cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Ololaelaps mooiensis Ryke
Creators: name: Halliday, R. B.
Publisher: name: Zenodo
Year: 2005
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Mesostigmata
Laelapidae
Ololaelaps
Ololaelaps mooiensis

description: Ololaelaps mooiensis Ryke
Ololaelaps mooiensis Ryke, 1962c: 126.
Pseudoparasitus mooiensis: Karg, 1978: 210; 1981a: 211.
Specimens examined: Site 94­13, 2 females; Site 94­14, 18 females.
Ololaelaps mooiensis was described from soil near Potchefstroom (Ryke, 1962c). Other species of Ololaelaps are found in soil and leaf litter, and in the nests of small mammals (Bregetova & Koroleva, 1964), where they are presumed to be predatory.
description: Published as part of Halliday, R. B., 2005, Predatory mites from crops and pastures in South Africa: potential natural enemies of redlegged earth mite Halotydeus destructor (Acari: Penthaleidae), pp. 11-64 in Zootaxa 1079 on page 36, DOI: 10.5281/zenodo.170355
Cynoscion microlepidotus
Creators: name: Ceríaco, Luis M. P.
name: Santos, Bruna S.
name: Semedo, Thiago B. F.
name: Garcia, Lucas Canes
name: Moreira, Cristiano Rangel
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Perciformes
Sciaenidae
Cynoscion
Cynoscion microlepidotus

description: Cynoscion microlepidotus (Cuvier 1830)
Extant specimens: MCUC ZOO.0000001 (Fig. 57a), MCUC ZOO.0000022 (Fig. 57b), and MCUC ZOO.0000046 (Fig. 57c).
Classification on the specimen: “P. Th. Labrus laevis ” (MCUC ZOO.0000001) and “P. Th. Labrus ” (MCUC ZOO.0000022 and MCUC ZOO.0000046).
Common names on the specimen (Portuguese/Tupi): “Pescadinha” (MCUC ZOO.0000001)/ None.
Comments: See Comments of Cynoscion acoupa. This species was undescribed at the time Veloso prepared it. Cynoscion microlepidotus occurs in the western Atlantic from Venezuela to Paraná (Brazil) (Menezes & Figueiredo 1980).
description: Published as part of Ceríaco, Luis M. P., Santos, Bruna S., Semedo, Thiago B. F., Garcia, Lucas Canes & Moreira, Cristiano Rangel, 2023, The fish collection of José Mariano da Conceição Veloso (1742 - 1811) and the beginning of ichthyological research in Brazil, with a taxonomic description of the extant specimens, pp. 1-85 in Zootaxa 5391 (1) on page 73, DOI: 10.11646/zootaxa.5391.1.1, http://zenodo.org/record/10434709
Additional file 7: Figure S4. of The efficacy, safety, and feasibility of inhaled amikacin for the treatment of difficult-to-treat non-tuberculous mycobacterial lung diseases
Creators: name: Yagi, Kazuma
name: Ishii, Makoto
name: Namkoong, Ho
name: Asami, Takahiro
name: Iketani, Osamu
name: Asakura, Takanori
name: Suzuki, Shoji
name: Sugiura, Hiroaki
name: Yoshitake Yamada
name: Tomoyasu Nishimura
name: Fujiwara, Hiroshi
name: Funatsu, Yohei
name: Uwamino, Yoshifumi
name: Kamo, Tetsuro
name: Sadatomo Tasaka
name: Betsuyaku, Tomoko
name: Hasegawa, Naoki
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Infectious Diseases
subject: FOS: Health sciences

description: Time course changes of the nebulizing speeds. (DOCX 312Â kb)
Limonia subaequalis Savchenko 1979
Creators: name: Ÿ, Jaroslav Star
name: Oosterbroek, Pjotr
Publisher: name: Zenodo
Year: 2008
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Limoniidae
Limonia
Limonia subaequalis

description: Limonia subaequalis Savchenko, 1979
Material examined: Turkey: Artvin, 4–6 km NW Meydancik, 1250 m, 3.–4. VI.1995, 2 ɗ, 1Ψ, H. v. Oorschot, H. v.d. Brink & P. Oosterbroek leg., J. Starý det.
Distribution: Ukraine (Crimea), Russia (North Caucasus), Armenia, Azerbaijan, Georgia. First record for Turkey.
description: Published as part of Ÿ, Jaroslav Star & Oosterbroek, Pjotr, 2008, New records of West Palaearctic Limoniidae, Pediciidae and Cylindrotomidae (Diptera) from the collections of the Zoological Museum, Amsterdam, pp. 1-20 in Zootaxa 1922 on page 16, DOI: 10.5281/zenodo.184739
Additional file 5: Figure S2. of Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism
Creators: name: Broman, Elias
name: SjĂśstedt, Johanna
name: Jarone Pinhassi
name: Dopson, Mark
Publisher: name: Figshare
Year: 2017
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Phylogenetic tree showing OTUs derived from the 16S rRNA gene analysis. Included OTUs had a relative abundance higher than 1% in one or more samples derived from the top 1-cm sediment surface sliced in the field and at the end of the incubation experiment. Sequences downloaded from NCBI GenBank have been marked with a dashed line in the heat map. The tree was rooted with a marine Actinomycete (NCBI accession: AJ866956.1). (PDF 456Â kb)
Lutjanus kasmira
Creators: name: Andréfouët, Serge
name: Chen, Wei-Jen
name: Kinch, Jeff
name: Mana, Ralph
name: Russell, Barry C.
name: Tully, Dean
name: White, William T.
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Perciformes
Lutjanidae
Lutjanus
Lutjanus kasmira

