cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Medicago minima Linnaeus 1754
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Fabales
Fabaceae
Medicago
Medicago minima

description: Medicago minima (Linnaeus) Linnaeus, Flora Anglica: 21. 1754, nom. inval.
Type not relevant.
 Current name:  Medicago minima  (L.) Bartal. (Fabaceae: Faboideae).
 Note: Shinners (in Rhodora 58: 3. 1956) questioned whether the recombination of var. minima at species rank was made by Linnaeus (in Fl. Anglica: 21. 1954). Shinners suggested that this is an error of interpretation, as Linnaeus subsequently continued to treat the taxon as a variety of M. polymorpha. Shinners accepted Bartalini (1776) as the first to make the combination at species rank, as did Stearn (Introd. Ray’s Syn. Meth. Stirp. Brit.  (Ray Soc. ed.): 57. 1973). Greuter (in Candollea 44: 563. 1989) disagreed, arguing that the combination dates from 1754. Brummitt & Meikle (in Watsonia 19: 181-183. 1993) argued, however, that there are typographical variants of the thesis which make it unreasonable to interpret names such as this (though they focussed particularly on two names in Primula) as a new combination.
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part M), pp. 651-689 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 659, DOI: 10.5281/zenodo.291971
Tragulus napu
Creators: name: Thu, Aye Myat
name: Lwin, Ye Htet
name: Quan, Rui-Chang
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Artiodactyla
Tragulidae
Tragulus
Tragulus napu

description: 313. Tragulus napu (F. Cuvier, 1822)
Common name: Greater Indo-Malayan Chevrotain Myanmar name:
Distribution: Brunei Darussalam, Indonesia, Malaysia, Singapore and Thailand. In Myanmar, recorded in Tanintharyi Region (Htaung Pru RF and Lenya Proposed NP).
description: Published as part of Thu, Aye Myat, Lwin, Ye Htet & Quan, Rui-Chang, 2024, Mammals of Myanmar: an annotated checklist, pp. 147-197 in Mammalia (Warsaw, Poland) (Warsaw, Poland) 88 (3) on page 186, DOI: 10.1515/mammalia-2023-0098, http://zenodo.org/record/13913939
title: Zooplankton distribution in a hypoxic eddy in the Eastern Tropical North Atlantic - an “open ocean dead zone'?
Creators: name: Hauss, Helena
name: Christiansen, Svenja
name: Kiko, Rainer
name: Lima, Miryan Edvam
name: Rodrigues, Elizandro
name: Schütte, Florian
name: DamianGrundle
name: Karstensen, Johannes
name: Löscher, Carolin
name: Körtzinger, Arne
name: Fiedler, Björn
Publisher: name: ASC 2015 - Theme session R
Year: 2024
Subjects: Ecosystem observation, processes and dynamics
Pressures, impacts, conservation, and management

description: No abstracts are to be cited without prior reference to the author.The recent discovery of mesoscale eddies in the Eastern Tropical North Atlantic (ETNA) that harbor an intense oxygen minimum zone (OMZ) just below the mixed layer has led us to conduct an interdisciplinary eddy hunt. In spring 2014, an anticyclonic mode water eddy passing north of Cape Verde was tracked using satellite data and gliders, followed by ship-based sampling. The eddy was characterized by increased nitrate and Chl-a, along with a 1.5 to 2-fold increase in total area-integrated zooplankton abundance. O2 concentrations were as low as 4.5 μmol kg-1 (85 to 120 m depth). In this depth range, a marked reduction in target strength (shipboard ADCP, 75 kHz) at nighttime was evident. Acoustic scatterers were avoiding this zone and were compressed at the surface. However, vertically stratified multinet hauls and Underwater Vision Profiler (UVP5) image data revealed that this depth range was not completely void of metazoan life. Many of the smaller and/or less mobile organisms targeted by the multinet were able to tolerate conditions in the shallow OMZ. In particular, Oncaea spp., ostracods, eucalanoid copepods and siphonophores seemed to favor this zone, while e.g. euphausiids appeared to avoid it.
Medicago polymorpha Linnaeus 1753
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Fabales
Fabaceae
Medicago
Medicago polymorpha

description: Medicago polymorpha Linnaeus, Species Plantarum 2: 779, 1200. 1753.
"Habitat [p. 1200:] Europa australi." RCN: 5720.
 Lectotype (Heyn in Bull. Res. Council Israel, Sect. D, Bot. 7: 163. 1959): Herb. Clifford: 378, Medicago 11 δ (BM-000646786).
 Current name:  Medicago polymorpha  L. (Fabaceae: Faboideae).
 Note: Shinners (in Rhodora 58: 5-7. 1956) provided an extensive discussion, concluding "[the name] is here typified by the element later named var. nigra ", but he cited no specimen or illustration to serve as the type. Heyn (1959) subsequently designated Clifford material as the type. However, Greuter (in Boissiera 13: 80. 1967) argued that an implicit typification by Krocker in 1790 meant that the name must be regarded as a nomen ambiguum. Lambinon (in Taxon 30: 363. 1981) subsequently proposed the rejection of the name but this was not approved by the Committee for Spermatophyta (in Taxon 35: 560. 1986).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part M), pp. 651-689 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 660, DOI: 10.5281/zenodo.291971
Tragulus williamsoni Kloss 1916
Creators: name: Thu, Aye Myat
name: Lwin, Ye Htet
name: Quan, Rui-Chang
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Artiodactyla
Tragulidae
Tragulus
Tragulus williamsoni

