27 research outputs found
Conogethes sahyadriensis Shashank, Kammar, Mally & Chakravarthy 2018
No full text652. Conogethes sahyadriensis Shashank, Kammar, Mally & Chakravarthy, 2018: 217, figs 1–2, 6, 9, 12, 15, 17, 19, 21, 237 Type locality: India, Chikmagalur, Mudigere, 12°25’11”N 75°43’48”E, 980 m Distribution. Indian records: Southwest India (Karnataka, Kerala) (Shashank et al. 2018). Global records: Sri Lanka (Shashank et al. 2018).Published as part of Singh, Navneet, Ranjan, Rahul, Talukdar, Avishek, Joshi, Rahul, Kirti, Jagbir Singh, Chandra, Kailash & Mally, Richard, 2022, A catalogue of Indian Pyraloidea (Lepidoptera), pp. 1-423 in Zootaxa 5197 (1) on page 266, DOI: 10.11646/zootaxa.5197.1.1, http://zenodo.org/record/725229
Conogethes sahyadriensis Shashank & Kammar & Mally & Chakravarthy 2018, sp. nov.
No full textConogethes sahyadriensis sp. nov. (Figs 1–2, 6, 9, 12, 15, 17, 19, 21, 23) Diagnosis. Conogethes sahyadriensis and C. pluto are identical in the colouration of the labial palps (Figs 6–7), in the presence of two dark spots on the dorsal metathorax (Figs 9–10), and in the wing maculation (Figs 1–3), and cannot be distinguished based on these characters. The two species can be distinguished by the male genitalia: the dorsal tegumen roof has a more pronounced bulge in C. pluto (Fig. 13); the clasper base of C. pluto is broader, with a trapezoid shape (Fig. 13), whereas the clasper of C. sahyadriensis has a narrower, rectangular base (Fig. 12); the valva sides towards the apex form a blunt right angle in C. sahyadriensis, whereas in C. pluto the valva apex is evenly arched. Conogethes evaxalis (Walker, 1859) has a broad brown band across the labial palps like C. sahyadriensis, but the metathorax has three dark spots dorsally, the distal tarsus of the male hindlegs comprises a distinct tuft of dark hairs, the hindwing has a large dark spot in the anal area, in the male genitalia the transtilla are enlarged and strongly sclerotised and the phallus has a short sclerotised section instead of a needle-shaped cornutus, and in the female genitalia the antrum is larger and the central ductus bursae is sclerotised. Conogethes sahyadriensis is distinguished from the sympatric C. punctiferalis (Figs 4–5, 8, 11, 14, 16, 18, 20, 22–23) by: second segment of labial palp always broadly tinted with black fuscous (Fig.6); metathorax dorsally with two spots of black scales (Fig.9) instead of three (Fig. 11); hair-pencils with slender phylliform hair scales (sensu Kimura et al. 2002) (broad ovate in C. punctiferalis); clasper with broad, rectangular base and abruptly narrowed tip, clasper oriented ventrad (Fig. 12), whereas the slim clasper of C. punctiferalis points anteroventrad (Fig. 14); phallus shorter and not strongly curved at the base (Fig. 12); ductus bursae shorter, corpus bursae irregular ovate, smaller in size (Fig. 15). The two species do not differ in morphology and chaetotaxy of the larva and the pupa, but scanning electron microscopic studies reveal differences in surface sculpturing of the chorion, with C. sahyadriensis eggs exhibiting a network of threads resembling a fishing net (Figs 17, 19, 21), while the network on the egg surface of C. punctiferalis is irregular, and the surface is rather smooth (Figs 18, 20, 22). Conogethes sahyadriensis is distinguished from C. parvipunctalis by the larger wing size, the larger discocellular black spots on the hind wing and in the female genitalia by the longer ovipositor, anterior apophyses, and eighth abdominal segment. Conogethes sahyadriensis is distinguished from C. pinicolalis by the pale-yellow apex on the ventral side of the forewing, which is tinted brown in C. pinicolalis, sometimes also with the area between postmedial and submarginal series tinted brown, and by the absence of a large tuft of fuscous scales on the male hindlegs distal tibia and first tarsus segment. The DNA barcode of C. sahyadriensis is not shared with other species (Fig. 23), and it differs in the p—distance in average by 5.56–6.00% from its nearest neighbour C. pluto and by 6.00–6.89% from C. punctiferalis; the lowest p—distance is to C. semifascialis (Walker, 1866) clade 1 with 5.11–6.00% (see also Supplementary Table 1). Description. Head. Male and female colouration similar. Frons pale yellowish, vertex with dense whitish yellow scales. Antenna filiform, brownish, covered with pale yellowish scales and between each flagellomere with short cilia. Labial palp yellowish, three-segmented, upturned, second segment outside always broadly tinted with black fuscous (Fig. 6). Maxillary palp short, filiform. Basal scaling of proboscis black fuscous. Thorax. Patagium with black spot on either side. Tegula pale yellowish. Prothorax dorsum pale yellowish, with two black spots anterolaterally. Mesothorax dorsum with two black spots dorsolaterally. Mesoscutum strawyellow with large round black spot dorsally. Metathorax dorsum with two spots dorsolaterally (Fig. 9). Legs yellowish-white, with few scattered dark scales; foreleg femur, tibia and proximal tarsus as well as