description: Lutjanus kasmira (Forsskål in Niebuhr 1775) —Blue-lined snapper
Status at New Ireland. First recorded from Drei Inseln Harbour, New Hanover by Munro (1958: 191). Previously misidentified from Carteret Harbour, Lambom, New Ireland as Lutjanus bengalensis (non Bloch 1790) by Peters (1877: 831); subsequently from Lihir Group, Namatamai District by Fry et al. (2006: 129). Specimens photographed on 2 June 2013, first dive, during ACIAR Aquarium Survey at Kavieng. Specimens photographed at Lissenung Island by Dietmar Amon on 28 Mar. 2007.
Distribution and habitat. New Ireland: 1, 2, 3, 5.—General distribution: Red Sea, East Africa, Madagascar and Mascarenes east to Kiribati (Line Islands) and Pitcairn Group, north to southern Japan and Ogasawara Islands, south to northern New Zealand and Rapa; introduced in Hawaiian Islands. Adults found in coral and rocky reefs, juveniles in seagrass beds or patch reefs, 0–265 m depth. Marine.
description: Published as part of Andréfouët, Serge, Chen, Wei-Jen, Kinch, Jeff, Mana, Ralph, Russell, Barry C., Tully, Dean & White, William T., 2019, Checklist of the marine and estuarine fishes of New Ireland Province, Papua New Guinea, western Pacific Ocean, with 810 new records, pp. 1-360 in Zootaxa 4588 (1) on page 153, DOI: 10.11646/zootaxa.4588.1.1, http://zenodo.org/record/2988163
Public hearing before assembly regulatoryoversight committee "review progress of the Board ofPublic Utilities in regulations to implement P.L. 1994, c.188 underground facilities protection act"
Creators: name: No Name Supplied
Publisher: name: No Publisher Supplied
Year: 1995

description: The public hearing was held to hear the following issue:Review progress of the Board of Public Utilities inregulations to implement P.L. 1994, c. 118, "UndergroundFacility Protection Act." The following is the transcript of that hearing.
Leptolaelaps lambda Evans
Creators: name: Halliday, R. B.
Publisher: name: Zenodo
Year: 2005
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Mesostigmata
Leptolaelapidae
Leptolaelaps
Leptolaelaps lambda

description: Leptolaelaps lambda Evans
Leptolaelaps lambda Evans, 1957: 47.
Leptolaelaps lambda: Karg, 1983: 391; 1997: 216.
Specimens examined: Site 94­1, 1 female.
Leptolaelaps lambda was described from 3 specimens from Knysna (Evans, 1957), and is now recorded from a single specimen from Cape Town. The species is presumed to be predatory, but is obviously rare.
description: Published as part of Halliday, R. B., 2005, Predatory mites from crops and pastures in South Africa: potential natural enemies of redlegged earth mite Halotydeus destructor (Acari: Penthaleidae), pp. 11-64 in Zootaxa 1079 on page 36, DOI: 10.5281/zenodo.170355
Exploration of FARO freestyle 3D laser scanners as a method for estimating surface fuel loading for wildland fire management
Creators: name: Rua, Joseph
Publisher: name: No Publisher Supplied
Year: 2018

description: To evaluate the effectiveness of the FARO 3D handheld LiDAR unit, I determined when ambient light affected the LiDAR’s detection capability. I then used standard destructive harvest methods combined with LiDAR data to examine the relationship between the number of pixels captured by the LiDAR unit with the log transformed dry biomass of the harvest fuels in both leaf-on and leaf-off conditions. Using a Bayesian regression model with a non-informative prior, the analysis showed a weak relationship between pixels and log biomass in leaf-on conditions with an R2 of 0.22 and a moderately strong relationship between pixels and log biomass in leaf-off conditions with an R2 of 0.67. The results suggest that handheld LiDAR units have the potential to replace destructive harvest methods under certain conditions, but may not serve as a tool for fire managers to utilize as a regular tool for estimate surface fuel loading.
Additional file 1: of Equine skeletal muscle adaptations to exercise and training: evidence of differential regulation of autophagosomal and mitochondrial components
Creators: name: Bryan, Kenneth
name: McGivney, Beatrice
name: Farries, Gabriella
name: McGettigan, Paul
name: McGivney, Charlotte
name: Gough, Katie
name: MacHugh, David
name: Katz, Lisa
name: Hill, Emmeline
Publisher: name: Figshare
Year: 2017
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological 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: Marine Biology
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Supplementary Information Main Document. (DOCX 110Â kb)
Limonia trivittata Schummel 1829
Creators: name: Ÿ, Jaroslav Star
name: Oosterbroek, Pjotr
Publisher: name: Zenodo
Year: 2008
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Limoniidae
Limonia
Limonia trivittata

description: Limonia trivittata (Schummel, 1829)
Material examined: Turkey: Kars, Sarikamis, 2000 m, 6. VII.1986, 1 ɗ, 1 Ψ, J.A.W. Lucas leg, J. Starý det. Distribution: Widespread in the West Palaearctic except for North Africa, also known from Georgia, Russia (West Siberia,? Far East), Kazakhstan, Kyrgyzstan and Uzbekistan. First record for Turkey.
description: Published as part of Ÿ, Jaroslav Star & Oosterbroek, Pjotr, 2008, New records of West Palaearctic Limoniidae, Pediciidae and Cylindrotomidae (Diptera) from the collections of the Zoological Museum, Amsterdam, pp. 1-20 in Zootaxa 1922 on page 17, DOI: 10.5281/zenodo.184739
Validation and application of advanced soil constitutive models in numerical modelling of soil and soil-structure interaction under seismic loading
Creators: name: Kowalczyk, Piotr Jozef
Publisher: name: Universit� degli studi di Trento
Year: 2020