description: 314. Tragulus williamsoni Kloss, 1916
Common name: Northern Chevrotain
Myanmar name:
Distribution: Brunei Darussalam, Cambodia, Indonesia, Laos, Malaysia, Singapore, Northern Thailand and possibly in Southern China, Laos, Vietnam and Southeastern Myanmar.
Remarks: Although this taxon was regarded as a distinct species, its distribution range remains unclear and further taxonomic study is needed (Meijaard et al. 2017).
description: Published as part of Thu, Aye Myat, Lwin, Ye Htet & Quan, Rui-Chang, 2024, Mammals of Myanmar: an annotated checklist, pp. 147-197 in Mammalia (Warsaw, Poland) (Warsaw, Poland) 88 (3) on page 186, DOI: 10.1515/mammalia-2023-0098, http://zenodo.org/record/13913939
ECOLOGY OF THE VELVET SWIMMING CRAB LIOCARCINUS PUBER (L.) (BRACHYURA: PORTUNIDAE)
Creators: name: NORMAN, CHRISTOPHER PAUL
Publisher: name: University of Plymouth
Year: 1989

description: Currently, Liocarcinus puber is commercially fished in the United Kingdom and exported to Southern Europe. The species appears particularly vulnerable to overfishing and has a history of overexploitation. The present study has examined the reproduction, growth and diet of L. puber, to provide information on which to manage this fishery. Immature Liocarcinus puber were first observed in late summer at a size of 6-10mm long carapace width (LCW). Growth in immature crabs was rapid, and sexual maturity occurred after approx. one year at 45mm (for males) and 40mm (for females) LCW. To differentiate the modal growth of mature crabs, probit analysis and computer models (ELEFAN) have been used. The life expectancy for L. puber is estimated at between 4-6 years, with males attaining a maximum size of approx. 95-100mm LCW and females 85-90mm LCW. From the end of the second year, moulting in both sexes was annual, and occurred in early summer for males and later in the year (generally late summer to autumn) for females. The reproductive cycle was also strongly seasonal with mating occurring at the time of the female moult. Evidence from the seasonal occurrence of different egg stages, and the ovarian development of ovigerous females, suggests that older females (II+ years) produce more than one brood each breeding season (January to July). Stomach analyses established that the diet of Liocarcinus puber contained quantities of both animal and algal material, however, algae were the most abundant prey item. Animal prey items included a broad range of benthic organisms and variation in the diet was noted between depth zones, with the availability of prey items appearing to largely determine the diet. Analysis of laminarinase activity in the hepatopancreatic tissue showed levels comparable to the highest recorded for any crustacean. L. puber can survive for extended periods, and moult on an algal diet, however, it appears that an algal diet contains insufficient protein to fully support long-term growth in this crab.
title: Genetic variation in the physiological performance of F. vesiculosus: Does the genotype matter?
Creators: name: Rothäusler, Eva
name: Sjöroos, Joakim
name: Jormalainen, Veijo
Publisher: name: ASC 2015 - Theme session Q
Year: 2024
Subjects: Baltic Sea (ICES Ecoregion)
Ecosystem observation, processes and dynamics

description: No abstracts are to be cited without prior reference to the author.The rocky littoral of the Baltic Sea is typically compromised of Fucus vesiculosus, and genetic diversity within this species may play an analogous role to species diversity. Especially important is the amount of genetic variation in the key traits of F. vesiculosus because it will determine their persistence. To study genetic variation, we grew replicated vegetative fronds (clones) of F. vesiculosus genotypes in common gardens. We quantified their genetic variation using photosynthetic parameters, growth, and osmotic stress responses by exposing fronds to desiccation, freezing and hyposalinity. Genetic variation among genotypes was apparent for some photosynthetic parameters and growth. After recovering from freezing, genotypes responded with different high photosynthetic efficiency but no such genetic variation was evident for genotypes treated with hyposalinity and desiccation. Our results revealed minor desiccation tolerance but very good ability to withstand freezing and short-term hyposalinity, implying that there is strong selection for stress tolerant genotypes. Conversely, the encountered genetic variation in photosynthesis and growth among F. vesiculosus genotypes highlights their potential to adapt to novel environments.
Moschus fuscus Li 1981
Creators: name: Thu, Aye Myat
name: Lwin, Ye Htet
name: Quan, Rui-Chang
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Artiodactyla
Moschidae
Moschus
Moschus fuscus

description: 315. Moschus fuscus Li, 1981
Common name: Black Musk Deer
Myanmar name:
Distribution: Bhutan, Southern China, Northeastern India and Nepal. In Myanmar, a sample was recorded in Putao Township, Kachin State (Lwin et al. 2021).
Remarks: The species was described as Siberian musk deer M. moschiferus in “ Wild Mammals of Myanmar ”; however, M. moschiferus is distributed in Northeast Asia. Thus, the musk deer in Myanmar could possibly be M. fuscus (Pan et al. 2015), however, further taxonomic study is needed. This species is an endangered and completely protected species of Myanmar.
description: Published as part of Thu, Aye Myat, Lwin, Ye Htet & Quan, Rui-Chang, 2024, Mammals of Myanmar: an annotated checklist, pp. 147-197 in Mammalia (Warsaw, Poland) (Warsaw, Poland) 88 (3) on page 186, DOI: 10.1515/mammalia-2023-0098, http://zenodo.org/record/13913939
Studies on the filamentous gliding bacteria Vitreoscilla stercoraria
Creators: name: Biggs, Laura Frances
Publisher: name: University of Plymouth
Year: 2003

