cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Ologamasus Berlese
Creators: name: Moraes, De
Publisher: name: Zenodo
Year: 2007
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Mesostigmata
Ologamasidae
Ologamasus

description: Key to species of Ologamasus Berlese (females)
1 Ventrianal shield totally fused with dorsal shield, except for lateral area .................................................. 2
1´Ventrianal shield fused with dorsal shield only by a narrow area behind anus ........................................... 5
2 Dorsal setae distally expanded.................................................................................................................... 3
2´Dorsal setae setiform ...................................................................................... O. simplicior (Berlese, 1914)
3 Tectum with only one pointed prong; sternal shield with parallel, longitudinal striation ............................ .......................................................................................................................... O. aberrans (Berlese, 1888)
3´Tectum with a central larger, and lateral, shorter, prongs; sternal shield reticulate .................................... 4
4 Seta Zv4 (seta ISv of Lee, 1970) present; setae s1 and s2 absent; tectum with 2 pairs of lateral prongs in addition to the central prong ...................................................................................... O. foliatus Karg, 1976
4´Seta Zv4 absent; setae s1 and s2 present; tectum with one pair of lateral prongs in addition to the central prong ............................................................................................................................... O. cananeiae sp. n.
5 Sternal shield with longitudinal striae ............................................................. O. membranosus Karg, 1976
5´Sternal shield without longitudinal striae ................................................................................................... 6
6 Ventrianal shield reticulate ............................................................................. O. striolatosimilis Karg, 1976
6´Ventrianal shield smooth ................................................................................... O. striolatus (Berlese, 1916)
description: Published as part of Moraes, De, 2007, A new species of Ologamasus (Acari: Ologamasidae) from Brazil, pp. 61-68 in Zootaxa 1462 on page 67, DOI: 10.5281/zenodo.176465
Additional file 1: Figure S1. of Genome-wide methylation profiling of ovarian cancer patient-derived xenografts treated with the demethylating agent decitabine identifies novel epigenetically regulated genes and pathways
Creators: name: Tushar Tomar
name: Jong, Steven De
name: Alkema, Nicolette
name: Rieks Hoekman
name: Meersma, Gert
name: Klip, Harry
name: Zee, Ate
name: G. Wisman
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Plant Biology

description: a Clinicopathological features of transplanted HGSOC tumors. b Representation of patients and their corresponding PDX tumor samples used in this study. c All preprocessing of 450 K data of each sample. d DNA methylation level of each sample type according to HIL CpG classes [38] for PDX-36, -37, and -56 for all generation tumors (F0, F1, F2, and F3), p
Amorphinopsis
Creators: name: Rützler, Klaus
name: Piantoni, Carla
name: Van, Rob W. M.
name: Díaz, Cristina
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Porifera
Demospongiae
Halichondrida
Halichondriidae
Amorphinopsis

description: Amorphinopsis sp.
Synonymy and references. Nailondria de Laubenfels, 1954: 182, fig. 121. Amorphinopsis Carter, 1887: Erpenbeck and van Soest (2002): 790, fig. 1.
Material. USNM 1229083, Curlew Bank forereef cave, ceiling, 1 m from entrance, 20 m; C. Piantoni and M. Parrish col. 22 Aug 2012.
Comparative material studied: USNM 23083 Nailondria maza de Laubenfels, 1954 (holotype, West-Central Pacific).
External morphology. Filling cavities and crevices in coral rock, 3–15 mm below the substratum surface. No epilithic structures were seen except small, white tubules and fistules that turned out to belong to a co-occurring Siphonodictyon. From calcareous fragments and pitting of the substratum it seems that the sponge is excavating. Color white.
Skeleton structure. Cavernous tissue filling the rock cavities, including densely packed spicules without orientation (criss-cross). No spongin visible on a histological section, only a variety of cells, including small (18 µm) choanocyte chambers.
Spicules. Strongyles of great size range but may be lumped into three size classes. Most are bent more or less sharply, once, twice, or three times in the same or in opposing directions (wavy). Some of the thinner ones show oxeote modifications, but are rare and assumed to be developmental stages rather than a different spicule type. Strongyles I: 430–1020 x 20–48 (789 x 29) µm; II: 440–940 x 6–15 (620 x 10) µm; III: 240–420 x 5–10 (343 x 7) µm.
Ecology. Inhabiting and (possibly) excavating cavities in coral rock of a framework cave ceiling, 20 m. The sponge is closely associated with other sponges, that is, specimens of Agelas sventres and Siphonodictyon coralliphagum.
Distribution. Belize.
Comments. Our material does not show ectosomal differentiation, but the choanosomal skeleton agrees with the definition of Amorphinopsis and the type species of its synonym Nailondria, N. maza de Laubenfels, which however has oxeas or strongyloxeas and styles for spicules (Erpenbeck and van Soest, 2002). The only other Amorphinopsis known from the Atlantic Ocean is A. atlantica Carvalho, Hajdu, Mothes and van Soest, which is usually grayish green and has oxeas and styles as spicules.
description: Published as part of Rützler, Klaus, Piantoni, Carla, Van, Rob W. M. & Díaz, Cristina, 2014, Diversity of sponges (Porifera) from cryptic habitats on the Belize barrier reef near Carrie Bow Cay, pp. 1-129 in Zootaxa 3805 (1) on pages 74-75, DOI: 10.11646/zootaxa.3805.1.1, http://zenodo.org/record/249983
Additional file 4: Figure S3. of Genome-wide methylation profiling of ovarian cancer patient-derived xenografts treated with the demethylating agent decitabine identifies novel epigenetically regulated genes and pathways
Creators: name: Tushar Tomar
name: Jong, Steven De
name: Alkema, Nicolette
name: Rieks Hoekman
name: Meersma, Gert
name: Klip, Harry
name: Zee, Ate
name: G. Wisman
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences

description: a, b Validation of global methylation using bisulfite pyrosequencing of LINE-1 (a) and ALU-Yb8 (b) in PDX samples treated with either vehicle or cisplatin (4 mg/kg/week) for 4 weeks (n = 3 mice per group). Each bar represents average methylation (%) ± SD of five CpG sites for LINE-1 and ALU-Yb8 in the indicated PDX samples. c, d Effect of cisplatin and carboplatin treatment on global methylation in various ovarian cancer cell lines using bisulfite pyrosequencing LINE-1 (c) and ALU-Yb8 (d). Each bar represents average methylation (%) ± SD of five CpG sites for LINE-1 and ALU-Yb8 in the indicated cell lines. Each cell line was treated with either cisplatin or carboplatin at the indicated dose for 72 h. (PDF 225 kb)
Topsentia bahamensis Diaz, Pomponi
Creators: name: Rützler, Klaus
name: Piantoni, Carla
name: Van, Rob W. M.
name: Díaz, Cristina
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Porifera
Demospongiae
Halichondrida
Halichondriidae
Topsentia
Topsentia bahamensis

description: Topsentia bahamensis Diaz, Pomponi & van Soest, 1993
(Figure 2 b)
Synonymy and references. Topsentia bahamensis Diaz, Pomponi & van Soest, 1993: 290, fig. 11, 14.
Material. USNM 1229089, Curlew Bank forereef cave, 20 m; C. Piantoni col. 2 Jul 2007. USNM 1229090, Carrie Bow Cay forereef crevice, on wall, 25 m; M. C. Diaz col. 8 Sep 2009. USNM 1229091, Curlew Bank, forereef cave, ceiling, 1 m from entrance, 20 m; C. Piantoni and M. Parrish col. 22 Aug 2012. USNM 1229092, Curlew Bank forereef cave, 18 m; C. Piantoni and M. Parrish col. 25 Aug 2012.
External morphology. A whitish knob, plate, or cup protruding from the cave wall, also penetrating crevices in rock, up to 3 cm thick, 9–12 cm maximum width by length. Very hard, brittle consistency, macroscopically no obvious oscula or ostia. Color white, to off-white (grayish to brown), with yellow-orange symbiotic zoanthids (Parazoanthus swiftii) covering part of the surface.
Skeleton structure. Spicules densely packed in criss-cross fashion throughout the body, generally directed in some angle toward the sponge surface. Many of the smaller spicules tend to be near or in the ectosome, more or less tangential.
Spicules. Fusiform oxeas, straight or curved, with sharp points. Size varies greatly but two main classes can be distinguished, I: 540–890 x 15–32 (721 x 23) Μm; II: 115–300 x 3–12 (243 x 8) Μm
Ecology. On deep reef and rock bottoms, more shallow in caves, 18– 160 m.
Distribution. Bahamas and Caribbean.
Comments. The type material was collected my manned submersibles from deep-reef areas in the Bahamas (40–160 m). These are the first samples from shallower cave habitats.
description: Published as part of Rützler, Klaus, Piantoni, Carla, Van, Rob W. M. & Díaz, Cristina, 2014, Diversity of sponges (Porifera) from cryptic habitats on the Belize barrier reef near Carrie Bow Cay, pp. 1-129 in Zootaxa 3805 (1) on pages 75-76, DOI: 10.11646/zootaxa.3805.1.1, http://zenodo.org/record/249983
Additional file 2: Figure S2. of Genome-wide methylation profiling of ovarian cancer patient-derived xenografts treated with the demethylating agent decitabine identifies novel epigenetically regulated genes and pathways
Creators: name: Tushar Tomar
name: Jong, Steven De
name: Alkema, Nicolette
name: Rieks Hoekman
name: Meersma, Gert
name: Klip, Harry
name: Zee, Ate
name: G. Wisman
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Developmental Biology
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences

description: a Systematic representation of F3 PDXs and their treatment schedule. b Global distribution of 450 K methylation probes of the raw data of PDX-36, untreated or treated, tumor samples. c DNA methylation level of each sample type according to HIL CpG classes [38] for PDX-36, untreated or treated tumor samples; *p  ﻿0.﻿﻿1)﻿ of SKOV3 cells after DAC treatment. f Comparative analysis of significantly differentially methylated CpG probes (percentages) in ovarian cancer patients [43] and PDX tumors treated with DAC in comparison with untreated control ones. g Supervised clustering analysis of significantly genome-wide demethylated sites (p
ABCE Student-led Research Symposium 2024 Programme
Creators: name: Dawes, George
name: Sodha, Kuldeep Singh Sodha
Publisher: name: Loughborough University
Year: 2024
Subjects: classificationCode: 4005
subject: Civil engineering
subject: FOS: Civil engineering
classificationCode: 400501
subject: Architectural engineering
classificationCode: 400502
subject: Civil geotechnical engineering
classificationCode: 400504
subject: Construction engineering
classificationCode: 400508
subject: Infrastructure engineering and asset management
classificationCode: 400510
subject: Structural engineering
classificationCode: 400512
subject: Transport engineering
classificationCode: 400599
subject: Civil engineering not elsewhere classified
classificationCode: 400513
subject: Water resources engineering

description: This supplementary document was issued as a handbook or programme of events and presentations at the 2nd annual Student-led Research Symposium in the School of Architecture, Building and Civil Engineering (ABCE). Issued and run by the ABCE Hub Committee, the event is a celebration and promotion of the research done by early-career researchers working across disciplines towards Creating Better Futures in the Built Environment across Loughborough University.Hosted in the Sir Frank Gibb Building, the event was well attended with over 60 attendees including 40 Doctoral researchers from the school alone, alongside technical and support staff and members of the senior leadership team.The day also featured support from C-DICE (The Centre for Postdoctoral Development in Infrastructure, Cities and Energy) - hosted in ABCE, alongside the wellbeing and careers teams from the central university.We were fortunate to have been provided with excellent keynote talks about the importance of research and innovation, research culture and internationally renowned research in the built environment from:Professor Steven Christie, Associate Pro Vice Chancellor (Doctoral College), Loughborough UniversityProfessor Daniel Parsons, Pro Vice Chancellor for Research and Innovation (PVCRI), Loughborough UniversityProfessor Shimul Haque, Director of Smart Transport Safety Research Lab (STSRLab), Queensland University of Technology (QUT), Australia
Agelas citrina Gotera & Alcolado 1987
Creators: name: Rützler, Klaus
name: Piantoni, Carla
name: Van, Rob W. M.
name: Díaz, Cristina
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Porifera
Demospongiae
Agelasida
Agelasidae
Agelas
Agelas citrina

description: Agelas citrina Gotera & Alcolado, 1987
Synonymy and references. Agelas citrina Gotera & Alcolado, 1987: 2, figs 1-2; Parra-Velandia et al., 2014: 331, figs. 1C, 1G, 13 (including synonymy).
Material. USNM 1191322, Carrie Bow Cay forereef slope, 15–35 m; K. Ruetzler, col. 26 Apr 1974. USNM 1191323, Carrie Bow Cay forereef slope, 21 m; C. Piantoni, col. 27 Jun 2007. USNM 1191324, Carrie Bow Cay forereef slope, 21 m; C. Piantoni, col. 2 Jul 2007. USNM 1229096, Curlew Bank forereef slope (wall), small cave, 20 m; C. Piantoni and M. Parrish, col. 23 Aug 2012.
External morphology. Small (2–6 cm diameter) cushions with smooth or knobby surface structure and few (1–3) circular oscular openings of 2–4 mm diameter. The color is yellow to yellow orange.
Skeleton structure. As usual in this genus, the skeleton consists of coarse, ascending primary and interconnecting secondary and tertiary spongin fibers. The fibers are partly cored, partly echinated by the spicules.
Spicules. Characteristic acanthostyles with verticillated spines. Spicules in this species are the longest of all agelasids examined. They measure148–360 x 18–20 (226 x 19) Μm with 14–29 (17) whorls of spines. The longer spicules tend to show a reduction of spine length and density along the center portion of the shaft.
Ecology. Collected from lower surfaces of platy coral rock (Agaricia) and inside a framework cave, 15– 35 m.
Distribution. Common on reefs throughout the Caribbean region (Parra-Velandia et al., 2014)
Comments. The length of spicules in our material exceeds that of all specimens previously studied in Belize and elsewhere in the Caribbean (Parra-Velandia et al., 2014). Unlike these authors, we find acanthostyles with reduced spines along the middle of the shaft, a characteristic thought to be unique to Agelas schmidti (Wilson, 1902) and A. sventres (Lehnert & van Soest, 1996) (see below). However, examining illustrations and specimens of other, not yellow-orange species, for instance, Agelas conifera (Schmidt, 1870) (Wiedenmayer, 1977), we find similar spine reductions. This raises the possibilities that the morphological aberration is age- or environmentrelated and not a useful taxonomic feature.
description: Published as part of Rützler, Klaus, Piantoni, Carla, Van, Rob W. M. & Díaz, Cristina, 2014, Diversity of sponges (Porifera) from cryptic habitats on the Belize barrier reef near Carrie Bow Cay, pp. 1-129 in Zootaxa 3805 (1) on page 76, DOI: 10.11646/zootaxa.3805.1.1, http://zenodo.org/record/249983
Additional file 7: Figure S3. of Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis
Creators: name: Cloete, Ruben
name: Ekow Oppon
name: Murungi, Edwin
name: Wolf-Dieter Schubert
name: Christoffels, Alan
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases
subject: 60506 Virology
subject: Computational Biology