description: This thesis presents validation and application of advanced soil constitutive models in cases of seismic loading conditions. Firstly, results of three advanced soil constitutive models are compared with examples of shear stack experimental data for free field response in dry sand for shear and compression wave propagation. Higher harmonic generation in acceleration records, observed in experimental works, is shown to be possibly the result of soil nonlinearity and fast elastic unloading waves. This finding is shown to have high importance on structural response, real earthquake records and reliability of conventionally employed numerical tools. Finally, short study of free field response in saturated soil reveals similar findings on higher harmonic generation. Secondly, two advanced soil constitutive models are used, and their performance is assessed based on examples of experimental data on piles in dry sand in order to validate the ability of the constitutive models to simulate seismic soil-structure interaction. The validation includes various experimental configurations and input motions. The discussion on the results focuses on constitutive and numerical modelling aspects. Some improvements in the formulations of the models are suggested based on the detailed investigation. Finally, the application of one of the advanced soil constitutive models is shown in regard to temporary natural frequency wandering observed in structures subjected to earthquakes. Results show that pore pressure generated during seismic events causes changes in soil stiffness, thus affecting the natural frequency of the structure during and just after the seismic event. Parametric studies present how soil permeability, soil density, input motion or a type of structure may affect the structural natural frequency and time for its return to the initial value. In addition, a time history with an aftershock is analysed to investigate the difference in structural response during the earthquake and the aftershock.
Lutjanus lunulatus
Creators: name: Andréfouët, Serge
name: Chen, Wei-Jen
name: Kinch, Jeff
name: Mana, Ralph
name: Russell, Barry C.
name: Tully, Dean
name: White, William T.
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Perciformes
Lutjanidae
Lutjanus
Lutjanus lunulatus

description: Lutjanus lunulatus (Park 1797) —Lunartail snapper
Status at New Ireland. First recorded from Kalili, New Ireland by Kailola (1987b: 295).
Distribution and habitat. New Ireland: 3.—General distribution: Pakistan east to Philippines, Papua New Guinea and Vanuatu. Found in coral reefs and on seaward reef slopes, 10–30 m depth. Marine.
description: Published as part of Andréfouët, Serge, Chen, Wei-Jen, Kinch, Jeff, Mana, Ralph, Russell, Barry C., Tully, Dean & White, William T., 2019, Checklist of the marine and estuarine fishes of New Ireland Province, Papua New Guinea, western Pacific Ocean, with 810 new records, pp. 1-360 in Zootaxa 4588 (1) on page 154, DOI: 10.11646/zootaxa.4588.1.1, http://zenodo.org/record/2988163
Micropogonias furnieri
Creators: name: Ceríaco, Luis M. P.
name: Santos, Bruna S.
name: Semedo, Thiago B. F.
name: Garcia, Lucas Canes
name: Moreira, Cristiano Rangel
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Perciformes
Sciaenidae
Micropogonias
Micropogonias furnieri

description: Micropogonias furnieri (Desmarest 1823)
Extant specimens: MCUC ZOO.0000011 (Fig. 59).
Classification on the specimen: “P. T [sic] Labrus cromis ”.
Common names on the specimen (Portuguese/Tupi): “Corvina”/ “Guatucupa ”.
Comments: This species was undescribed at the time Veloso prepared it. Labrus cromis Linnaeus 1766 (= Pogonias cromis) is a sciaenid occurring in northwestern Atlantic. Veloso describe this species in the Ichthyologia Fluminensis manuscript and listed the same common names as the ones on the herbarium sheet. There are 112 herborized specimens of Labrus in the Ajuda’s inventory, and one specimen of Labrus cromis is mentioned in the transference document to the Lisbon Academy of Sciences, and three in the transference to the University of Coimbra, one of which is extant. The Portuguese common name is still used nowadays. Micropogonias furnieri occurs in the Western Atlantic from Antilles and Costa Rica to Argentina (Menezes & Figueiredo 1980).
description: Published as part of Ceríaco, Luis M. P., Santos, Bruna S., Semedo, Thiago B. F., Garcia, Lucas Canes & Moreira, Cristiano Rangel, 2023, The fish collection of José Mariano da Conceição Veloso (1742 - 1811) and the beginning of ichthyological research in Brazil, with a taxonomic description of the extant specimens, pp. 1-85 in Zootaxa 5391 (1) on page 73, DOI: 10.11646/zootaxa.5391.1.1, http://zenodo.org/record/10434709
Additional file 2: Table S2. of Prevalence, awareness, treatment and control of dyslipidemia in older persons in urban and rural population in the Astana region, Kazakhstan
Creators: name: Supiyev, Adil
name: Nurgozhin, Talgat
name: Zhaxybay Zhumadilov
name: Peasey, Anne
name: Hubacek, Jaroslav
name: Bobak, Martin
Publisher: name: Figshare
Year: 2017
Subjects: subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Factors associated with serum cholesterols in Astana region, Kazakhstan, OR (95% CI). (DOC 92 kb)
Macrocheles caelatus Berlese
Creators: name: Halliday, R. B.
Publisher: name: Zenodo
Year: 2005
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Mesostigmata
Macrochelidae
Macrocheles
Macrocheles caelatus

description: Macrocheles caelatus Berlese
Macrocheles (Coprholaspis) caelatus Berlese, 1918: 157. Macrocheles caelatus: Walter & Krantz, 1986: 283.
Specimens examined: Site 94­13, 12 females; Site 94­14, 2 females.
Macrocheles caelatus was described from East Africa (Berlese, 1918) and subsequently collected from Zaire and Rwanda (Walter & Krantz, 1986). The records of this species from New Zealand, Fiji and Malaysia (Ramsay, 1970; Emberson, 1973) represent misidentification of M. peniculatus Berlese. M. caelatus is a member of the Macrocheles glaber species group, which prey on nematodes and insect eggs and larvae wherever organic matter is decomposing. The Australian fauna includes at least 6 species in this group, not including M. caelatus (Halliday, 2000b).
description: Published as part of Halliday, R. B., 2005, Predatory mites from crops and pastures in South Africa: potential natural enemies of redlegged earth mite Halotydeus destructor (Acari: Penthaleidae), pp. 11-64 in Zootaxa 1079 on page 36, DOI: 10.5281/zenodo.170355
Distinct and shared endothermic strategies in the heat producing tissues of tuna and other teleosts
Creators: name: 武宝生(Baosheng Wu)
Publisher: name: CNGB
Year: 2024
Subjects: Genome sequencing and assembly
Raw sequence reads
Genome sequencing
Assembly
Multiisolate
Evolution