midleg central tibia homogenous dark brown; mid- and hind-tibiae sometimes with tarsus blackish, dusted with yellowish white outwardly. Wings (Figs 1–2). Wing span male 25.66± 1.22 mm (Mean±SD; n=10), female 27.55± 1.87 mm (Mean±SD; n=10). Male with one frenulum bristle, female with two fused frenulum bristles with the apex ending in two thin free tips. Forewings ground colour light yellow to orange yellow, ventral side paler. Costal margin with black and yellow scales, apical to anal margin with pale yellow fringed scales. Five black spots at the base of forewing: one at central wing base, two close to each other on the costa, one below proximal discal cell, and another spot on the inner wing margin. Discal cell with central black spot and with black transverse dash on discocellular vein. Series of antemedial, medial, postmedial and submarginal black spots present. Antemedial series consists of three black spots situated outwardly oblique from costa to inner margin. Medial series with four black spots arising from posterior angle of cell, leading obliquely inward toward inner margin. Postmedial series with twelve spots, of which four form an convex curve between costa and M1, almost forming a continuous band, the other eight spots arranged between vein M1 and inner margin in two rows of four spots each, the inner, straight row running obliquely towards inner wing margin, the outer row forming a convex curve towards inner margin. Submarginal series with six spots which are moderately excurved between R4 and CuA2, with the third spot from the apex being significantly displaced inward between vein M1 and M2, paralleling the outer series of spots of the postmedial series. Hind wings paler than forewings. Discocellular with large black spot. Antemedial series consists of three almost coalesced spots, placed between CuA2 and 2A. Postmedial series with eight spots present between vein Rs and 1A, with the spots between M1 and M2, and CuA1 and CuA2 displaced inward. A submarginal series of six roundish spots placed between vein Rs to CuA2, of which the spot placed between M1 and M2 is displaced inward. Ventral side of forewings with costa tinted dark brown from base to subapex; proximal half of cell tinted brown, with subcentral spot and central dash much broader than on dorsal forewing side; postmedial and submarginal series as on the dorsal forewing side, but with the spots of the postmedial series enlarged except for the four outer row spots between M1 and inner margin. Ventral side of hindwings with spots as on dorsal side, but postmedial series with spots more clearly. Abdomen. Abdomen orange yellow dorsally, whitish yellow ventrally. First abdominal tergite whitish yellow, without any black spots. Second to fifth tergites with three black spots, one on dorsal and other the two dorsolateral. Sixth tergite with one dorsal black spot. No black spots ventrally. Male anal tuft faded black,with sparse hairs. Male genitalia (Figs 12). Anterior margin of the tegumen completely sclerotized and lateral arms narrow. Uncus narrow, slender, ventrally curved, apical third swollen, dorsally densely covered with bifurcate setae, apically sparsely with simple setae, apex with two sclerotized processes, their ventral side bearing simple setae, their dorsal side protruded into thin, broadly ovate lobes. Gnathos formed by a broad, strongly sclerotized band, mesally fused with the subscaphium. Transtillum arms somewhat elongate, mesally connected with each other via a short dorsal and a long ventral process protruding from the transtillum apex. Saccus of vinculum U-shaped with conically pointed apex. Anterior connection of tegumen and vinculum with a round sclerite densely studded with hairs, forming a corema; outer margin of coremata hair pencil formed by simple long, lanceolate hairs and a few broad, flat hairs, centre of coremata with thin brown, easily removable, felting hairs. Juxta narrow elongate, tapering dorsad. Valve broad ovate, margins and inner surface sparsely covered with long setae, distally of clasper forming a dense field. Costa broad tubular, convex, dorsal costa base forming a straight elongate, ventrally directed rod whose apex serves as the dorsal joint of the valve with the vinculum (the ventral joint is formed by the sacculus base). Sacculus elongate triangular, distal half with a protruding ridge along valva margin; a small hook-shaped process near clasper curving dorsad; distal sacculus sclerotisation broadened and fused with the sclerotized areas leading from the costa and the medial valve sclerotisation from which the clasper emerges. Clasper short, sclerotized, decurved with blunt tip, overlapping with the hook-shaped process of the distal sacculus, clasper emerges from a broad triangular base which ispart of an elongate sclerotisation on the central inner valve, parallel to the sacculus. Phallus long, slender and strongly curved near anterior end; phallus apodeme membranous apart from a narrow, sclerotized band along ventral side; vesica with a thin, needle-shaped cornutus of almost the