description: KEGG metabolic pathway map for Nicotinate and Nicotinamide metabolism in M. tuberculosis H37rV strain. Rv2421c or nadD selected for investigation is shown in red highlighted box and involved in step 2.7.7.18 of this specific pathway. Known drug resistance gene Rv2043c or pncA is shown in blue highlighted box and involved in step 3.5.1.19 of this pathway. M. tuberculosis specific genes are coloured in green. (PDF 106 kb)
Agelas dispar Duchassaing & Michelotti 1864
Creators: name: Rützler, Klaus
name: Piantoni, Carla
name: Van, Rob W. M.
name: Díaz, Cristina
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Porifera
Demospongiae
Agelasida
Agelasidae
Agelas
Agelas dispar

description: Agelas dispar Duchassaing & Michelotti, 1864
Synonymy and references. Agelas dispar Duchassaing & Michelotti, 1864: 76, pl. 15 fig. 1; Parra-Velandia et al., 2014: 306, figs. 1D, 2, 15C, 15E (including synonymy).
Material. USNM 1191325, Carrie Bow Cay, North Channel, 6 m; K. Ruetzler, col. 23 May 1979. USNM 1191326, 1191327, Curlew Bank forereef, framework cave, 20 m; C. Piantoni, col. 27 Jun 2007. USNM 1229097, Curlew Bank forereef slope (wall), small cave, 20 m; C. Piantoni & M. Parrish, col. 23 Aug 2012.
External morphology. Massive, thickly encrusting, or lobate, 10–20 cm in diameter. One specimen (USNM 1191327) growing at the ceiling of a cave had brain-like ridges and depressions. Porous to cavernous interior. Oscula scattered, 2-4 mm in diameter, a few merged, key-hole-like. Color is grayish to reddish brown and brownish orange.
Skeleton structure. Interconnected spongin fibers, cored and echinated by spicules.
Spicules. Acanthostyles with spines in equidistant whorls. They measure 110–210 x 10–25 (158 x 18) Μm, with 7–17 (12) whorls of spines; no reduced spines were noted.
Ecology. Found under coral rock and on ceiling and walls of framework caves, 6– 20 m.
Distribution. The species has been reported from several locations in the eastern and southern Caribbean (Parra-Velandia et al., 2014).
Comments. The brain-like morphology of specimen USNM 1191327 is unusual but might have been caused by healed fish or sea turtle bites. Spicule dimensions and characteristics were very close to those of the other samples.
description: Published as part of Rützler, Klaus, Piantoni, Carla, Van, Rob W. M. & Díaz, Cristina, 2014, Diversity of sponges (Porifera) from cryptic habitats on the Belize barrier reef near Carrie Bow Cay, pp. 1-129 in Zootaxa 3805 (1) on page 77, DOI: 10.11646/zootaxa.3805.1.1, http://zenodo.org/record/249983
Additional file 10: Figure S5. of Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis
Creators: name: Cloete, Ruben
name: Ekow Oppon
name: Murungi, Edwin
name: Wolf-Dieter Schubert
name: Christoffels, Alan
Publisher: name: Figshare
Year: 2016
Subjects: subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: RMSD of the backbone atoms of model Rv1712 (green) and substrate C5P (red) during the 30000Â ps simulation. Generated using Gnuplotv4.2 [41]. (PDF 198 kb)
Generative architectural plan drawings for early design decisions: data grounding and additional training for specific use cases
Creators: name: Choi, Soohyung
name: Kim, Youngchae
name: Nam, Taesik
name: Hong, Seung-Wan
name: Lee, Jin-Kook
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified

description: This study shows the development of models for generating architectural plan drawings to support early design decisions in time – and cost-effective housing projects. Plan drawings are communicated through a combination of visual representations and accompanying textual descriptions. These elements play a crucial role in communicating design specifications to project stakeholders. In particular, by exploring the benefits of early decision-making during the planning phase, this paper explores specific use cases and demonstrates how existing data can be processed for additional training in image-generative models. These models have significantly advanced architectural visualization as a synthetic medium for visual representation. The methodology follows a structured approach: (1) evaluating the efficacy of default base models in generating plan drawings to determine the need for additional data grounding and training; (2) defining the scope of research through a theoretical examination of design requirements for specific use cases for training; (3) systematizing and generalizing the additional training process including data grounding (preparing and preprocessing data suitable for specific use cases), optimizing hyperparameters, and training (implementing models capable of generating images with the desired quality); and (4) demonstrating the proposed applications using the additional training model, specifically within the use case of ‘Korean urban residential housing projects’. This methodology aims to improve the efficiency of design communication during the initial stages of architectural design. By doing so, it enables more effective and strategic planning across a wide range of use cases and scenarios.
Additional file 12: Figure S7. of Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis
Creators: name: Cloete, Ruben
name: Ekow Oppon
name: Murungi, Edwin
name: Wolf-Dieter Schubert
name: Christoffels, Alan
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: RMS fluctuations of all CÎą residues for Rv1712 over the 30000Â ps simulation. (PDF 55 kb)
Additional file 6: Figure S2. of Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis
Creators: name: Cloete, Ruben
name: Ekow Oppon
name: Murungi, Edwin
name: Wolf-Dieter Schubert
name: Christoffels, Alan
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Marine Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Computational Biology