description: Although most fishes are ectothermic, some, including tuna and billfish, achieve endothermy through special heat producing tissues, which are modified muscles. How these heat producing tissues evolved, and whether they share convergent molecular mechanisms, is unresolved. Here, we generated a high-quality mackerel tuna (Euthynnus affinis) genome, and investigated the heat producing tissue of this fish through single-nucleus and bulk RNA sequencing. Compared with other teleosts, tuna-specific genetic changes are highly associated with muscle differentiation. Single-nucleus RNA-Seq revealed a high proportion of specific slow skeletal muscle subtype cells in the heat producing tissues of tuna. The marker genes of this cell subtype are associated with the relative sliding of actin and myosin, suggesting that endothermy in tuna relies mainly on shivering thermogenesis. In contrast, cross-species transcriptome analysis indicated that endothermy in billfish relies mainly on non-shivering thermogenesis. Nonetheless, the heat producing tissues of the different species do share some tissues specifically expressed genes, including vascular-related and mitochondrial genes. These results imply that both distinct and shared molecular mechanisms are employed by organisms to achieve the same goals, in this case endothermy in teleosts.
Cynoscion Gill 1861
Creators: name: Ceríaco, Luis M. P.
name: Santos, Bruna S.
name: Semedo, Thiago B. F.
name: Garcia, Lucas Canes
name: Moreira, Cristiano Rangel
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Perciformes
Sciaenidae
Cynoscion

description: Cynoscion sp., probably Cynoscion jamaicensis (Vaillant & Bocourt 1883)
Extant specimens: MCUC ZOO.0000023 (Fig. 58).
Classification on the specimen: None.
Common names on the specimen (Portuguese/Tupi): None.
Comments: Two species of the genus Cynoscion with truncate caudal fin and ctenoid scales occur in the southwestern Atlantic, C. guatucupa and C. jamaicensis (Menezes & Figueiredo 1980; Chao 2002). Cynoscion jamaicensis can be distinguished from C. guatucupa by a higher number of dorsal-fin rays (22–27 in C. jamaicensis vs. 18–21 in C. guatucupa) and by a higher number of scales above lateral line (68–73 in C. jamaicensis vs. 63–66 in C. guatucupa) (Menezes & Figueiredo 1980; Chao 2002). The specimen analyzed has more than 23 dorsal-fin rays, however, due to its poor conditions, it is not possible to count the scales, hindering a proper identification of this specimen.
description: Published as part of Ceríaco, Luis M. P., Santos, Bruna S., Semedo, Thiago B. F., Garcia, Lucas Canes & Moreira, Cristiano Rangel, 2023, The fish collection of José Mariano da Conceição Veloso (1742 - 1811) and the beginning of ichthyological research in Brazil, with a taxonomic description of the extant specimens, pp. 1-85 in Zootaxa 5391 (1) on page 73, DOI: 10.11646/zootaxa.5391.1.1, http://zenodo.org/record/10434709
Lipsothrix nobilis Loew 1873
Creators: name: Ÿ, Jaroslav Star
name: Oosterbroek, Pjotr
Publisher: name: Zenodo
Year: 2008
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Limoniidae
Lipsothrix
Lipsothrix nobilis

description: Lipsothrix nobilis Loew, 1873
Material examined: Turkey: Rize, 5 km SE Ayder, 1600 m, 31. V.1995, 1 ɗ; Rize, Ayder, 1300 m, 30. V.1995, 1 ɗ; Rize, 2 km NW Ikizdere, 550 m, 29. V.1995, 1 ɗ, all H. v. Oorschot, H. v.d. Brink & P. Oosterbroek leg., J. Starý det.
Distribution: Scattered records from Europe, also known from Georgia and possibly Azerbaijan. First records for Turkey.
Note: For the time being, it is advisable to consider Lipsothrix iranica Alexander, 1975, of Iran, a distinct species (cf. Starý 2007).
description: Published as part of Ÿ, Jaroslav Star & Oosterbroek, Pjotr, 2008, New records of West Palaearctic Limoniidae, Pediciidae and Cylindrotomidae (Diptera) from the collections of the Zoological Museum, Amsterdam, pp. 1-20 in Zootaxa 1922 on page 17, DOI: 10.5281/zenodo.184739
Additional file 2: Figure S2. of Genome-wide analysis of LTR-retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.)
Creators: name: Mascagni, Flavia
name: Giordani, Tommaso
name: Ceccarelli, Marilena
name: Cavallini, Andrea
name: Natali, Lucia
Publisher: name: Figshare
Year: 2017
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Hematology
subject: Virology

description: Distance tree of LTR-Copia RT domains of 10 species and one subspecies of Helianthus subjected to NJ analysis. Bootstrap values higher than 0.6 are shown with asterisk. Bar represents the nucleotide distance. Outgroups are RT domains of other species. Distance tree of LTR-Gypsy RT domains of 10 species and one subspecies of Helianthus subjected to NJ analysis. Bootstrap values higher than 0.6 are shown with asterisk. Bar represents the nucleotide distance. Outgroups are RT domains of other species. (PDF 487 kb)
Lutjanus lutjanus lutjanus Bloch 1790
Creators: name: Andréfouët, Serge
name: Chen, Wei-Jen
name: Kinch, Jeff
name: Mana, Ralph
name: Russell, Barry C.
name: Tully, Dean
name: White, William T.
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Perciformes
Lutjanidae
Lutjanus
Lutjanus lutjanus