length of the phallus, and with fine denticulate granulation. Hair-pencil situated on each side of the genital, attached anterior at the joint of tegumen and vinculum, different hair scale types present (see Kimura et al. 2002), with the outer, phylliform hair scales slender and spatulate. Female genitalia (Fig. 15). Ovipositor triangular, covered with long and short setae. Apophyses anteriores about as long as, but somewhat thicker than A. posteriores. Ostium narrow, funnel-shaped, membranous, somewhat granulose at transition onto antrum. Antrum tubular, sclerotized, almost twice as long as broad, dorsal side with broad longitudinal non-sclerotised gap. Ductus bursae long, narrow, in anterior part with granulose sclerotisations; ductus seminalis emerges anterior the antrum. Corpus bursae usually ovate, irregular in shape, about half the length of the ductus bursae,with membranous appendix bursae attached laterally. Signum absent, but posterior half of corpus bursae lightly granulose. Immature stages. The immature stages are described in detail in Shashank (2012) as C. punctiferalis feeding on cardamom. Eggs. Eggs whitish, flattened and measuring 0.86± 0.006 mm and 0.81± 0.007 mm in length, and 0.47± 0.005 mm and 0.44± 0.008 mm in width in cohort one and two, respectively. Scanning electron microscopic studies reveal differences in the surface sculpturing on the chorion, appearing like a network of threads and resembling a fishing net (Figs 17–22). Larvae. Larvae eruciform, polypod, pinkish white, 25.01± 0.155mm in length and 4.12± 0.02 mm in width. Head light brown. Body wall transparent, studded with dark grey tubercles and long setae arising from pinacula. Pupae. Pupae light brown, obtect type. Male pupae are 15.66± 0.20 mm long and 2.84± 0.05 mm broad, female pupae are 16.91± 0.22 mm long and 79± 0.02 mm broad (n=30). Head in both investigated pupae represented by vertex and frontoclypeus, with compound eyes prominent. Antennae arise from the dorsal margin of the compound eyes and proceed ventrally to the tip of wing pad. Labial palpi prominent on either side of the mid-ventral line. All three thoracic segments dorsally clear, ventrally concealed by the appendages. Dorsally ten and ventrally six abdominal segments are evident. Distribution. Southwest India (Karnataka, Kerala), Sri Lanka. Material studied. Type material: Holotype ♂, INDIA, Chikmagalur, Mudigere, 12°25'11"N, 75°43'48", 980 m, 18.vii.2011, cardamom, Shashank, P.R.; Paratypes (21 specimens): 1♂, 1♀ same data as holotype, 1♂ (same locality as Holotype), 13.x.2010, cardamom, Shashank, P.R., 1♂ (same locality as Holotype), 12.x.2010, cardamom, Shashank, P.R., 3♂ (same locality as Holotype), 25.x.2015, cardamom, Vasudev K., 2♂, 1♀ (same locality as Holotype), 25.x.2015, cardamom, Kumar, K.P., 7♂, 4♀ (same locality as Holotype), 11.xi.2016, cardamom, Kumar, K.P.; all type specimens are deposited in NPC. Additional material: 1♂, 1♀, CEYLON [Sri Lanka], Kandy District, Kandy, 2100 ft, Udawattakele Sanctuary, 10–23.i.1970, Davis & Rowe, genitalia slides USNM 114050, RM1139 (USNM), 1♀, CEYLON [Sri Lanka], Kandy District, Kandy, 28.ii.1971, Piyadasa & Somapala, genitalia slide USNM 114051 (USNM), 1♂, CEYLON [Sri Lanka] Kandy District, Peredeniya, 2300 ft, Upper Hantane Hill, 12–16.i.1970, Davis & Rowe, genitalia slide RM1138 (USNM). Etymology. This species is named after the Sanskrit word ' sahyadri', meaning "The Benevolent Mountains" which is another name for the western Ghats, the type locality of this species. Biology. Conogethes sahyadriensis undergoes five larval instars and completes its life cycle in around 39 days. The detailed biology of C. sahyadriensis is given in Doddabasappa et al. (2014) under C. punctiferalis feeding on cardamom. Phylogenetic analysis. The best-fitting model for the sequence data was the GTR+G+I model. The two parallel MrBayes runs had sufficiently converged after 5 Mio. generations. Most effective sampling size (ESS) values were well above 1000, except for pinvar with ESS =509 and alpha with ESS =981, indicating a sufficiently large sampling size from which the marginal likelihood was estimated. In the Bayesian analysis (Fig. 23), C. sahyadriensis forms a distinct clade, with C. pluto as nearest neighbour. The topology of the tree is as follows: C. tharsalea is found as sister to all other Conogethes species included in the dataset. The latter split into two groups: one comprising C. haemactalis + C. cf. haemactalis which are sister to (C. evaxalis + Conogethes sp. 2) + Conogethes sp. 3 + Conogethes sp. 4, and the other group comprising C. ersealis + C. diminutiva which are sister to a tritomy of Conogethes sp. 1, the C. punctiferalis — C. semifascialis species complex, and C. pluto + C. sahyadriensis. The C. punctiferalis — C. semifascialis species complex comprises (C. punctiferalis + C. semifascialis clade 1) + C. cf. semifascialis, and C. cf. punctiferalis + C. semifascialis clade 2. COI analysis revealed that the percent of interspecific sequence variation, measured as p—distance, is 5.56– 6.00% between C. sahyadriensis and C. pluto, and 6.00–6.89% between C. sahyadriensis and C. punctiferalis. The lowest p—distance of C. sahyadriensis is that to C. semifascialis clade 1 with 5.11–6.00%; the closest p—distance of the C. semifascialis clade 1, however, is to C. punctiferalis with 2.00–3.11%. Supplementary Table 1 summarises the intra- and interspecific p—distances of all sampled species.Published as part of Shashank, P. R., Kammar, Vasudev, Mally, Richard & Chakravarthy, A. K., 2018, A new Indian species of shoot and capsule borer of the genus Conogethes (Lepidoptera: Crambidae), feeding on cardamom, pp. 215-234 in Zootaxa 4374 (2) on pages 217-221, DOI: 10.11646/zootaxa.4374.2.3, http://zenodo.org/record/115432