description: KEGG metabolic pathway map for Oxidative phosphorylation in M. tuberculosis H37rV strain. Rv2984 or ppk selected for investigation is shown in blue highlighted box and involved in step 2.7.4.1 of this specific pathway. Rv2194 or qcrC selected for investigation is shown in the red highlighted box. Both Rv1305 (atpE) and Rv1311 (atpC) selected for investigation are shown in brown highlighted box and involved in step 3.6.3.14 of this specific pathway. Rv2195 or qcrA selected for investigation is shown in the yellow highlighted box involved in cytochrome C reductase. Rv1456c or COX15 selected for investigation is shown in the magenta highlighted box involved in cytochrome C oxidase. Rv1622c or CydB selected for investigation is shown in the light blue highlighted box involved in cytochrome C oxidase. Known drug resistance gene Rv1854c or ndh is shown in orange highlighted box and involved in step 1.6.99.3 of this pathway. M. tuberculosis specific genes are coloured in green. (PDF 157 kb)
Additional file 11: Figure S6. of Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis
Creators: name: Cloete, Ruben
name: Ekow Oppon
name: Murungi, Edwin
name: Wolf-Dieter Schubert
name: Christoffels, Alan
Publisher: name: Figshare
Year: 2016
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: The variation in total (green) and potential energy (red) for the Rv1712-C5P complex during the 30000Â ps simulation. Generated using Gnuplotv4.2 [41]. (PDF 69 kb)
Topsentia ophiraphidites
Creators: name: Rützler, Klaus
name: Piantoni, Carla
name: Van, Rob W. M.
name: Díaz, Cristina
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Porifera
Demospongiae
Halichondrida
Halichondriidae
Topsentia
Topsentia ophiraphidites

description: Topsentia ophiraphidites (de Laubenfels, 1934)
Synonymy and references. Topsentia ophiraphidites (de Laubenfels, 1934): Diaz, van Soest & Pomponi, 1993: 290, figs. 6, 12..
Material. SNM 1229093, Carrie Bow Cay south back reef, Acropora palmata coral plate in exposed zone behind reef crest, 1 m; K. Ruetzler col. 6 Mar 2006. USNM 1229094, Curlew Bank forereef cave, 20 m; C. Piantoni col. 28 Jun 2007. USNM 1229095, Curlew Bank forereef cave, 20 m; C. Piantoni col. 29 Jun 2007.
External morphology. Small cushion to conical projection with lobate extensions, 35 mm long, 15 mm diameter. Lumpy surface, hard consistency. Color gray to purplish pink..
Skeleton structure. Large spicules in dense but confused-radial arrangement, smaller spicules in between but in highest concentration near the sponge surface.
Spicules. Fusiform, curved oxeas, some with styloid modifications, in great size range. Three size classes can be distinguished, but separation is not always easy because there are many transitions; the smallest kind often shows angular bends (kinks) or is wavy; I: 650–1050 x 17–35 (822 x 22) Μm; II: 420–580 x 8–20 (504 x 12) Μm; III: 190–360 x 4–9 (289 x 7) Μm.
Ecology. Occurs under shallow coral rubble and in forereef caves, 1–20 m; elsewhere reported from 40 m and below.
Distribution. Caribbean and off northeastern Brazil.
description: Published as part of Rützler, Klaus, Piantoni, Carla, Van, Rob W. M. & Díaz, Cristina, 2014, Diversity of sponges (Porifera) from cryptic habitats on the Belize barrier reef near Carrie Bow Cay, pp. 1-129 in Zootaxa 3805 (1) on page 76, DOI: 10.11646/zootaxa.3805.1.1, http://zenodo.org/record/249983
Additional file 14: Figure S9. of Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis
Creators: name: Cloete, Ruben
name: Ekow Oppon
name: Murungi, Edwin
name: Wolf-Dieter Schubert
name: Christoffels, Alan
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Superimposition of lowest DOPE score models for the initial and newly generated structures. The blue model represents the initial model without 3R20 used as a template while the red model consist of 3R20 used as a template for model construction. Ligands SO4 and CMP are shown as sticks. RMSD = 0.387 Å. (PDF 33 kb)
Cortical and subcortical gray matter volume and cognitive impairment in Parkinson’s disease
Creators: name: Moradi, Naser
name: Shahidi, Siamak
name: Ahmadpanah, Mohammad
name: Farashi, Sajjad
name: Roshanaei, Ghodratollah
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Science Policy
subject: Mental Health