description: Strains of Vitreoscilla stercoraria were isolated from the environment and characterised. Cell width, motility and requirement of each strain for sodium chloride were investigated. Two strains were selected for further study and the effect of monensin and FCCP on growth of the strains was investigated. One strain of Vitreoscilla (LB13) was chosen for further study, cells from strain LB 13 were found to be 1.38 µm ± 0.041 (± 1 SEM, n=10) wide, were motile by gliding and had an optimum requirement for sodium chloride for growth of 43 mM. The organism was grown in batch culture and respiratory membranes were isolated. Cytochrome bo was extracted from the respiratory membranes and further purification was achieved using column chromatography. A yield of 6.71 % was achieved with a purification factor of 18.5. The light sensitivity of Vitreoscilla stercoraria was investigated. Two strains of Vitreoscilla (LB13 and C1) were shown to be highly sensitive to UV-A (320-400 nm) with an LD50 of less than 20 kJmˉ². Superoxide dismutase and catalase were shown to provide protection from the effect of UV-A during exposure, either separately of together, indicating an involvement of reactive oxygen species. A photo-insensitive strain (LB13A) was isolated during an exposure experiment and originated from a culture of LB13. The possible sodium pumping activity of cytochrome bo from two strains of Vitreoscilla (LB13 and C1) was investigated. The Vmax of decylubiquinol oxidation by respiratory membranes from LB13 and C 1 were calculated and found to be 0.96 nmol sˉ¹ mg-1 and 13.33 nmol sˉ¹ mgˉ¹ respectively. The Km of decylubiquinol oxidation by LB13 membranes was found to be 9.8 µM. Quinol oxidation activity was tested for dependence on sodium chloride in both respiratory membranes and in the purified enzyme. No stimulation of activity was shown with either strain using decylubiquinol, duroquinol or menadiol as substrates. Given the lack of sodium sensitivity it is unlikely that the enzyme pumps sodium.
Axis porcinus
Creators: name: Thu, Aye Myat
name: Lwin, Ye Htet
name: Quan, Rui-Chang
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Artiodactyla
Cervidae
Axis
Axis porcinus

description: 316. Axis porcinus (Zimmermann, 1780)
Common name: Hog Deer
Myanmar name:
Distribution: Bangladesh, Bhutan, Cambodia, India, Nepal, Pakistan and possibly in China, Laos and Vietnam. In Myanmar, recorded in Kachin State (Hukaung Valley WS; Naing et al. 2015, Indawgyi Wetland WS; Lwin et al. 2018) and Kayin State (sighting record in the Kayin lowland forest area; Moo et al. 2017).
Remarks: This species is an endangered and completely protected species of Myanmar.
description: Published as part of Thu, Aye Myat, Lwin, Ye Htet & Quan, Rui-Chang, 2024, Mammals of Myanmar: an annotated checklist, pp. 147-197 in Mammalia (Warsaw, Poland) (Warsaw, Poland) 88 (3) on page 186, DOI: 10.1515/mammalia-2023-0098, http://zenodo.org/record/13913939
Medicago arabica Huds.
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Fabales
Fabaceae
Medicago
Medicago arabica

description: Medicago polymorpha Linnaeus var. arabica Linnaeus, Species Plantarum 2: 780. 1753.
RCN: 5720.
 Lectotype (Heyn in Bull. Res. Council Israel, Sect. D, Bot. 7: 167. 1959): [icon] "Medica cochleata minor polycarpos annua capsula majore, alba, folio cordato, macula fusca notato" in Morison, Pl. Hist. Univ. 2: 154, s. 2, t. 15, f. 12. 1680.
 Current name:  Medicago arabica  (L.) Huds. (Fabaceae: Faboideae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part M), pp. 651-689 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 660, DOI: 10.5281/zenodo.291971
title: Digesting in hypoxia: impact on gastric evacuation rate and postprandial metabolism (SDA) of Atlantic cod, Gadus morhua
Creators: name: Chabot, Denis
name: Behrens, Jane
name: Andersen, Niels
Publisher: name: ASC 2015 - Theme session R
Year: 2024
Subjects: Ecosystem observation, processes and dynamics
Pressures, impacts, conservation, and management

description: No abstracts are to be cited without prior reference to the author.Chronic hypoxia reduces both food consumption and growth rate of ﬁsh. As digestion results in increased oxygen uptake, the so?called speciﬁc dynamic action (SDA), a possible mechanism is that the reduction of aerobic metabolic scope imposed by hypoxia limits the increase in oxygen uptake during hypoxia. This in turn prolongs the SDA response and, conversely, decreases ingestion rate over time. However, nothing is known of the underlying processes in the stomach and the gut. This study investigates gastric evacuation (GE) rates at 3 levels of dissolved oxygen (90, 55 and 40% sat.) and the SDA response in normoxia and hypoxia (40 % sat.). GE proceeded signiﬁcantly slower at 55 and 40% sat. compared with normoxia, and, as digestion proceeded, the moisture content of the bolus increased more slowly at 55 and 40% sat. than in normoxia. Further analysis of the available SDA data will reveal to what extent these support the suppressing eﬀects of hypoxia on gastric performance.
Rucervus eldii M ' Clelland 1842
Creators: name: Thu, Aye Myat
name: Lwin, Ye Htet
name: Quan, Rui-Chang
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Artiodactyla
Cervidae
Rucervus
Rucervus eldii

description: 317. Rucervus eldii M ’ Clelland 1842
Common name: Brow-antlered Deer, Eld ’ s Deer, Thamin Myanmar name:
Distribution: China, Cambodia, India, Laos and Thailand. There are four recognized subspecies; R. e. thamin Thomas, 1918 is a subspecies that only occur in Central Myanmar (Chatthin and Shwesettaw WS, Popa Mountain Park and Chaungponkan WS; Thu et al. 2019). This is an endemic, endangered and completely protected species of Myanmar.
description: Published as part of Thu, Aye Myat, Lwin, Ye Htet & Quan, Rui-Chang, 2024, Mammals of Myanmar: an annotated checklist, pp. 147-197 in Mammalia (Warsaw, Poland) (Warsaw, Poland) 88 (3) on page 186, DOI: 10.1515/mammalia-2023-0098, http://zenodo.org/record/13913939
Site-specific structure and stability constrained substitution models improve phylogenetic inference
Creators: name: Bastolla, Ugo
name: Lorca, Ivan
name: Arenas, Miguel
Publisher: name: Zenodo
Year: 2024
Subjects: substitution model
protein folding stability
Protein structure conservation
Selection on protein structure

description: In previous studies, we presented site-specific substitution models of protein evolution based on selection on the folding stability of the native state (Stab-CPE), which predict more realistically the evolutionary variability across protein sites. However, those Stab-CPE present qualitative differences from observed data, probably because they ignore changes in the native structure, despite empirical studies suggesting that conservation of the native structure is a stronger selective force than selection on folding stability. 