Not Available
No full textNot AvailableConogethes sahyadriensis (Shashank PR, Kammar V, Mally R, Chakravarthy
AK, Zootaxa 4374(2):215–234, 2018) is a serious insect pest of zingiberaceous
spice crops such as cardamom (Elettaria cardamomum Maton), ginger (Zingiber
officinale Rosc.) and turmeric (Curcuma longa L.). On ginger and cardamom the
borer incurs up to 25% and 80% yield losses, respectively. On cardamom the
economic threshold level is fixed at 10% shoot infestation. The fecundity of
female moths and the duration for completing the generations varied with the
season, the spice crop and the habitat. C. sahyadriensis infesting spice crops in
South India has alternate wild Zingiberaceae plants, viz. species of Alpinia,
Amomum, Hedychium, Curcuma, Aframomum, etc. Over a dozen, promising
parasitoids and predators have been recorded on Conogethes larvae and pupae.
Therefore, need-based applications of selective insecticides are warranted. Use
of semiochemicals for borer management should be rendered practicable.Not Availabl
Broadband signal reconstruction for SHM: An experimental and numerical time reversal methodology
Get PDFStructural Health Monitoring (SHM) aims to shift aircraft maintenance from a time-based to a condition-based approach. Within all the SHM techniques, Acoustic Emission (AE) allows for the monitoring of large areas by analyzing Lamb waves propagating in plate like structures. In this study, the authors proposed a Time Reversal (TR) methodology with the aim of reconstructing an original and unaltered signal from an AE event. Although the TR method has been applied in Narrow-Band (NwB) signal reconstruction, it fails when a Broad-Band (BdB) signal, such as a real AE event, is present. Therefore, a novel methodology based on the use of a Frequencies Compensation Transfer Function (FCTF), which is capable of reconstructing both NwB and real BdB signals, is presented. The study was carried out experimentally using several sensor layouts and materials with two different AE sources: (i) a Numerically Built Broadband (NBB) signal, (ii) a Pencil Lead Break (PLB). The results were validated numerically using Abaqus/CAETM with the implementation of absorbing boundaries to minimize edge reflections.Structural Integrity & Composite
Low-Resource Deontic Modality Classification in EU Legislation
No full textIn law, it is important to distinguish between obligations, permissions, prohibitions, rights, and powers. These categories are called deontic modalities. This paper evaluates the performance of two deontic modality classification models, LEGAL-BERT and a Fusion model, in a low-resource setting. To create a generalized dataset for multi-class classification, we extracted random provisions from European Union (EU) legislation. By fine-tuning previously researched and published models, we evaluate their performance on our dataset against fusion models designed for low-resource text classification. We incorporate focal loss as an alternative for cross-entropy to tackle issues of class imbalance. The experiments indicate that the fusion model performs better for both balanced and imbalanced data with a macro F1-score of 0.61 for imbalanced data, 0.62 for balanced data, and 0.55 with focal loss for imbalanced data. When focusing on accuracy, our experiments indicate that the fusion model performs better with scores of 0.91 for imbalanced data, 0.78 for balanced data, and 0.90 for imbalanced data with focal loss
IDENTIFICATION OF CONSERVED FUNCTIONAL MOTIFS IN LACTOFERRIN USING MEME
No full textInternational Journal on Bioinformatics & Biosciences (IJBB) Vol.2, No.4, December 2012 DOI : 10.5121/ijbb.2012.2403 29 IDENTIFICATION OF CONSERVED FUNCTIONAL MOTIFS IN LACTOFERRIN USING MEME * Shashank Rana1 [email protected] Shrikant Sharma1 [email protected] 1. Research Scholar, Bioinformatics Facility, Department of Immunology, College of Biotechnology, Sardar VallabhBhai Patel University of Agriculture & Technology. Meerut (U.P.) Raghvendar Singh2 [email protected] 2. Head of Department, Bioinformatics Facility, Department of Immunology, College of Biotechnology, SardarVallabhBhai Patel University of Agriculture & Technology. Meerut (U.P.) Corresponding Author-*Shashank Rana ([email protected]) Abstract Lactoferrin is an iron binding globular protein with antimicrobial activity was