description: This study investigated the cortical and subcortical gray matter volume (GMV) and cognitive impairment (CI) in patients with Parkinson’s disease (PD). In this study, T1-weighted magnetic resonance imaging of the cortex and subcortex was conducted on 92 individuals diagnosed with PD and 92 healthy controls (HCs). PD patients were divided into three groups: PD with normal cognition (PD-NC, n = 21), PD with mild CI (PD-MCI, n = 43), and PD with severe CI (PD-SCI, n = 28). Differences in GMV were analyzed using voxel-based morphometry (VBM). Statistical analysis was conducted using SPSS 26. Compared to the HCs, the PD-NC group exhibited reduced GMV in the right middle frontal gyrus (RMFG), right precentral gyrus medial segment (RPGMS), left temporal pole, and right superior frontal gyrus medial segment (RSFGMS). In comparison to the HC and PD-NC groups, the PD-MCI and PD-SCI groups (respectively) demonstrated significant decreases in GMV in the right caudate, left hippocampus, left thalamus, RMFG, RPGMS, RSFGMS, and cerebellum (right crus I and left crus I). The regression analysis indicated that changes in the GMV of the frontal areas can predict cognitive test outcomes. Compared to HCs, PD patients with CI presented significant volume reductions in the RC, LH, LT, RMFG, RPGMS, RSFGMS, and the right and left crus I regions. Consequently, as average GMV atrophy increased in the specified regions, PD patients exhibited more severe cognitive impairment than the HC group. This may be attributed to the initial pathological loss of frontal GMV (especially in the RMFG and RPGMS regions), which could subsequently lead to subcortical dysfunction.
Agelas sventres Lehnert
Creators: name: Rützler, Klaus
name: Piantoni, Carla
name: Van, Rob W. M.
name: Díaz, Cristina
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Porifera
Demospongiae
Agelasida
Agelasidae
Agelas
Agelas sventres

description: Agelas sventres Lehnert & van Soest, 1996
Synonymy and references. Agelas sventres Lehnert & van Soest, 1996: 65, figs. 6, 22, 55; Parra-Velandia et al., 2014: 334, fig. 14 (including synonymy).
Material. USNM 1191330, Carrie Bow Cay back reef near crest, 0.3 m; inside and underside of A. palmata r ubble; K. Ruetzler, col. 23 Apr 1974. USNM 1191331, Carrie Bow back reef and reef flat, 1 m; in old conch shells; K. Ruetzler & C. Piantoni col. 23 Feb. 2006. USNM 1229100, Curlew Bank, forereef slope (wall), 50-150 cm inside framework cave, ceiling, 20 m; C. Piantoni & M. Parrish, col. 22 Aug 2012.
External morphology. Massive cushions, 6-8 cm in diameter, up to 3 cm thick. Surface smooth, with irregularly dispersed, circular openings, 2–6 mm in diameter. The color is bright orange red, only slightly duller in the cavernous interior.
Skeleton structure. Network of coarse spongin fibers cored and echinated by spicules.
Spicules. Acanthostyles with spines in whorls: 80–220 x 11–18 (152 x 14) Μm, 10–16 (12) whorls of spines. Some spicules, particularly the longer ones, have reduced spines along the center half of the shaft.
Ecology. In the survey area it occurs on lower surfaces of platy coral rock (Acropora palmata) and inside empty conch shells with apex cut off, 1 m or less deep. Elsewhere it is reported from reefs between 5– 30 m.
Distribution. Occurs on reefs throughout the Caribbean region (Parra-Velandia et al., 2014)
Comments. Because of its color, the species can be confused with some specimens of Agelas citrina and A. clathrodes (Schmidt, 1870) but we found that the former is easily distinguished by its substantially longer spicules, the latter by its particularly short acanthostyles (almost one third less than A. sventres); also, we did not encounter A. clathrodes in cave habitats we studied.
description: Published as part of Rützler, Klaus, Piantoni, Carla, Van, Rob W. M. & Díaz, Cristina, 2014, Diversity of sponges (Porifera) from cryptic habitats on the Belize barrier reef near Carrie Bow Cay, pp. 1-129 in Zootaxa 3805 (1) on page 78, DOI: 10.11646/zootaxa.3805.1.1, http://zenodo.org/record/249983
Additional file 9: Figure S4. of Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis
Creators: name: Cloete, Ruben
name: Ekow Oppon
name: Murungi, Edwin
name: Wolf-Dieter Schubert
name: Christoffels, Alan
Publisher: name: Figshare
Year: 2016
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: DOPE score energy profiles graph of the structural model for Rv1712 (red) and templates 1Q3T (green), 1CKE (dark blue), 1KDO (light blue) and 2H92 (purple). Generated using Gnuplotv4.2 [41]. (PDF 68 kb)
Agelas wiedenmayeri Alcolado 1984
Creators: name: Rützler, Klaus
name: Piantoni, Carla
name: Van, Rob W. M.
name: Díaz, Cristina
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Porifera
Demospongiae
Agelasida
Agelasidae
Agelas
Agelas wiedenmayeri