Here we present novel structurally constrained substitution models (Str-CPE) based on Julian Echave's model of the structural change due to a mutation as the linear response of the protein to a perturbation and on the explicit model of the perturbation generated by a specific amino-acid mutation. Compared to our previous Stab-CPE models, the novel Str-CPE models are more stringent (they predict lower sequence entropy and substitution rate), provide higher likelihood to multiple sequence alignments (MSA) that include one or more known structures, and better predict the observed conservation across sites. The models that combine Str-CPE and Stab-CPE models are even more stringent and fit the empirical MSAs better.

We refer collectively to our models as structure and stability constrained substitution models (SSCPE). Importantly in comparison to the traditional empirical substitution models, the SSCPE models infer phylogenetic trees of distantly related proteins more similar to reference trees based on structural information.

We implemented the SSCPE models in the program SSCPE.pl, freely available at https://github.com/ugobas/SSCPE, which infers phylogenetic trees under the SSCPE models with the program RAxML-NG from a concatenated alignment and a list of protein structures that overlap with it.
description: The files are text files that can be open with any text editor.
Funding provided by: Agencia Estatal de InvestigaciónROR ID: https://ror.org/003x0zc53Award Number: PID2019-109041GB-C22/10.13039/501100011033
Funding provided by: Agencia Estatal de InvestigaciónROR ID: https://ror.org/003x0zc53Award Number: PID2019-107931GA-I00/AEI/10.13039/501100011033
description: The data were generated by the programs tnm (torsional network model, Mendez and Bastolla 2010) and Prot_evol, whose last version is presented in the paper related with the dataset.
Rusa unicolor
Creators: name: Thu, Aye Myat
name: Lwin, Ye Htet
name: Quan, Rui-Chang
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Artiodactyla
Cervidae
Rusa
Rusa unicolor

description: 318. Rusa unicolor (Kerr, 1792)
Common name: Sambar
Myanmar name:
Distribution: Bangladesh, Bhutan, Brunei Darussalam, Cambodia, China, India, Indonesia, Laos, Malaysia, Nepal, Sri Lanka, Thailand and Vietnam. In Myanmar, recorded in Kachin State (Madwalrazi area, Bumphabum, Hponkanrazi,
Indawgyi Wetland and Hukaung Valley WS), Chin State (Natmataung NP), Sagaing Region (Alaungdawkathapa NP, Htamanthi and Proposed Mahamyaing WS), Kayin State, Rakhine State, Tanintharyi Region, Bago Yoma and Popa Mountain Park.
Remarks: This species is a vulnerable and normally protected species of Myanmar.
description: Published as part of Thu, Aye Myat, Lwin, Ye Htet & Quan, Rui-Chang, 2024, Mammals of Myanmar: an annotated checklist, pp. 147-197 in Mammalia (Warsaw, Poland) (Warsaw, Poland) 88 (3) on pages 186-187, DOI: 10.1515/mammalia-2023-0098, http://zenodo.org/record/13913939
Elaphodus cephalophus Milne-Edwards 1872
Creators: name: Thu, Aye Myat
name: Lwin, Ye Htet
name: Quan, Rui-Chang
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Artiodactyla
Cervidae
Elaphodus
Elaphodus cephalophus

description: 319. Elaphodus cephalophus Milne-Edwards, 1872
Common name: Tufted Deer
Myanmar name:
Distribution: Only occur in China and Northern Myanmar (Proposed Imawbum NP; Nijman 2015).
Remarks: This species is listed as completely protected species of Myanmar.
description: Published as part of Thu, Aye Myat, Lwin, Ye Htet & Quan, Rui-Chang, 2024, Mammals of Myanmar: an annotated checklist, pp. 147-197 in Mammalia (Warsaw, Poland) (Warsaw, Poland) 88 (3) on page 187, DOI: 10.1515/mammalia-2023-0098, http://zenodo.org/record/13913939
Medicago ciliaris All.
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Fabales
Fabaceae
Medicago
Medicago ciliaris

description: Medicago polymorpha Linnaeus var. ciliaris Linnaeus, Species Plantarum 2: 780. 1753.
RCN: 5720.
 Neotype (Lassen inTurland & Jarvis in Taxon 46: 475. 1997): France. Aude: Craboules, prés salés et bord des chemins, Jun 1889, Abbé Pons s.n.  [Magnier Fl. Select. Exsicc. 2353] (LD).
 Current name:  Medicago ciliaris  (L.) All. (Fabaceae: Faboideae).
 Note: Heyn (in Bull. Res. Council Israel, Sect. D, Bot. 7: 167. 1959) discussed the name but was unable to locate a suitable type. Lassen subsequently designated a neotype.
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part M), pp. 651-689 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 660, DOI: 10.5281/zenodo.291971
Structure and stability constrained substitution models outperform traditional substitution models used for evolutionary inference
Creators: name: Bastolla, Ugo
name: Lorca, Ivan
name: Arenas, Miguel
Publisher: name: Zenodo
Year: 2022
Subjects: substitution model
protein folding stability
Protein structure conservation
Selection on protein structure