firstly isolated in bovine milk. Lactoferrin (LF) is structurally similar to the transferrins. So it is also known as lactotransferrin (LTF) is a globular multifunctional protein. Our work was on motif discovery by using OOPS modal of MEME (Multiple EM for Motif Elicitation) tool. The aim of motif discovery is to detect short, highly conserved patterns in a collection of unaligned DNA or protein sequences. We have taken fifteen LTF AA sequencesfrom different resources.By analysis of these sequences, three motifs were retrieved. It is to be noted that all fifteen sequences contains all three motifs but start points of those are different. Each motif has 15 sites and 50 widths. On the bases of motif analysis, it is distinct that LTF retrieved from any milk recourse, have common conserved patterns. Keywords- MEME, LTF, OOPS, Conserved pattern, MAST Introduction Lactoferrin form bovine milk was first isolated by Sorenson and Sorenson firstly in 1939 [1]. It is well known fact that LF have an iron binding properties and it also have similarity with transferrin, therefore also called lactotransferrin. Lactoferrin is considered a multifunctional or multi-tasking protein. LF has antibacterial, antiviral, antifungal, anti-inflammatory, antioxidant and Immunomodulatory activities [2]. LF is reported to have metal transfer, antiviral, antiageing agents. Javed et. al. (2001) reported lactoferrin from camel has two lobs N (Iron binding) and C (discharge of Iron) [7]. We have taken fifteen protein sequences of LTF from different milk producing animals. The length of shortest sequence was 692 residues and the longest sequence 711 residues and the modal for motif generation was OOPS. The purpose of MEME (Multiple EM for Motif Elicitation) (rhymes with ‘team’) [5] is to allow users to discover signals (called ‘motifs’) in DNA or protein sequences. For motif study of lactoferrin, we use by default value as described by MEME suite. The MEME Suite is well known software package with a International Journal on Bioinformatics & Biosciences (IJBB) Vol.2, No.4, December 2012 30 unified web server interface that enables us to perform all four types of motif analysis wiz 1) motif discovery, 2) motif–motif database searching, 3) motif-sequence database searching and 4) assignment of function [6]. Figure-1: MEME overview Materials and Methods In present study, we have selected fifteen lactoferrin sequences (amino acid) in FASTA format retrieved from NCBI [8] (Table-1). Motif analysis in lactoferrin sequences was conducted by using OOPS model of MEME.. The output of this modal of MEME shows color graphical alignment as well as common regular expression of motifs. On the hand, the block represents start and end point of the amino acid sequences with motif length. This is well known fact that E-value describes the statistical significance of the motif. MEME [9] (ver.4.6.1) usually finds the most statistically significant (low E-value) motifs first. The E-value is an assessment of the probable number of motifs with the given log probability ratio (or higher) along with the same width and site count present, that one would find in a similarly sized set of random sequences. On the other hand, motif width defines that each motif describes a pattern of a fixed with as no gaps are allowed in MEME motifs. In MEME package, sites define the conserved regions present in the particular motifs. Site numbers are the important contributing factor to the construction of the motifs. The information content of the motif (In bits), is equal to the sum of the uncorrected information content, R (), in the columns of the LOGO as described in user manual of MEME suite and MEME suites follows position specific probability matrices that specify the probability of each possible letter appearing at each possible position in an occurrence of the motif and are displayed as "sequence LOGOS", containing stacks of letters at each position in the motif. It is to be noted that the total height of the stack is the "information content" of that position in the motif in bits. For identification of motifs in proteins, the categories are based on the biochemical properties of the various amino acids. Further we also analyse motif by using Motif Alignment and Search Tool [10] (MAST ver.4.6.1). . Results and Discussion According to Bailey et al. (2006), by default, MEME looks for up to three motifs, each of which may be present in some or all of the input sequences. MEME chooses the width and number of occurrences of each motif automatically in order to minimize the ‘E-value’ of the motif—the probability of finding an equally well-conserved pattern in random sequences. By default, only motif widths between 6 and 50 are considered, The MEME output is HTML and shows the motifs as local multiple alignments of (subsets of) the input sequences, as well as in several other formats. ‘Block diagrams’ show the relative positions of the motifs in each of the input sequences. After the submission of sequences in query box of MEME, results display in the form of graph and seq