description: Lutjanus lutjanus Bloch 1790 —Bigeye snapper
Status at New Ireland. New record, based on specimens photographed at Kavieng fish market by Barry C. Russell on 14 and 21 June 2014.
Distribution and habitat. New Ireland: 2.—General distribution: Red Sea and East Africa east to Vanuatu, north to Ryukyu Islands, south to northern Australia and New Caledonia. Found in coastal coral reefs and on seaward reef slopes, 10–90 m depth. Marine.
description: Published as part of Andréfouët, Serge, Chen, Wei-Jen, Kinch, Jeff, Mana, Ralph, Russell, Barry C., Tully, Dean & White, William T., 2019, Checklist of the marine and estuarine fishes of New Ireland Province, Papua New Guinea, western Pacific Ocean, with 810 new records, pp. 1-360 in Zootaxa 4588 (1) on page 154, DOI: 10.11646/zootaxa.4588.1.1, http://zenodo.org/record/2988163
Large-scale protease multispecificity
Creators: name: Rubenstein, Aliza
Publisher: name: No Publisher Supplied
Year: 2018

description: Proteases are ubiquitous and significant to both normal cellular functioning and disease states.  They are generally multispecific, cleaving a set of substrates without recognizing other peptides.  Computational methods to predict and design protease multispecificity would advance our understanding of the biophysical basis of protease specificity, enable the characterization of novel proteases, allow the identification of novel biological roles for proteases, elucidate protease specificity landscapes and ultimately further the design of custom proteases to serve as therapeutics or protein-level knockout reagents in cell culture.    Current methods of computational protease specificity prediction are limited in a variety of ways.  Techniques to classify substrates as cleaved or uncleaved are constrained by the quality of the input data, cannot be easily generalized to other proteases, and require large training data sets to learn correlations between substrate positions.  Methods that predict specificity profiles are computationally expensive and thus unable to be used directly within design.  While fitness landscapes have been explored experimentally and via low-resolution computational models, no methods have yet explored the full fitness landscape using chemically realistic atomic-resolution computations.     In this dissertation, we further the understanding of protease multispecificity via a variety of experimental and computational techniques that can be generalized to other proteases.  First, we develop a structure-based classifier that distinguishes robustly between cleaved and uncleaved substrates, benchmark the classifier performance for five model proteases, and apply the classifier in a blind test to identify novel substrates.  Second, we implement a mean-field structure-based algorithm (MFPred) to rapidly and accurately predict protease specificity profiles, benchmark MFPred performance on a range of protease and protein-recognition domains, and demonstrate that MFPred accurately predicts the impact of receptor-side mutations, thus showing putative utility in protease design.  Third, we construct a specificity landscape of hepatitis C virus NS3 protease using both experimental and computational methods and find evidence for a structural basis of mutational robustness.  Finally, we compare the Rosetta and Amber energy functions used in the computational prediction of protease multispecificity in a systematic benchmark.
Investigating the ubiquitin-proteasome system for targeted reversal of HIV-1 latency
Creators: name: Russnak, Timothy
Publisher: name: No Publisher Supplied
Year: 2018

description: HIV is a worldwide epidemic, remaining the ever-present specter among all matters regarding blood or other bodily fluids, such as sexual intercourse, healthcare, blood transfusions, or even surgery, particularly in resource-poor areas. While antiretroviral drug therapy is highly successful in suppressing the virus and preventing transmission, it cannot cure the infection due to latency – the ability of HIV to go into a silent state within cells; once drug therapy is stopped, reactivating latent virus will cause a surge of the viral load within days or weeks. Current drug therapies do not act on this latent reservoir, necessitating lifelong adherence to medication, which is both extremely costly and comes with negative side effects. The mainstay of research into HIV latency deals with teasing apart the mechanisms involved in establishing and maintaining latency, in the hopes of finding drug compounds which can efficiently reverse latency and thus purge the body of hidden HIV.  In searching for cellular pathways involved in latency, our lab has employed a genome-wide negative-selection screen, which indicated that the ubiquitin-proteasome system plays a role in maintaining latency. This led us to discover that proteasome inhibitors act as bifunctional antagonists of HIV, both reversing the latent state and reducing infectivity of virions. We went on to identify the specific ubiquitin-proteasome pathway that is involved in maintaining latency. We then investigated the activity of a small-molecule inhibitor of one component of the ubiquitin-proteasome system, showing its ability to reactivate latent HIV in both a primary cell model and in cells taken from aviremic HIV+ patients. These results are a proof-of-concept that inhibition of a specific ubiquitin-proteasome pathway can allow for specific reversal of HIV latency.
Additional file 3: Figure S3. of Genome-wide analysis of LTR-retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.)
Creators: name: Mascagni, Flavia
name: Giordani, Tommaso
name: Ceccarelli, Marilena
name: Cavallini, Andrea
name: Natali, Lucia
Publisher: name: Figshare
Year: 2017
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified

description: Sequence composition of LTR-Copia-RE-related clusters. The size of the rectangle is proportional to the genome proportion of a cluster for each species (acronyms as in Table 1). Bar plot in the top row shows the size of the clusters as number of reads in the comparative analysis. Upper lines label groups of clusters as asses by a hierarchical clustering of the results. The percentage of reads included in the group is shown in parentheses. The colour of the rectangles corresponds to the lineage of the Copia LTR-RE. All Copia-related repeats were shared among all the 10 species and one subspecies, with some peculiarities. In fact, differences were found even within lineages, producing 14 groups of RE sublineages with different abundance patterns, which accounted for 0.03 to 3.53% of the genome. For example, group 10, although being the most abundant (3.53% of the genome on the whole), was made up by nine clusters (eight annotated as Maximus/SIRE and one as Copia-unknown), that were represented in all species, but showed the largest abundance in H. porteri. On the contrary, the eight sublineages of group 12, annotated as Maximus as well, showed the highest genome proportions especially in H. agrestis and, to a lesser extent, in the Helianthus section. (PDF 454 kb)
Umbrina coroides Cuvier 1830
Creators: name: Ceríaco, Luis M. P.
name: Santos, Bruna S.
name: Semedo, Thiago B. F.
name: Garcia, Lucas Canes
name: Moreira, Cristiano Rangel
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Perciformes
Sciaenidae
Umbrina
Umbrina coroides