description: The current knowledge about how protein structures influence sequence evolution is rarely incorporated into substitution models adopted for phylogenetic inference, which are commonly based on independent with the same substitution process and ignore the known variation of the evolutionary rates across sites with different structural properties. In previous works, we presented site-specific substitution models of protein evolution based on selection on the folding stability of the native state (Stab-CPE), which predict more realistically the evolutionary variability across protein sites. However, those Stab-CPE present qualitative differences from observed data, probably because they ignore changes in the native structure, despite empirical studies suggesting that conservation of the native structure is a strong selective force. Here we present novel structurally constrained substitution models (Str-CPE) based on Julián Echave's model of the structural change due to a mutation as the linear response of the protein to a perturbation and on the explicit model of the perturbation generated by a specific amino-acid mutation. Compared to our previous Stab-CPE models, the novel Str-CPE models are more stringent (they predict lower sequence entropy and substitution rate), provide higher likelihood to multiple sequence alignments (MSA) of the wild-type protein, and better predict the observed substitution rates. Next, we combine Str-CPE and Stab-CPE models to obtain structure and stability constrained substitution models (SSCPE) that fit the empirical MSAs even better. Importantly, these SSCPE models present a relevant improvement of the phylogenetic likelihood for all ten protein families that we analyzed with the program RAxML-NG. We implemented the SSCPE models in the program Prot evol, freely available at https://github.com/ugobas/Prot_evol.
description: The files are text files that can be open with any text editor.Funding provided by: Agencia Estatal de Investigación
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100011033
Award Number: PID2019-109041GB-C22/10.13039/501100011033Funding provided by: Agencia Estatal de Investigación
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100011033
Award Number: PID2019-107931GA-I00/AEI/10.13039/501100011033
description: The data were generated by the programs tnm (torsional network model, Mendez and Bastolla 2010) and Prot_evol, whose last version is presented in the paper related with the dataset.
Muntiacus feae
Creators: name: Thu, Aye Myat
name: Lwin, Ye Htet
name: Quan, Rui-Chang
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Artiodactyla
Cervidae
Muntiacus
Muntiacus feae

description: 320. Muntiacus feae (Thomas and Doria, 1889)
Common name: Fea ’ s Muntjac
Myanmar name:
Distribution: Only occur in Thailand and Myanmar (Htaung Pru RF and Proposed Lenya NP, Proposed Imawbum NP and possibly in Kayin State).
Remarks: A photograph taken at 1250-m elevation in Hponkanrazi WS in Northern Myanmar shows a male with some features like M. feae and the trophies attributed to this species were observed in the villages in the Wusut Area, Hmai Hka catchment, Kachin State in 2010 (Nijman 2015). No further details are available and these records are best considered provisional at the moment though the distribution of this species is restricted to a small area in Southern Myanmar and Thailand (Nijman 2015). This species is listed as completely protected species of Myanmar.
description: Published as part of Thu, Aye Myat, Lwin, Ye Htet & Quan, Rui-Chang, 2024, Mammals of Myanmar: an annotated checklist, pp. 147-197 in Mammalia (Warsaw, Poland) (Warsaw, Poland) 88 (3) on page 187, DOI: 10.1515/mammalia-2023-0098, http://zenodo.org/record/13913939
title: Causes and consequences of the Baltic Sea hypoxia: the vicious circle revisited with models
Creators: name: Savchuk, Oleg P.
Publisher: name: ASC 2015 - Theme session R
Year: 2024
Subjects: Ecosystem observation, processes and dynamics
Pressures, impacts, conservation, and management

description: No abstracts are to be cited without prior reference to the author.Long-term dynamics of the Baltic Sea offshore hypoxia is governed by interplay between a sporadic natural aeration of the deep waters and man-enhanced oxygen demand. Variations of hypoxic zone bring forth biogeochemical alterations of the nitrogen and phosphorus pools interlocked in positive feedback where hypoxia is sustained with mineralization of primary production based on nitrogen fixed by cyanobacteria thriving on a P excess. The ecosystem consequences of these interactions are quantified with an aid of both extensive databases and simulations with mathematical models.
Empathy for the Devil: Can AI-Illustrated Vignettes Manipulate Affective Polarization and Democratic Values?
Creators: name: Peterlevitz, Tiago
Publisher: name: OSF Registries
Year: 2024
Subjects: subject: Comparative Politics
subject: Political Science
subject: FOS: Political science
subject: Social and Behavioral Sciences

description: This is the pre-analysis plan for a survey experiment investigating how AI-illustrated vignettes emphasizing tolerance and counter-stereotypes can foster empathy toward political adversaries.
title: Modeling the population-level effects of hypoxia on a coastal fish: implications of a spatially-explicit individual-based model
Creators: name: Rose, Kenneth A.
name: Creekmore, Sean
name: Thomas, Peter
name: Craig, J. Kevin
name: Miller-Neilan, Rachael
name: Rahman, Md. Saydur
name: Wang, Lixia
name: Justic, Dubravko
Publisher: name: ASC 2015 - Theme session R
Year: 2024
Subjects: Ecosystem observation, processes and dynamics
Pressures, impacts, conservation, and management