will displays in the form of sequence logo or regular expression(Bailey et al., 2006) (Table-2). Motif overview in figure-2 has shown 6.5e-590 E-value of motif one, 5.4e-541 E-value of motif two and 2.4e-515 E-value of motif three.In Results were analyzed on the bases International Journal on Bioinformatics & Biosciences (IJBB) Vol.2, No.4, December 2012 31 of e-value and p-value. Where second one defines about the conserved pattern of motifs and first one describe about the width of the same match. Higher p-value described the best match whereas lower the e-value better the results. E-value is defined as an estimate of the expected number of motifs with the given log likelihood ratio (or higher), and with the same width and site count, that one would find in a similarly sized set of random sequences. After the submission of multiple amino acid sequences to MEME, we find that all the sequences have all three motifs but the starts points of all these motifs are vary sequence to sequence. Figure-3, 5 and 7 represent the number of site which contributing to the construction of the motif. In each protein sequence define the site in colour format. These are shown aligned with each other. Every site is recognized by the name of the sequence where it occurs, the strand, and the Start position in the sequence where the site begins. The sites are listed in order of increasing statistical significance (p-value).In figure-4, 6 and 8 shown the block diagram of each site and represent the motif location. The occurrence of the motif in the protein sequences are shown as coloured blocks on a line. The block one , two and three represent all of fifteen sequences. One figure is printed for each sequence to show all the sites contributing to that motif in that particular sequence and the sequences were listed below in same order as in the input. The motif occurrences shown combined block diagram (Figure-9) might not be closely the similar as those reported in each motif segment because only motifs with a position p-value of 0.0001 that don't overlap other, more significant motif occurrences are shown in combined block.Following on, we were submit our MEME result in MAST (Figure-10).The combined block diagram represent on the bases of E-value. The sequence 1,2,3,5,6,8,9,10,11,12,13 and 14 were shown zero Evalue. Other than Sequence 7, 4 and 15 shown 4e-200, 8.8e-194 and 1.5e-164 E- value (Figure11). The sequence 1 is show higher similarity and sequence 15 show lower similarity in lactoferrin protein sequence. of E-value. The sequence 1,2,3,5,6,8,9,10,11,12,13 and 14 were shown zero E-value. Other than Sequence 7, 4 and 15 shown 4e-200, 8.8e-194 and 1.5e-164 Evalue (Figure-11). The sequence 1 is show higher similarity and sequence 15 show lower similarity in lactoferrin protein sequence. Table-1: Scientific name of different species Sequence No. Scientific Name 1 Homo sapiens 2 Pan troglodytes 3 Macaca cyclopis 4 Oryctolagus cuniculus 5 Camelus dromedarius 6 Equus caballus 7 Mus musculus 8 Sus scrofa 9 Ovis aries 10 Capra hircus 11 Bos taurus 12 Bos indicus x Bos taurus 13 Bos indicus 14 Bos grunniens 15 Rattus norvegicus International Journal on Bioinformatics & Biosciences (IJBB) Vol.2, No.4, December 2012 32 Table-2: motif information with sequence logo and regular expression Figure-2: Conserved pattern of Lactoferrin Figure-3: Site of Block one Figure-4: Block One Show the Motif Location in each Lactoferrin sequences Sr . N o. Mot if no. Widt h E Valu e Sit es Sequence logo Regular expression 1 1 50 6.5e590 15 TWNS[LV][KR][GD]K KSCHTAVDRTAG WNIPMGL[LI][FVA] NQTGSC[AK]FDE [FY]FSQSCAPG[AS]D 2 2 50 5.4e541 15 [QR]THYYAVAVVK KG[SG][NS]FQL[ND] [DE]LQG[LR]KSCHT GLGR [ST]AGW [NI][IV]P[IM]G[IT]LR P[FY]L[NS]W 3 3 50 2.4e515 15 FG[KR]NG][KS][DNR ]CP[DG][KE][FCLF] [KQR]S[EK]TKNLLF NDNTECLA[KR]L[G QH] G[KR][TP]TYE[KE]Y LG[TP][EQ]YV[TA] International Journal on Bioinformatics & Biosciences (IJBB) Vol.2, No.4, December 2012 33 Figure-5: Site of Block Two Figure-6: Block Two Show the Motif Location in each Lactoferrin sequences International Journal on Bioinformatics & Biosciences (IJBB) Vol.2, No.4, December 2012 34 Figure-7: Site of Block Three Figure-8: Block Three Show the Motif Location in each Lactoferrin sequences International Journal on Bioinformatics & Biosciences (IJBB) Vol.2, No.4, December 2012 35 Figure- 9: Combined block diagram show the Motif location of each block Figure-10: Submit motifs in MAST Figure-11:Block diagram show top scoring sequence International Journal on Bioinformatics & Biosciences (IJBB) Vol.2, No.4, December 2012 36 Conclusion At last,Our research explain that using multiple motifs gives much better database search results than using single motifs. Multiple motifs contain more information quality of the protein family than do single motifs.MEME easily accessible tobiologists who want to analyze their own sequences ofnucleic acids and proteins.This study suggest that lactoferrin sequence of different species show same conserver region. When these species were originate from different ancestor and different region. On the base of our result we assumed that lactoferrin illustrate similar function in all species. The MAST result also prove that lactoferrin have play same function in these species but their percentage is differ species to species. Homo sapiens contain higher concentration of lactoferrinwith 0.0 E-value and sequence15 Rattusnorvegicuswith E-value 1.5e164 have low concentration.As stated above MEMEdescribes that although lactoferrin present in different source of origin,they contains common patterns of amino acids. It is again noted that motifs may overlap withone another due to the reason of commonconsensus patterns. Reference 1. Sorensen, M., Sorensen, S.P.L., (1939). The proteins in whey. C. R. Lab. Carlsberg, 23, 55–99. 