description: Agelas wiedenmayeri Alcolado, 1984
Synonymy and references. Agelas wiedenmayeri Alcolado, 1984: 11, fig 7B, C, 8B; Parra-Velandia et al., 2014: 313, figs. 4, 15F (including synonymy).
Material. USNM 1191332, Carrie Bow Cay forereef cave, 20-28 m; M. C. Diaz col. 8 Sep 2009. USNM 1229101, Curlew Bank forereef slope (wall), framework cave, 18 m; C. Piantoni & M. Parrish, col. 25 Aug 2012.
External morphology. Groups of short tubes or hollow lobes (5–12 cm) protruding from crevices in coral rock. Apical openings of the tubes measure 5–15 mm, on the lobes they are also apical but scattered and small (1–3 mm). Color is brown to reddish brown, cream in the interior of the sponge.
Skeleton structure. Interconnected spongin fibers, cored and echinated by spicules.
Spicules. Acanthostyles with spines in equidistant whorls: 88–200 x 8–18 (139 x 14) Μm, 9–15 (12) whorls of spines.
Ecology. Found under platy coral rock and in framework caves, 5– 28 m.
Distribution. The species seems to occur throughout the Caribbean region.
Comments. This is the species erroneously described as Agelas schmidti, from the Bahamas (Wiedenmayer (1977: 13, fig. 137; pl. 27, fig. 1). We confirmed the identity with our material by examining a microscope slide made from a fragment of the holotype of A. wiedenmayeri, generously provided by P. Alcolado (USNM 39266); spicule dimensions and number of whorls are nearly identical. A slight reduction of spine size in the middle of some of the largest spicules was evident but far less obvious than in the real A. schmidti and in A. sventres.
description: Published as part of Rützler, Klaus, Piantoni, Carla, Van, Rob W. M. & Díaz, Cristina, 2014, Diversity of sponges (Porifera) from cryptic habitats on the Belize barrier reef near Carrie Bow Cay, pp. 1-129 in Zootaxa 3805 (1) on page 78, DOI: 10.11646/zootaxa.3805.1.1, http://zenodo.org/record/249983
Additional file 5: Figure S1. of Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis
Creators: name: Cloete, Ruben
name: Ekow Oppon
name: Murungi, Edwin
name: Wolf-Dieter Schubert
name: Christoffels, Alan
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: KEGG metabolic pathway map for Nucleotide metabolism (pyrimidine metabolism) in M. tuberculosis H37rV strain. Rv1712 or cmk selected for investigation is shown in red highlighted boxes and involved in step 2.7.4.14 of this specific pathway. Known drug resistance gene Rv0667 or rpoB is shown in blue highlighted box and involved in step 2.7.7.6 of this pathway. M. tuberculosis specific genes are coloured in green. (PDF 111 kb)
Additional file 13: Figure S8. of Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis
Creators: name: Cloete, Ruben
name: Ekow Oppon
name: Murungi, Edwin
name: Wolf-Dieter Schubert
name: Christoffels, Alan
Publisher: name: Figshare
Year: 2016
Subjects: subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Radius of gyration of all bacbone atoms for Rv1712 over the 30000Â ps simulation. (PDF 29 kb)
Additional file 1: Table S1. of Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis
Creators: name: Cloete, Ruben
name: Ekow Oppon
name: Murungi, Edwin
name: Wolf-Dieter Schubert
name: Christoffels, Alan
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: KEGG pathways for genes known to be associated with 1st and 2nd line drug resistance. The 10 mutations (eight genes) indicated in bold were verified by the BROAD institute, while the remainder were identified from literature. Abbreviations used: A-Adenine, Ala-Alanine, Arg-Arginine, Asn-Glutamine, Asp-Aspartate, Gly-Glycine, His-Histidine, indel-insertion deletion, Ileu-Isoleucine, Leu-Leucine, Met-Methionine, N.A-Not available, Pro-Proline, Ser-Serine, T-Thymidine, Thr-Threonine, Tyr-Tyrosine, Val-Valine. (PDF 143 kb)
Additional file 2: of Association of anticardiolipin, antiphosphatidylserine, anti-Î˛2 glycoprotein I, and antiphosphatidylcholine autoantibodies with canine immune thrombocytopenia
Creators: name: Chen, Yu-Chen
name: Lang-Ming Chi
name: Kuan-Chih Chow
name: Shiow-Her Chiou
name: Fan, Yi-Hsin
name: Ho, Shu-Peng
name: Hsu, Yu-Chen
name: Yu-Chyi Hwang
name: Meng-Xing Wu
name: Lee, Wei-Ming
name: Shiun-Long Lin
name: Chau-Loong Tsang
name: Mao, Frank
Publisher: name: Figshare
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Antiplatelet antibodies measurement. (PDF 99Â kb)
Batrachophthalmum Hendel 1911
Creators: name: De, Claudio J. B.
name: Wolff, Marta
name: Wendt, Lisiane D.
Publisher: name: Zenodo
Year: 2011
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Richardiidae
Batrachophthalmum