description: No abstracts are to be cited without prior reference to the author.The northwestern Gulf of Mexico currently experiences a large hypoxic area (“dead zone”) during the summer. We developed a spatially-explicit, individual-based model to analyze how hypoxia effects on individual croaker in the northwestern Gulf of Mexico could lead to population-level responses. The model follows the hourly growth, mortality, reproduction, and movement of individuals for 140 years on a 300 x 800 spatial grid representing the bottom habitat. Chlorophyll-a concentration, water temperature, and dissolved oxygen (DO) were specified daily for each grid cell and repeated for each year of the simulation. For some simulations, chlorophyll was adjusted from baseline based on the severity (mild or severe) of the hypoxia in each year. Hypoxia effects were imposed by exposure to low DO reducing growth, survival, and annual fecundity. Simulations were performed that used random sequences of hypoxia years, with and without coupling to chlorophyll concentrations. The population was predicted to decline by 10 to 25% due to hypoxia. The negative effects of reduced food under a 25% reduction in nutrients were offset by the positive effects of moderate reductions in hypoxia. Our results highlight how the population-level responses are a function of the combined effects of nutrient-driven food supply and hypoxia.
Muntiacus gongshanensis Ma 1990
Creators: name: Thu, Aye Myat
name: Lwin, Ye Htet
name: Quan, Rui-Chang
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Artiodactyla
Cervidae
Muntiacus
Muntiacus gongshanensis

description: 321. Muntiacus gongshanensis Ma, 1990
Common name: Gongshan Muntjac
Myanmar name:
Distribution: Southwest China and Northern Myanmar (Hponkanrazi WS, Hkakaborazi and Proposed Imawbum NP; Lwin et al. 2021; Nijman 2015; Zhang et al. 2021).
Remarks: This species is listed as completely protected species of Myanmar.
description: Published as part of Thu, Aye Myat, Lwin, Ye Htet & Quan, Rui-Chang, 2024, Mammals of Myanmar: an annotated checklist, pp. 147-197 in Mammalia (Warsaw, Poland) (Warsaw, Poland) 88 (3) on page 187, DOI: 10.1515/mammalia-2023-0098, http://zenodo.org/record/13913939
An evaluation of multivariate statistical techniques for the analysis of yield from barley (Hordeum vulgare L.) breeding trials data
Creators: name: ABDULLAH, AHMED
Publisher: name: University of Plymouth
Year: 2007

description: This project involved two locations (Breda and Tel Hadya) over two seasons (1993 and 1994). Yield was found to have been affected by many factors including environment, genotype and morphological characters. A genotype-environment interaction (GEl) was also discovered. To investigate the influence of morphological characters on yield parameters, multivariate statistical techniques (canonical analysis, factor analysis and multiple regression analysis (linear and exponential)) were used. Multivariate statistical techniques were applied to three hybrids (Hybrid 1, 2 and 3) in replicated field plots at two locations (Breda and Tel Hadya) in two seasons. Canonical analysis and factor analysis revealed a significant relationship between yield parameters and morphological characters. However, this relationship was not significant for each hybrid because there were insufficient data for each hybrid. Stepwise multiple regression analysis showed that plant height, vegetative duration and length of growing season were the significant factors influencing yield parameters, while leafiness was not. The relationship can approximate nonlinear in that it gives more realistic predictions. Consequently, stepwise multiple exponential equation fitted the data better than stepwise multiple linear equation. The relationship between yield parameters and morphological characters was affected by environment but not by genotype.
Medicago coronata Bartal.
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Fabales
Fabaceae
Medicago
Medicago coronata

description: Medicago polymorpha Linnaeus var. coronata Linnaeus, Species Plantarum 2: 780. 1753.
RCN: 5720.
 Lectotype (Heyn in Bull. Res. Council Israel, Sect. D, Bot. 7: 167. 1959): [icon] "Medica coronata Cherleri, parva" in Bauhin & Cherler, Hist. Pl. Univ. 2: 386. 1651.
 Current name:  Medicago coronata  (L.) Bartal. (Fabaceae: Faboideae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part M), pp. 651-689 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 660, DOI: 10.5281/zenodo.291971
Muntiacus putaoensis Amato, Egan and Rabinowitz 1999
Creators: name: Thu, Aye Myat
name: Lwin, Ye Htet
name: Quan, Rui-Chang
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Artiodactyla
Cervidae
Muntiacus
Muntiacus putaoensis

description: 322. Muntiacus putaoensis Amato, Egan and Rabinowitz, 1999
Common name: Leaf Muntjac
Myanmar name:
Distribution: China and Northern Myanmar (Hkakaborazi NP and Hponkanrazi WS; Lwin et al. 2021) and adjacent area of India.
Remarks: This species is listed as a completely protected species of Myanmar.
description: Published as part of Thu, Aye Myat, Lwin, Ye Htet & Quan, Rui-Chang, 2024, Mammals of Myanmar: an annotated checklist, pp. 147-197 in Mammalia (Warsaw, Poland) (Warsaw, Poland) 88 (3) on page 187, DOI: 10.1515/mammalia-2023-0098, http://zenodo.org/record/13913939
BYUDJET - SOLIQ SIYOSATI
Creators: name: Qo'ldoshev, Asadbek
Publisher: name: Zenodo
Year: 2024

description: Siyosatning juda ko‘p yoki xilma-xil tur (ko‘rinish)lari mayjud. Ulardan biri byudjet-soliq siyosatidir. Bu siyosat pul mablag‘larining harakati bilan bevosita bogliq. Byudjet-soliq siyosati bir tomondan, byudjet daromadlarini (oqilona) shakllantirish va ikkinchi tomondan, byudjet xarajatlarini (samarali) sarflash bilan bog‘liq. Aslida byudjet siyosati tom ma'noda o‘z ichiga soliq siyosatini ham qamrab oladi. Biroq amaliyotda ko‘pchilik hollarda, byudjet daromadlarini shakllantirishga qaratilgan siyosatni, odatda, soliq siyosati va byudjet xarajatlarini sarflashga qaratilgan siyosatni esa byudjet siyosati, deb yuritiladi. Shu ma’noda byudjet-soliq siyosatini shartli ravishda bir-biridan va nisbiy jihatdan mustaqil bo'lgan byudjet va soliq siyosatlarining majmuyi sifatida ham e'tirof etish mumkin.
title: Dead zones relate to the body condition of the Baltic Sea cod
Creators: name: Casini, Michele
name: Käll, Filip
name: Hansson, Martin
name: Karlsson, Olle
name: Hjelm, Joakim
Publisher: name: ASC 2015 - Theme session R
Year: 2024
Subjects: Ecosystem observation, processes and dynamics
Pressures, impacts, conservation, and management