description: Umbrina coroides Cuvier 1830
Extant specimens: MCUC ZOO.0000033 (Fig. 60).
Classification on the specimen: “P. Th. Labrus ”.
Common names on the specimen (Portuguese/Tupi): None.
Comments: This species was undescribed at the time Veloso prepared it. While there are 112 herborized specimens of Labrus in the Ajuda’s inventory, no name that would fit this species could be found in the transference documents to the Lisbon Academy of Sciences or the University of Coimbra.Also, no description fitting this species is found in the Ichthyologia Fluminensis manuscript. Umbrina coroides occurs in the Western Atlantic from Florida (USA) to Santa Catarina (Brazil) (Menezes & Figueiredo 1980).
Order Spariformes
description: Published as part of Ceríaco, Luis M. P., Santos, Bruna S., Semedo, Thiago B. F., Garcia, Lucas Canes & Moreira, Cristiano Rangel, 2023, The fish collection of José Mariano da Conceição Veloso (1742 - 1811) and the beginning of ichthyological research in Brazil, with a taxonomic description of the extant specimens, pp. 1-85 in Zootaxa 5391 (1) on page 74, DOI: 10.11646/zootaxa.5391.1.1, http://zenodo.org/record/10434709
Acugamasus grahami Ryke
Creators: name: Halliday, R. B.
Publisher: name: Zenodo
Year: 2005
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Mesostigmata
Ologamasidae
Acugamasus
Acugamasus grahami

description: Acugamasus grahami (Ryke)
Cyrtolaelaps (Gamasellus) grahami Ryke, 1962b: 38. Acugamasus grahami: Lee, 1970: 144.
Specimens examined: Site 94­1, 1 DN; Site 94­5, 8 females, 2 males, 3 DN; Site 94­30, 2 females, 2 males, 2 DN; Site 94­31, 9 females, 9 males, 6 DN; Site 94­33, 5 males, 1 DN.
Acugamasus grahami was described from soil at Bathurst and Grahamstown (Ryke, 1962b), and transferred to Acugamasus Lee by Lee (1970). Nothing is known of the biology of this species, except that it is presumed to be a predator by analogy with other species of Ologamasidae (Lee, 1974).
description: Published as part of Halliday, R. B., 2005, Predatory mites from crops and pastures in South Africa: potential natural enemies of redlegged earth mite Halotydeus destructor (Acari: Penthaleidae), pp. 11-64 in Zootaxa 1079 on page 41, DOI: 10.5281/zenodo.170355
Evidence for presynaptic protein at the calyx of held nerve terminal
Creators: name: Scarnati, Matthew Steven
Publisher: name: No Publisher Supplied
Year: 2018

description: Presynaptic activity requires the localization and maintenance of thousands of proteins that are typically thought to be synthesized in the soma and transported to nerve terminals. However, local protein synthesis occurs at dendritic locations and local presynaptic protein synthesis has recently been shown to occur in an inhibitory neuron in the brain, but the small size of most nerve terminals complicates further studies. Here, we study presynaptic protein synthesis at the calyx of Held nerve terminal, located in the mammalian brain. The size of this terminal, its long axon, and high firing frequency make it an ideal choice to study presynaptic protein synthesis. We show a major ribosomal component, 5.8S ribosomal RNA is present in this presynaptic nerve terminal. To verify the presence of functional presynaptic ribosomes, we used the surface sensing of translation (SUnSET) technique. This produced well-defined fluorescent signals in presynaptic terminals and postsynaptic cell bodies, and the fluorescent signal was eliminated by inhibiting protein synthesis. To determine the effects on synaptic transmission, we measured electrical activity. After inhibiting translation, the initial frequency of spontaneous events increased by ~2-fold but the amplitude was unaffected, indicating a presynaptic mechanism. In addition, we find that evoked responses show less depression during high frequency firing (≥ 100 Hz). The reduction in depression is not consistent with effects on desensitization but is well explained by presynaptic changes in neurotransmitter release. These findings further indicate that presynaptic protein synthesis occurs, that it can affect spontaneous and evoked release of neurotransmitter, and it affects neurotransmitter release at high firing frequencies.
Metalimnobia (Metalimnobia) tenua Savchenko 1976
Creators: name: Ÿ, Jaroslav Star
name: Oosterbroek, Pjotr
Publisher: name: Zenodo
Year: 2008
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Limoniidae
Metalimnobia
Metalimnobia tenua

description: Metalimnobia (Metalimnobia) tenua Savchenko, 1976
Material examined: Italy: Lombardia, 2 km E Bagolino (BS), 600 m, 4. VI.1997, 1 ɗ, 1Ψ, P. Oosterbroek & C. Hartveld leg., J. Starý det.
Distribution: Recorded from a few countries in Europe (Austria, Czech Republic, Finland and Slovakia), from Russia (East Siberia, Far East) and Japan. First record for Italy.
description: Published as part of Ÿ, Jaroslav Star & Oosterbroek, Pjotr, 2008, New records of West Palaearctic Limoniidae, Pediciidae and Cylindrotomidae (Diptera) from the collections of the Zoological Museum, Amsterdam, pp. 1-20 in Zootaxa 1922 on page 17, DOI: 10.5281/zenodo.184739
Lobotes surinamensis
Creators: name: Ceríaco, Luis M. P.
name: Santos, Bruna S.
name: Semedo, Thiago B. F.
name: Garcia, Lucas Canes
name: Moreira, Cristiano Rangel
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Perciformes
Lobotidae
Lobotes
Lobotes surinamensis