description: Batrachophthalmum Hendel, 1911
(Figs. 1–10)
Type-species: Batrachophthalmum rufiventre Hendel, 1911
Diagnosis. Head wider than high. All femora with apicoventral rows of setae, spinose setae on fore femur stronger than those on mid and hind femora. Mid and hind legs longer and slender than fore leg. R2+3 sinuous just before margin; r-m at distal ¾ of cell dm. Prosternum weakly ciliated. Metasternum bare. Postcoxal metathoracic bridge developed.
Head. Wider than high. Clypeus well developed; arista pubescent with longest cilia as long as the arista base diameter; frons normal, not produced; lunula developed (Figs. 5, 9); ocellar seta present; medial and lateral vertical setae present; distance between posterior ocelli ½ distance to anterior ocellus. Scape slightly developed, length about ½ length of pedicel. Genal and pos-genal setae absent (Fig. 4).
Thorax. Postpronotal seta absent (Fig. 10); proepimeral seta weak; notopleura with 2 setae, posterior seta strong, twice length of anterior seta; scutum with 1 supra-alar seta, 1 long and strong postalar seta, 1 weak intraalar seta; 1–2 dorsocentral setae, well apart from scutellum and aligned with postalar seta. Two pairs of scutellar setae. Katepisternal seta weak. Katatergite bare and totally pollinose. Prosternum weakly ciliated. Metasternum bare. Metathoracic spiracle with differentiated setulae on posterior portion of spiracle. Postcoxal metathoracic bridge developed. Legs: all femora with apicoventral rows (anterior and posterior) of black stout setae; mid and hind legs very long and slender; fore femur with spinose setae stronger than those on mid and hind femora (Figs. 2, 7). Wing (Figs. 1, 8): veins bare; R2+3 sinuous just before margin; r-m at distal ¾ of cell dm; vein A1+CuA2 long, becoming weaker towards margin; alula present.
Abdomen (Figs. 2, 7). Shorter than thorax in lateral view; syntergite 1–2 twice length of tergite 3, with 2–4 pairs of lateral setae disposed obliquely in relation to margin of syntergite; tergites 3–5 similar in length.
Remarks: The wing venation is very important to distinguish among richardiid genera, and the pattern of wing bands is very useful to separate among species. Each genus has a unique venation pattern, which is relatively constant among its species (with a few exceptions, for instance Setellia Robineau-Desvoidy). In species of Batrachophthalmum, vein R2+3 is uniquely sinuous throughout (Figs. 1, 8).
Batrachophthalmum was proposed for B. rufiventre Hendel, a species that has males with swelled eyes. The type-species was examined only through photographs (Figs. 1–5).
description: Published as part of De, Claudio J. B., Wolff, Marta & Wendt, Lisiane D., 2011, A new stalk-eyed species of Batrachophthalmum Hendel (Diptera, Richardiidae) from Colombia, pp. 41-46 in Zootaxa 2932 on page 42, DOI: 10.5281/zenodo.278067
Agelas schmidti Wilson 1902
Creators: name: Rützler, Klaus
name: Piantoni, Carla
name: Van, Rob W. M.
name: Díaz, Cristina
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Porifera
Demospongiae
Agelasida
Agelasidae
Agelas
Agelas schmidti

description: Agelas schmidti Wilson, 1902
Synonymy and References. Agelas schmidti Wilson, 1902: 398. Parra-Velandia et al., 2014: 329, fig.12 (including synonymy).
Material. USNM 1191328, Carrie Bow Cay, forereef cave, 18 m; K. Ruetzler, col. 19 May 1979. USNM 1191329, Curlew Bank, framework cave, 20 m; C. Piantoni, col. 1 July 2007. USNM 1229098, Curlew Bank, forereef slope (wall), 50-150 cm inside framework cave, ceiling, 20 m; C. Piantoni & M. Parrish, col. 22 Aug 2012. USNM 1229099 Curlew Bank forereef slope (wall), framework cave, 18 m; C. Piantoni & M. Parrish, col. 25 Aug 2012.
External morphology. Coalescent tubes filling coral crevices and protruding as hollow cones (1–3 cm at the base) and tapering to terminal oscula, 4–10 mm in diameter. The base is yellow orange, exposed apical parts are orange red.
Skeleton structure. Interconnected spongin fibers, cored and echinated by spicules.
Spicules. Acanthostyles with spines in whorls. They measure 103–230 x 8–20 (151 x 16) Μm, with 9–15 (13) whorls; spines can be reduced in length or missing along the mid-portion of the spicules.
Ecology. Common in small framework caves on the forereef, 18– 20 m. Exposed surfaces are generally covered by encrusting coralline algae and sponges, for instance the bright red Clathria campecheae.
Distribution. The species is common throughout the Caribbean and the Gulf of Mexico (Rützler et al., 2009; Parra-Velandia et al., 2014).
Comments. We compared the spicules with those of the holotype from St. Thomas, U. S. Virgin Islands, and found them to be nearly identical in dimensions and number of whorls, as well as reduction of spines in the center region of some.
description: Published as part of Rützler, Klaus, Piantoni, Carla, Van, Rob W. M. & Díaz, Cristina, 2014, Diversity of sponges (Porifera) from cryptic habitats on the Belize barrier reef near Carrie Bow Cay, pp. 1-129 in Zootaxa 3805 (1) on page 77, DOI: 10.11646/zootaxa.3805.1.1, http://zenodo.org/record/249983