 2022, Revisiting the taxonomy of Exacum courtallense (Gentianaceae) and recognizing E. courtallense var. laxiflorum at the species rank, pp. 185-192 in Phytotaxa 559 (2) on page 190, DOI: 10.11646/phytotaxa.559.2.7, http://zenodo.org/record/702160
A time- and message-optimal distributed algorithm for minimum spanning trees
No full textThis paper presents a randomized (Las Vegas) distributed algorithm that constructs a minimum spanning tree (MST) in weighted networks with optimal (up to polylogarithmic factors) time and message complexity. This algorithm runs in Õ(D + √n) time and exchanges Õ(m) messages (both with high probability), where n is the number of nodes of the network, D is the diameter, and m is the number of edges. This is the first distributed MST algorithm that matches simultaneously the time lower bound of Ω(D + √n) [Elkin, SIAM J. Comput. 2006] and the message lower bound of Ω(m) [Kutten et al., J. ACM 2015], which both apply to randomized Monte Carlo algorithms.The prior time and message lower bounds are derived using two completely different graph constructions; the existing lower bound construction that shows one lower bound does not work for the other. To complement our algorithm, we present a new lower bound graph construction for which any distributed MST algorithm requires both Ω(D + √n) rounds and Ω(m) messages
Revisiting the taxonomy of Exacum courtallense (Gentianaceae) and recognizing E. courtallense var. laxiflorum at the species rank
No full textGeethakumary, M.P., Deepu, S., Kissling, J., Pandurangan, A.G. (2022): Revisiting the taxonomy of Exacum courtallense (Gentianaceae) and recognizing E. courtallense var. laxiflorum at the species rank. Phytotaxa 559 (2): 185-192, DOI: 10.11646/phytotaxa.559.2.
A translational study of the mechanisms of accumulation and activation of T cells in human asthmatic airway
No full textEThOS - Electronic Theses Online ServiceGBUnited Kingdo
On the distributed complexity of large-scale graph computations
No full textMotivated by the increasing need to understand the distributed algorithmic foundations of large-scale graph computations, we study some fundamental graph problems in a message-passing model for distributed computing where k ≥ 2 machines jointly perform computations on graphs with n nodes (typically, n ≫ k). The input graph is assumed to be initially randomly partitioned among the k machines, a common implementation in many real-world systems. Communication is point-to-point, and the goal is to minimize the number of communication rounds of the computation. Our main contribution is the General Lower Bound Theorem, a theorem that can be used to show non-trivial lower bounds on the round complexity of distributed large-scale data computations. This result is established via an information-theoretic approach that relates the round complexity to the minimal amount of information required by machines to solve the problem. Our approach is generic, and this theorem can be used in a “cookbook” fashion to show distributed lower bounds for several problems, including non-graph problems. We present two applications by showing (almost) tight lower bounds on the round complexity of two fundamental graph problems, namely, PageRank computation and triangle enumeration. These applications show that our approach can yield lower bounds for problems where the application of communication complexity techniques seems not obvious or gives weak bounds, including and especially under a stochastic partition of the input. We then present distributed algorithms for PageRank and triangle enumeration with a round complexity that (almost) matches the respective lower bounds; these algorithms exhibit a round complexity that scales superlinearly in k, improving significantly over previous results [Klauck et al., SODA 2015]. Specifically, we show the following results: • PageRank: We show a lower bound of Ω (n/k2 ) rounds and present a distributed algorithm that computes an approximation of the PageRank of all the nodes of a graph in Õ (n/k2 ) rounds. • Triangle enumeration: We show that there exist graphs with m edges where any distributed algorithm requires Ω (m/k5/3 ) rounds. This result also implies the first non-trivial lower bound of Ω (n1/3 ) rounds for the congested clique model, which is tight up to logarithmic factors. We then present a distributed algorithm that enumerates all the triangles of a graph in Õ (m/k5/3 + n/k4/3 ) rounds
Single-cell analysis to understand the diversity of immune cell types that drive disease pathogenesis
No full textSingle-cell next-generation sequencing assays are powerful tools to understand the nature of the immune cells that drive disease pathogenesis. In this brief review we explain the value of performing assays at single-cell resolution to better understand the pathogenesis of allergy, asthma, and other lung diseases. We explain the challenges in performing single-cell studies of airways and lung samples from patients with lung diseases. A major limitation comes from the amount of diseased tissue that can be used for research purposes. Finally, we discuss which sequencing strategies can be used to successfully investigate airway and lung diseases at single-cell resolution.</p
RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps
No full textMotivation: To better analyze low-resolution cryo electron microscopy maps of macromolecular assemblies, component atomic structures frequently have to be flexibly fitted into them. Reaching an optimal fit and preventing the fitting process from getting trapped in local minima can be significantly improved by identifying appropriate rigid bodies in the fitted component.