2. Adlerova, L., Bartoskova, A. and Faldyna, M. (2008), Lactoferrin: a review. Veterinarni Medicina, 53: 457-468. 3. Baker, E.N., Baker, H.M., Kidd, R.D.,(2002). Lactoferrin and transferrin: Functional variations on a common structural framework. Biochem.Cell Biol.,80, 27-34.PMID: 11908640. 4. Baker, E.N., Baker, H.M., (2005). Molecular structure, binding properties and dynamics of lactoferrin. Cellular and Molecular Life Sciences, 62, 2531–2539.PMID: 16261257. 5. Bailey, T.L., Elkan, C.,(1995). The value of prior knowledge in discovering motifs with MEME.Molecular biology. 3, 21–29. PMID: 7584439. 6. Bailey TL, Williams N, Misleh C, Li WW.(2006) Meme: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res.,34, W369–W373. PMID: 16845028. 7. Javed A. Khan, Pravindra Kumar, M. Paramasivam, Raghvendra S. Yadav, Mohan S. Sahani, Sujata Sharma, Srinivasan A. , Singh, Tej P., (2001). Camel lactoferrin, a transferrin-cumlactoferrin: crystal structure of camel apolactoferrin at 2.6 Å resolution and structural basis of its dual role. Journal of Moecluar Biology, Vol.309, issue 3,751-761. 8. http://www.ncbi.nlm.nih.gov/ 9. http://meme.nbcr.net/meme4_6_1/cgi-bin/meme.cgi 10. http://meme.nbcr.net/meme4_6_1/cgi-bin/mast.cg
Remarks on the conjectures of Capparelli, Meurman, Primc and Primc
Get PDFIn a sequence of two papers, S. Capparelli, A. Meurman, A. Primc, M. Primc
(CMPP) and then M. Primc put forth three remarkable sets of conjectures,
stating that the generating functions of coloured integer partition in which
the parts satisfy restrictions on the multiplicities admit simple infinite
product forms. While CMPP related one set of conjectures to the principally
specialised characters of standard modules for the affine Lie algebra
, finding a Lie-algebraic interpretation for the remaining
two sets remained an open problem. In this paper, we use the work of Griffin,
Ono and the fourth author on Rogers-Ramanujan identities for affine Lie
algebras to solve this problem, relating the remaining two sets of conjectures
to non-standard specialisations of standard modules for
and . We also use their work to formulate conjectures
for the bivariate generating function of one-parameter families of CMPP
partitions in terms of Hall-Littlewood symmetric functions. We make a detailed
study of several further aspects of CMPP partitions, obtaining (i) functional
equations for bivariate generating functions which generalise the well-known
Rogers-Selberg equations, (ii) a partial level-rank duality in the
case, and (iii) (conjectural) identities of the
Rogers-Ramanujan type for .Comment: 37 page
To NER or Not to NER? A Case Study of Low-Resource Deontic Modalities in EU Legislation
No full textDeontic modality (obligation, permission, prohibition) in legal documents can convey critical information, and identification of deontic modalities is often performed using Natural Language Processing (NLP) techniques as a 'Deontic Modality Classification' (DMC) text classification task. As deontic modalities in legal text are not mutually exclusive, a key challenge with DMC is that it classifies the provided text into a single modality while in reality it might have multiple deontic modalities. To address this, this study analyzes the feasibility of performing deontic modality identification as a Named Entity Recognition (NER) task over DMC task approaches in a low-resource data setting with EU legislation. Low-resource NLP approaches can offer solutions to tackle the problem of scarce data. In this paper, we use a rule-based approach with modal verbs and a Decision Tree classifier for DMC task. For NER, we utilize Conditional Random Fields (CRFs) in a low-resource setting and report on the reliability and precision for identification of deontic modality. Our experiments reveal that simpler models, like decision trees, out perform larger models in the low-resource setting of DMC obtaining macro-F1 score of 0.83. For the NER task, the CRF models show consistent performance for 'obligation' labels with an F1-score of 0.51 but have wavering results for other classes with a max F1-score of 0.26 for 'permission', and 0.08 for 'prohibition'
Results for 14 articles with human annotations provided by both authors and non-authors, and computational predictions provided by the CRF (SIS) model.