description: Lobotes surinamensis (Bloch 1790)
Extant specimens: MCUC ZOO.0000064 (Fig. 61).
Classification on the specimen: None.
Common names on the specimen (Portuguese/Tupi): None.
Comments: This species was undescribed at the time Veloso prepared it. This species cannot be assigned to any listed species in any documentation related to this collection. Also, no description fitting this species is found in the Ichthyologia Fluminensis manuscript. Lobotes surinamensis occurs in tropical and temperate waters circumglobally (Carpenter 2002c).
description: Published as part of Ceríaco, Luis M. P., Santos, Bruna S., Semedo, Thiago B. F., Garcia, Lucas Canes & Moreira, Cristiano Rangel, 2023, The fish collection of José Mariano da Conceição Veloso (1742 - 1811) and the beginning of ichthyological research in Brazil, with a taxonomic description of the extant specimens, pp. 1-85 in Zootaxa 5391 (1) on page 76, DOI: 10.11646/zootaxa.5391.1.1, http://zenodo.org/record/10434709
Lutjanus malabaricus
Creators: name: Andréfouët, Serge
name: Chen, Wei-Jen
name: Kinch, Jeff
name: Mana, Ralph
name: Russell, Barry C.
name: Tully, Dean
name: White, William T.
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Perciformes
Lutjanidae
Lutjanus
Lutjanus malabaricus

description: Lutjanus malabaricus (Bloch & Schneider 1801) —Malabar snapper
Status at New Ireland. New record, based on specimens observed by Jeff Kinch during CFMDP Survey at Kavieng fish market in 2004–2005, and by Barry C. Russell on 14 and 21 June 2014.
Distribution and habitat. New Ireland: 2.—General distribution: Persian Gulf east to Philippines and Papua New Guinea, north to Taiwan, south to northern Australia. Juveniles in coastal and seaward reefs, adults in deep water, 10–40 m depth. Marine.
description: Published as part of Andréfouët, Serge, Chen, Wei-Jen, Kinch, Jeff, Mana, Ralph, Russell, Barry C., Tully, Dean & White, William T., 2019, Checklist of the marine and estuarine fishes of New Ireland Province, Papua New Guinea, western Pacific Ocean, with 810 new records, pp. 1-360 in Zootaxa 4588 (1) on page 154, DOI: 10.11646/zootaxa.4588.1.1, http://zenodo.org/record/2988163
Gamaselliphis potchefstroomensis Ryke
Creators: name: Halliday, R. B.
Publisher: name: Zenodo
Year: 2005
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Mesostigmata
Ologamasidae
Gamaselliphis
Gamaselliphis potchefstroomensis

description: Gamaselliphis potchefstroomensis (Ryke)
Cyrtolaelaps (Gamaselliphis) potchefstroomensis Ryke, 1961: 101. Gamaselliphis potchefstroomensis: Lee, 1970: 57.
Specimens examined: Site 94­11, 7 females, 4 males; Site 94­13, 1 male; Site 94­14, 19 females, 10 males; Site 94­31, 1 male; Site 94­33, 1 female, 1 male.
Gamaselliphis potchefstroomensis was described from humus at Potchefstroom (Ryke, 1961) and has not been reported since, except when Lee (1970) promoted Gamaselliphis Ryke 1961 from a subgenus to the status of a full genus. Nothing is known of the biology of this species and the next, except that they are presumed to be predatory by analogy with other species of Ologamasidae. The genus includes only five described species, all of which were described by Ryke (1961). The male is known for only three of these.
The collection also includes three specimens of another apparently undescribed species of Gamaselliphis, which has some distinctive features (site 94­31, 2 males, 1 DN). However, I refrain from attempting a description because the female is unknown.
description: Published as part of Halliday, R. B., 2005, Predatory mites from crops and pastures in South Africa: potential natural enemies of redlegged earth mite Halotydeus destructor (Acari: Penthaleidae), pp. 11-64 in Zootaxa 1079 on page 41, DOI: 10.5281/zenodo.170355
Rhipidia (Rhipidia) ctenophora Loew 1871
Creators: name: Ÿ, Jaroslav Star
name: Oosterbroek, Pjotr
Publisher: name: Zenodo
Year: 2008
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Limoniidae
Rhipidia
Rhipidia ctenophora

description: Rhipidia (Rhipidia) ctenophora Loew, 1871
Material examined: Spain: Teruel, 25–30 km SW Alcaniz, 350 m, 10. VII.1972, 1 ɗ, M.J. & J.P. Duffels leg., J. Starý det.
Distribution: Known from Europe except for Fennoscandia and Russia. First record for Spain.
description: Published as part of Ÿ, Jaroslav Star & Oosterbroek, Pjotr, 2008, New records of West Palaearctic Limoniidae, Pediciidae and Cylindrotomidae (Diptera) from the collections of the Zoological Museum, Amsterdam, pp. 1-20 in Zootaxa 1922 on page 17, DOI: 10.5281/zenodo.184739
Archosargus rhomboidalis
Creators: name: Ceríaco, Luis M. P.
name: Santos, Bruna S.
name: Semedo, Thiago B. F.
name: Garcia, Lucas Canes
name: Moreira, Cristiano Rangel
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Perciformes
Sparidae
Archosargus
Archosargus rhomboidalis