Results: Here we present the RIBFIND server, a tool for identifying rigid bodies in protein structures. The server identifies rigid bodies in proteins by calculating spatial proximity between their secondary structural elements.
Availability: The RIBFIND web server and its standalone program are available at http://ribfind.ismb.lon.ac.uk
Fast distributed algorithms for connectivity and MST in Large Graphs
No full text
Motivated by the increasing need to understand the algorithmic foundations of distributed large-scale graph computations, we study a number of fundamental graph problems in a message-passing model for distributed computing where
k
≥2 machines jointly perform computations on graphs with
n
nodes (typically,
n
>
k
). The input graph is assumed to be initially randomly partitioned among the
k
machines, a common implementation in many real-world systems. Communication is point-to-point, and the goal is to minimize the number of communication rounds of the computation.
Our main result is an (almost) optimal distributed randomized algorithm for graph connectivity. Our algorithm runs in Õ(
n
/
k
2
) rounds (Õ notation hides a polylog(
n
) factor and an additive polylog(
n
) term). This improves over the best previously known bound of Õ(
n
/
k
) [Klauck et al., SODA 2015] and is optimal (up to a polylogarithmic factor) in light of an existing lower bound of Ω
˜
(
n
/
k
2
). Our improved algorithm uses a bunch of techniques, including linear graph sketching, that prove useful in the design of efficient distributed graph algorithms. Using the connectivity algorithm as a building block, we then present fast randomized algorithms for computing minimum spanning trees, (approximate) min-cuts, and for many graph verification problems. All these algorithms take Õ(
n
/
k
2
) rounds and are optimal up to polylogarithmic factors. We also show an almost matching lower bound of Ω
˜
(
n
/
k
2
) rounds for many graph verification problems by leveraging lower bounds in random-partition communication complexity.
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Identification of significant chromatin contacts from HiChIP data by FitHiChIP
No full textHiChIP/PLAC-seq is increasingly becoming popular for profiling 3D chromatin contacts among regulatory elements and for annotating functions of genetic variants. Here we describe FitHiChIP, a computational method for loop calling from HiChIP/PLAC-seq data, which jointly models the non-uniform coverage and genomic distance scaling of contact counts to compute statistical significance estimates. We also develop a technique to filter putative bystander loops that can be explained by stronger adjacent loops. Compared to existing methods, FitHiChIP performs better in recovering contacts reported by Hi-C, promoter capture Hi-C and ChIA-PET experiments and in capturing previously validated promoter-enhancer interactions. FitHiChIP loop calls are reproducible among replicates and are consistent across different experimental settings. Our work also provides a framework for differential HiChIP analysis with an option to utilize ChIP-seq data for further characterizing differential loops. Even though designed for HiChIP, FitHiChIP is also applicable to other conformation capture assays.</p
Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change
No full textFitting of atomic components into electron cryo-microscopy (cryoEM) density maps is routinely used to understand the structure and function of macromolecular machines. Many fitting methods have been developed, but a standard protocol for successful fitting and assessment of fitted models is still to be agreed upon among the experts in the field. Here, we created and tested a protocol that highlights important issues related to homology modelling, density map segmentation, rigid and flexible fitting, as well as the assessment of fits. As part of it, we use two different flexible fitting methods (Flex-EM and iMODfit) and demonstrate how combining the analysis of multiple fits and model assessment could result in an improved model. The protocol is applied to the case of the mature and empty capsids of Coxsackievirus A7 (CAV7) by flexibly fitting homology models into the corresponding cryoEM density maps at 8.2Å and 6.1Å resolution. As a result, and due to the improved homology models (derived from recently solved crystal structures of a close homolog – EV71 capsid – in mature and empty forms), the final models present an improvement over previously published models. In close agreement with the capsid expansion observed in the EV71 structures, the new CAV7 models reveal that the expansion is accompanied by ∼5° counterclockwise rotation of the asymmetric unit, predominantly contributed by the capsid protein VP1. The protocol could be applied not only to viral capsids but also to many other complexes characterised by a combination of atomic structure modelling and cryoEM density fitting
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