No full text<p>(a) Contingency table of human annotations.</p><p>(b) Per-article average recall, precision and F1 score of non-author human annotations and computational predictions using author annotations as ground truth.</p
The American Society of Pain and Neuroscience (ASPN) Evidence-Based Clinical Guideline of Interventional Treatments for Low Back Pain
No full textDawood Sayed,1 Jay Grider,2 Natalie Strand,3 Jonathan M Hagedorn,4 Steven Falowski,5 Christopher M Lam,1 Vinicius Tieppo Francio,6 Douglas P Beall,7 Nestor D Tomycz,8 Justin R Davanzo,9 Rohit Aiyer,10 David W Lee,11 Hemant Kalia,12,13 Soun Sheen,13 Mark N Malinowski,14,15 Michael Verdolin,16 Shashank Vodapally,17 Alexios Carayannopoulos,18– 20 Sameer Jain,21 Nomen Azeem,22,23 Reda Tolba,24,25 George C Chang Chien,26,27 Priyanka Ghosh,28 Anthony J Mazzola,29 Kasra Amirdelfan,30 Krishnan Chakravarthy,31,32 Erika Petersen,33 Michael E Schatman,34,35 Timothy Deer36 1Department of Anesthesiology and Pain Medicine, The University of Kansas Medical Center, Kansas City, KS, USA; 2University of Kentucky, Lexington, KY, USA; 3Interventional Pain Management, Mayo Clinic, Scottsdale, AZ, USA; 4iSpine Pain Physicians, Maple Grove, MN, USA; 5Functional Neurosurgery, Neurosurgical Associates of Lancaster, Lancaster, PA, USA; 6Department of Rehabilitation Medicine, University of Kansas Medical Center, Kansas City, KS, USA; 7Comprehensive Specialty Care, Edmond, OK, USA; 8AHN Neurosurgery, Allegheny General Hospital, Pittsburgh, PA, USA; 9AHN Neurosurgery, Forbes Hospital, Monroeville, PA, USA; 10Interventional Pain Management and Pain Psychiatry, Henry Ford Health System, Detroit, MI, USA; 11Physical Medicine & Rehabilitation and Pain Medicine, Fullerton Orthopedic Surgery Medical Group, Fullerton, CA, USA; 12Rochester Regional Health System, Rochester, NY, USA; 13Department of Physical Medicine & Rehabilitation, University of Rochester, Rochester, NY, USA; 14Adena Spine Center, Adena Health System, Chillicothe, OH, USA; 15Ohio University Heritage College of Osteopathic Medicine, Athens, OH, USA; 16Anesthesiology and Pain Medicine, Pain Consultants of San Diego, San Diego, CA, USA; 17Physical Medicine and Rehabilitation, Michigan State University, East Lansing, MI, USA; 18Department of Physical Medicine and Rehabilitation, Rhode Island Hospital, Newport Hospital, Lifespan Physician Group, Providence, RI, USA; 19Comprehensive Spine Center at Rhode Island Hospital, Newport Hospital, Providence, RI, USA; 20Neurosurgery, Brown University, Providence, RI, USA; 21Interventional Pain Management, Pain Treatment Centers of America, Little Rock, AR, USA; 22Department of Neurology, University of South Florida, Tampa, FL, USA; 23Florida Spine & Pain Specialists, Riverview, FL, USA; 24Pain Management, Cleveland Clinic, Abu Dhabi, United Arab Emirates; 25Anesthesiology, Cleveland Clinic Lerner College of Medicine, Cleveland, OH, USA; 26Pain Management, Ventura County Medical Center, Ventura, CA, USA; 27Center for Regenerative Medicine, University Southern California, Los Angeles, CA, USA; 28Remedy Medical Group, San Francisco, CA, USA; 29Mount Sinai Health System, New York City, NY, USA; 30IPM Medical Group, Inc., Walnut Creek, CA, USA; 31Division of Pain Medicine, Department of Anesthesiology, University of California San Diego, San Diego, CA, USA; 32Va San Diego Healthcare, San Diego, CA, USA; 33Department of Neurosurgery, University of Arkansas for Medical Science, Little Rock, AR, USA; 34Department of Anesthesiology, Perioperative Care, and Pain Medicine, NYU Grossman School of Medicine, New York, New York, USA; 35Department of Population Health - Division of Medical Ethics, NYU Grossman School of Medicine, New York, New York, USA; 36The Spine and Nerve Center of the Virginias, Charleston, WV, USACorrespondence: Dawood Sayed, The University of Kansas Health System, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA, Tel +1 913-588-5521, Email [email protected]: Painful lumbar spinal disorders represent a leading cause of disability in the US and worldwide. Interventional treatments for lumbar disorders are an effective treatment for the pain and disability from low back pain. Although many established and emerging interventional procedures are currently available, there exists a need for a defined guideline for their appropriateness, effectiveness, and safety.Objective: The ASPN Back Guideline was developed to provide clinicians the most comprehensive review of interventional treatments for lower back disorders. Clinicians should utilize the ASPN Back Guideline to evaluate the quality of the literature, safety, and efficacy of interventional treatments for lower back disorders.Methods: The American Society of Pain and Neuroscience (ASPN) identified an educational need for a comprehensive clinical guideline to provide evidence-based recommendations. Experts from the fields of Anesthesiology, Physiatry, Neurology, Neurosurgery, Radiology, and Pain Psychology developed the ASPN Back Guideline. The world literature in English was searched using Medline, EMBASE, Cochrane CENTRAL, BioMed Central, Web of Science, Google Scholar, PubMed, Current Contents Connect, Scopus, and meeting abstracts to identify and compile the evidence (per section) for back-related pain. Search words were selected based upon the section represented. Identified peer-reviewed literature was critiqued using United States Preventive Services Task Force (USPSTF) criteria and consensus points are presented.Results: After a comprehensive review and analysis of the available evidence, the ASPN Back Guideline group was able to rate the literature and provide therapy grades to each of the most commonly available interventional treatments for low back pain.Conclusion: The ASPN Back Guideline represents the first comprehensive analysis and grading of the existing and emerging interventional treatments available for low back pain. This will be a living document which will be periodically updated to the current standard of care based on the available evidence within peer-reviewed literature.Keywords: back pain, intervention, clinical guideline, spinal cord stimulation, minimally invasive spine procedure, lumbar disorder, epidural steroid injection, radiofrequency ablatio