description: Archosargus rhomboidalis (Linnaeus 1758)
Extant specimens: MCUC ZOO.0000051 (Fig. 62).
Classification on the specimen: “P. Th. Sparus maculatus ” (see Comments).
Common names on the specimen (Portuguese/Tupi): None/ “Canhanha” (see Comments).
Comments: This species has been subsequently reidentified as Sparus argentatus, with the new specific name written over the old one, which is crossed out. Although the specific name “ maculatus ” is a common specific name, we were unable to identify any species name available during Veloso’s time that corresponds to this specific name, and that fits this species. Consequently, it is likely that Veloso intended to assign a new name to this species. The reidentification Sparus argentatus is most likely a misspelling of Sparus argenteus Bloch & Schneider 1801 (= Pagrus pagrus) which is a similar sparid and that also occurs in the western Atlantic. Veloso described Sparus maculatus in the Ichthyologia Fluminensis manuscript. There are 67 herborized specimens of Sparus listed in the Ajuda’s inventory, and no Sparus maculatus is mentioned in the transference document to the University of Coimbra. However, two specimens of S. maculatus are mentioned in the transference to the Lisbon Academy of Sciences. The Tupi common name is inscribed in the lower left corner, typically reserved for the Portuguese common name. Presently, Canhanha continues to be employed as the common name for this species. Archosargus rhomboidalis occurs in the Western Atlantic from New Jersey (USA) to São Paulo (Brazil) (Menezes & Figueiredo 1980; Carpenter 2002d).
description: Published as part of Ceríaco, Luis M. P., Santos, Bruna S., Semedo, Thiago B. F., Garcia, Lucas Canes & Moreira, Cristiano Rangel, 2023, The fish collection of José Mariano da Conceição Veloso (1742 - 1811) and the beginning of ichthyological research in Brazil, with a taxonomic description of the extant specimens, pp. 1-85 in Zootaxa 5391 (1) on pages 76-78, DOI: 10.11646/zootaxa.5391.1.1, http://zenodo.org/record/10434709
Inhibition of histone deacetylase 3 via RGFP966 facilitates exceptionally specific and enduring memory for excitatory and inhibitory sound-signal associations
Creators: name: Shang, Andrea
Publisher: name: No Publisher Supplied
Year: 2018

description: Epigenetic mechanisms that modulate gene expression are key to regulating long-term memory (LTM) formation, and are known to exert control on memory formation in multiple systems of the adult brain, including the sensory cortex. Chromatin modifications have been shown to have powerful effects on experience-dependent transcription for neuroplasticity underlying memory processes. One mechanism for chromatin modification is histone acetylation. Histone acetyltransferases (HATs) generally facilitate LTM formation by promoting gene expression, while histone deacetylases (HDACs) tend to have gene silencing effects, and negatively regulate LTM. Thus, blocking the action of HDACs has been shown to facilitate LTM formation. Because sensory cortex undergoes learning-induced remodeling over a lifetime, here we aimed to identify the ways in which HDAC-inhibition acts to facilitate LTM using a standard model of auditory memory and cortical plasticity. Auditory cortical plasticity in particular has been extensively studied in learning and memory processes. Representational plasticity in primary auditory cortex (A1) is known to reflect the formation of strong and sound-selective associative memory for behaviorally relevant sound features. In this present study, we used RGFP966, a class I HDAC inhibitor with selectivity for HDAC3 that has been shown to modulate associative learning-induced A1 plasticity (Bieszczad et al., 2015), to facilitate memory consolidation in rats learning a 2-tone sound frequency discrimination (2TD) task. We found that systemic treatments of the HDAC3-inhibitor early in 2TD task training facilitated associative learning for both excitatory (CS+) and inhibitory (CS-) sound signals, and altered the LTM formed in two ways that were independent of the final performance level achieved, which was equivalent between groups. We found that HDAC3-inhibition enhanced memory specificity for the sound-frequency of the two pure-tone CS cues, and strengthened memory for the excitatory and inhibitory sound-specific associations. Moreover, the behavioral effects of an initial, limited bout of HDAC3-inhibitor were long-lasting, enduring for at least weeks following the last administration of RGFP966. The present results support a role for HDAC3 during auditory memory consolidation by regulating the specificity and strength of newly learned sound-signal associations. This conclusion complements existing research on the effects of HDAC-inhibitors by providing a potential behavioral explanation for long-term memory enhancements.
Lutjanus monostigma
Creators: name: Andréfouët, Serge
name: Chen, Wei-Jen
name: Kinch, Jeff
name: Mana, Ralph
name: Russell, Barry C.
name: Tully, Dean
name: White, William T.
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Perciformes
Lutjanidae
Lutjanus
Lutjanus monostigma

description: Lutjanus monostigma (Cuvier in Cuvier & Valenciennes 1828) —Onespot snapper
Status at New Ireland. First recorded from Edmago Island, Kavieng, New Ireland by Munro (1958: 188). Specimens observed by Jeff Kinch during CFMDP Survey at Kavieng fish market in 2004–2005, and by Barry C. Russell on 21 June 2014; a video of a specimen taken from Alexander Passage, off southeastern New Hanover, 5– 14 m depth, at St. KR 96, in 2014 (identified by Barry C. Russell).
Distribution and habitat. New Ireland: 1, 2.—General distribution: East Africa, Madagascar and Mascarenes east to Kiribati (Line Islands) and Pitcairn, north to Ryukyu Islands, south to off northern Australia, New Caledonia and Rapa. Found in coral reefs, usually close to shelter, 1–60 m depth. Marine.
description: Published as part of Andréfouët, Serge, Chen, Wei-Jen, Kinch, Jeff, Mana, Ralph, Russell, Barry C., Tully, Dean & White, William T., 2019, Checklist of the marine and estuarine fishes of New Ireland Province, Papua New Guinea, western Pacific Ocean, with 810 new records, pp. 1-360 in Zootaxa 4588 (1) on page 154, DOI: 10.11646/zootaxa.4588.1.1, http://zenodo.org/record/2988163