description: No abstracts are to be cited without prior reference to the author.Investigating the factors regulating fish individual growth is crucial in the management of exploited fish populations. The growth and body condition of cod has decreased dramatically during the past 3 decades in the Baltic Sea, an area at present severely affected by phenomena of hypoxia and anoxia (i.e. “dead zones”). Here, we statistically investigated using GAMs the factors that have driven The Eastern Baltic cod body condition during the past 25 years using fishery-independent biological data and hydrological observations. We evidenced a combination of biological and abiotic factors driving cod condition, operating both in space and time. The results in fact showed that the temporal decrease in cod condition was mainly related to the dramatic increase in the extent of dead zones, although the abundance of pelagic fish prey were also significant explanatory factors in the models. Dead zones can act on cod condition through different mechanisms, related directly to species physiology, or to behaviour and trophic interactions, that will be presented and discussed in the oral presentation.
Muntiacus vaginalis
Creators: name: Thu, Aye Myat
name: Lwin, Ye Htet
name: Quan, Rui-Chang
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Artiodactyla
Cervidae
Muntiacus
Muntiacus vaginalis

description: 323. Muntiacus vaginalis (Boddaert, 1785)
Common name: Northern Red Muntjac
Myanmar name:
Distribution: Bangladesh, Bhutan, Brunei Darussalam Cambodia, China, India, Indonesia, Laos, Malaysia, Nepal, Pakistan, Sri Lanka, Thailand and Vietnam. In Myanmar, widely distributed and recorded in most of the PAs and RF.
Remarks: M. vaginalis is considered as a subspecies of M. muntjac; however, by their distribution range, the muntjac species in Myanmar could be identified as M. vaginalis (Zhang et al. 2021). In Myanmar, presence is uncertain as the red muntjac of Myanmar is identified as “ northern red muntjac M. vaginalis ” (Zhang et al. 2021); however, possibly distributed in southern Tanintharyi Region (Proposed Lenya NP and its extension; Grindley 2019). This species is listed as a seasonally protected species of Myanmar.
description: Published as part of Thu, Aye Myat, Lwin, Ye Htet & Quan, Rui-Chang, 2024, Mammals of Myanmar: an annotated checklist, pp. 147-197 in Mammalia (Warsaw, Poland) (Warsaw, Poland) 88 (3) on page 187, DOI: 10.1515/mammalia-2023-0098, http://zenodo.org/record/13913939
Medicago minima Linnaeus 1754
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Fabales
Fabaceae
Medicago
Medicago minima

description: Medicago polymorpha Linnaeus var. hirsuta Linnaeus, Species Plantarum 2: 780. 1753.
RCN: 5720.
 Lectotype (Heyn in Bull. Res. Council Israel, Sect. D, Bot. 7: 168. 1959): [icon] "Medica echinata hirsuta" in Bauhin & Cherler, Hist. Pl. Univ. 2: 386. 1651.
 Current name:  Medicago minima  (L.) L. (Fabaceae: Faboideae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part M), pp. 651-689 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 660, DOI: 10.5281/zenodo.291971
EMP-A 2024 TRAINNING (Onsset Track) Report
Creators: name: Karim, Deliornica
name: Sankoh, Martin Sidi
Publisher: name: Zenodo
Year: 2024

description: EMP-A -2024 

This report constitutes the outcome of a three-weeks capacity building activity on GEP-OnSSET as part of the 2024 Energy Modelling Platform for Africa workshop. The authors collected input data, set parameters, calibrated the model, and run electrification investment scenarios for Sierra Leone in order to explore pathways leading to the achievement of electrification targets. The results of this analysis are not conclusive, but rather the output of experimentation with the model and thus only indicative. You may contact the author for more information and/or questions about the methodology, limitations, and follow-up activities of this study.
Bos gaurus C. H. Smith 1827
Creators: name: Thu, Aye Myat
name: Lwin, Ye Htet
name: Quan, Rui-Chang
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Artiodactyla
Bovidae
Bos
Bos gaurus

description: 324. Bos gaurus C.H. Smith, 1827
Common name: Gaur, Indian Bison
Myanmar name:
Distribution: Bhutan, Cambodia, China, India, Laos, Malaysia, Nepal, Thailand, Vietnam, and possibly in Sri Lanka and Bangladesh. In Myanmar, recorded in Kachin and Shan States (Hponkanrazi, Bumphabum and Hukaung Valley WS, Momeik and Mabein Townships), Sagaing Region (Alaungdawkathapa NP, Htamanthi WS), Paunglaung catchment, Rakhine State (Rakhine Yoma Elephant Range WS; Cremonesi et al. 2021), Bago Region (North Zamari WS; Hein et al. 2020), Kayin State (Moo et al. 2017), Tanintharyi Region (Tanintharyi Nature Reserve, Htaung Pru RF and Proposed Lenya NP; Grindley 2019) and possibly in Shweudaung WS.
Remarks: The wild species of gaur was considered as B. gaurus, while referring to the domestic form (Mythun, Mithan or Gayal) as B. frontalis Lambert, 1804 (Gentry et al. 2004). B. g. readei is regarded as Myanmar ’ s subspecies, it is a vulnerable and completely protected species of Myanmar.
description: Published as part of Thu, Aye Myat, Lwin, Ye Htet & Quan, Rui-Chang, 2024, Mammals of Myanmar: an annotated checklist, pp. 147-197 in Mammalia (Warsaw, Poland) (Warsaw, Poland) 88 (3) on pages 187-188, DOI: 10.1515/mammalia-2023-0098, http://zenodo.org/record/13913939
title: Food web structure and small pelagic fish interactions in hypoxic conditions
Creators: name: Nikolioudakis, Nikolaos
name: Tsagaraki, Tatiana M.
name: Pirounaki, Myrto M.
name: Giannoulaki, Marianna
name: Machias, Athanasios
name: Somarakis, Stylianos
Publisher: name: ASC 2015 - Theme session R
Year: 2024
Subjects: Ecosystem observation, processes and dynamics
Pressures, impacts, conservation, and management

description: No abstracts are to be cited without prior reference to the author.Small pelagic fish (SPF) depend heavily on environmental changes (e.g. hypoxia) and when combined with human-induced pressures (e.g. high exploitation rates) the sustainable management of the stocks is challenged. To enhance our understanding on how combined pressures affect SPF, impacts on the pelagic niche were studied in a coastal area of the Eastern Mediterranean as part of the PERSEUS project. Two sites with different levels of disturbance and hydrographic characteristics were sampled during two periods (thermal stratification and mixing) following an integrated pelagic ‘end-to-end’ sampling approach that involved concurrent measurements of abiotic and biotic variables. The considerably higher anthropogenic pressures exerted at site A, combined with its topographic and hydrographic characteristics, caused hypoxia below the summer thermocline, leading to a different overall community structure and function compared to site B. More importantly, the ‘compacted’ vital space for SPF caused by hypoxia, confined their diel vertical migration range to the oxygen-rich layer, consequently altering their predator vulnerability. However, SPF densities in site A were extremely higher than in site B with large numbers of juvenile fish. The combined results suggest that complex interactions taking place in hypoxic areas can result in them functioning as nursery grounds despite their severe degradation.
Evaluation of Haematococcus pluvialis as a natural dietary source of the carotenoid astaxanthin for rainbow trout flesh pigmentation
Creators: name: Lagocki, Stephen
Publisher: name: University of Plymouth
Year: 2001

description: The efficacy of the lipid soluble carotenoid astaxanthin (biosynthesised as a secondary metabolite by the microalga Haematococcus pluvialis) as a source of pigment to enhance the aesthetic appeal of the flesh of farmed salmonid species has been investigated, using rainbow trout (Oncorhynchus mykiss) as a model. Accretion of astaxanthin within rainbow trout epaxial white muscle was primarily shown to be dependent on dietary inclusion and the type of diet used as a pigment carrier. Different dietary inclusion rates demonstrated a dose response. Cold pressed low oil and commercially extruded high oil diets containing similar astaxanthin concentration were tested, fish receiving the latter obtained higher growth rates and retained higher concentrations of astaxanthin within their flesh as compared to those receiving the former. Assessment of intact encysted H. pluvialis cells and processed H. pluvialis cells which had been mechanically treated to ruptured their cell wall revealed that the astaxanthin retained within the cells is only bioavailable to rainbow trout when the cell wall has been breached. The carotenoid profile of H. pluvialis confirmed that its astaxanthin was in three forms, i.e. free (5.9%), mono-esterified (82.3%) and di-esterified (11.8 %) to fatty acid moieties. Assessment of H. pluvialis purified mono and di-esterified astaxanthin extracts fed to rainbow trout demonstrated that astaxanthin mono-esters were more bioavailable than di-esters. Image analysis confirmed the major colour component of pigmented rainbow trout fillets is red and the distribution of astaxanthin within fillets varies greatly, with the head region having the lightest hue, which gradually increases towards the tail region. The addition of 2-palmitoylaminoproprionic acid (Corbinol) as a feed additive to diets containing synthetic astaxanthin had no effect on increasing the deposition of astaxanthin in the epaxial white muscle. Nevertheless, none of the in vivo trials incorporating H. pluvialis cells or H. pluvialis derived astaxanthin extracts demonstrated any detrimental effects on rainbow trout, in terms of feed utilisation, growth performance or health. Also, the protection afforded to astaxanthin by ruptured H. pluvialis cysts was demonstrated (during in vitro experiments) to provide increased stability as compared to synthetic astaxanthin, with respect to diet storage, exposure to emulated sunlight and loss in a turbulent water column. The present studies contribute to the awareness of Haematococcus pluvialis as a source of natural astaxanthin for salmonid species, by highlighting both negative and positive aspects with respect to its use in the aquaculture industry.
Bos javanicus d'Alton 1823
Creators: name: Thu, Aye Myat
name: Lwin, Ye Htet
name: Quan, Rui-Chang
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Artiodactyla
Bovidae
Bos
Bos javanicus

description: 325. Bos javanicus d ’ Alton, 1823
Common name: Banteng
Myanmar name:
Distribution: Cambodia, China, Indonesia, Laos, Malaysia, Thailand and Vietnam. In Myanmar, recorded in Sagaing Region (Alaungdawkathapa NP and Proposed Mahamyaing WS), Bago Region (North Zamari WS; Hein et al. 2020), and Tanintharyi Region (Tanintharyi Nature Reserve and Proposed Lenya NP; Grindley 2019).
Remarks: There are three subspecies; B. j. birmanicus is regarded as Myanmar subspecies. This is an endangered and completely protected species of Myanmar.
description: Published as part of Thu, Aye Myat, Lwin, Ye Htet & Quan, Rui-Chang, 2024, Mammals of Myanmar: an annotated checklist, pp. 147-197 in Mammalia (Warsaw, Poland) (Warsaw, Poland) 88 (3) on page 188, DOI: 10.1515/mammalia-2023-0098, http://zenodo.org/record/13913939