cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1568474
title: Phylogenetic revision of the South American notopithecines (Mammalia: Notoungulata)

description: A phylogenetic analysis of all Eocene taxa assigned to Notopithecinae has been conducted, evaluating relationships amongst notopithecines, basal interatheriids and Interatheriinae. Other groups of native ungulates were also included. New dental and postcranial characters are considered with respect to previously published data; some characters are evaluated in notoungulates for the first time. Two different searches were performed under parsimony and equal weights. The inclusion of postcranial characters strongly influenced tree topology. The most significant result of the phylogenetic analysis was the identification of a novel monophyletic group, including species traditionally grouped as Patagonian Notopithecinae. The ‘notopithecid’ name is linked to the new clade defined as the clade stemming from the most recent common ancestor of the species <i>Notopithecus adapinus, Antepithecus brachystephanus, Transpithecus obtentus</i> and <i>Guilielmoscottia plicifera</i>. This phylogeny supports the main morphological differences of the new clade with respect to Interatheriinae Interatheriidae. In consequence, a diagnosis is proposed based on phylogenetic results, to which some other morphological characters are added. The Chilean basal interatheriids <i>Johnbell</i> and <i>Ignigena</i> as well as <i>Punapithecus</i> (Argentinean Puna) are excluded from the notopithecid clade, implying biostratigraphical and biogeographical changes. Notopithecid distribution now becomes restricted to the middle–late Eocene part of the Sarmiento Formation outcropping in central Chubut and north-east Santa Cruz provinces, Argentina. Other extra-Patagonian records of notopithecids are not confirmed. The resulting phylogeny resolves some relationships within basal interatheriids differently from previous analyses. Interatheriinae is not recovered as a monophyletic group, and Oldfieldthomasiidae and Henricosborniid are paraphyletic. The position of the Archaeopithecidae <i>Acropithecus rigidus</i> is controversial; it appears at the base of the Typotheria lineage or in the notopithecid clade, but systematic taxonomy and phylogenetic relationships amongst members of Archaeopithecidae remain to be established.
DOI: 10.6084/m9.figshare.1568470
title: Spatial and temporal variation of bird dawn chorus and successive acoustic morning activity in a Mediterranean landscape

description: Ecoacoustic techniques using multiple acoustic sensors and two metrics of the acoustic community – the acoustic complexity index (ACI) and the chorus ratio (CR) – were successfully used to describe and characterize the morning acoustic activity of birds according to three equal temporal intervals during spring 2013: Dawn Chorus, Post Chorus 1, and Post Chorus 2.The metrics were applied across five Italian Mediterranean locations (Valenza, Madonna dei Colli, Monte Curto, Virolo, Croce di Tergagliana) that differed by land-cover typologies. Results from the ACI metrics showed a peak during the Dawn Chorus and a visible lull close to sunrise between Dawn Chorus and Post Chorus 1.The lull was evident in all localities except Valenza, where singing activity was relatively constant across the successive morning intervals. Temperature and vegetation structure were confirmed as important factors associated with morning acoustic activities. Vegetation evenness and temperature across the season was negatively correlated with ACI, whereas CR was positively correlated with temperature and vegetation diversity. Of the 33 species of birds identified during the maximum dawn chorus activity, Blackcap, Blackbird, European Robin, and Great Tit were acoustically dominant and their activity was significantly higher before sunrise except for Blackcap, whose acoustic activity showed no significant differences across time intervals. The dawn chorus is one of the most conspicuous behaviours of birds, engendering much speculation but no definitive, univocal explanations. The ecoacoustic approach opens a new perspective for investigating this complex phenomenon.
DOI: 10.6084/m9.figshare.1568471
title: Biased signaling: potential agonist and antagonist of PAR2

description: Protease activated receptor 2 (PAR2) has emerged as one of the promising therapeutic targets to inhibit rapidly metastasizing breast cancer cells. However, its elusive molecular mechanism of activation and signaling has made it a difficult target for drug development. In this study, in silico methods were used to unfold PAR2 molecular mechanism of signaling based on the concept of GPCR receptor plasticity. Although, there are no conclusive evidences of the presence of specific endogenous ligands for PAR2, the efficacy of synthetic agonist and antagonist in PAR2 signaling has opened up the possibilities of ligand-mediated signaling. Furthermore, it has been proved that ligands specific for one GPCR can induce signaling in GPCRs belonging to other subfamilies. Therefore, the aim of this study was to identify potential agonists and antagonists from the GPCR ligand library (GLL), which may induce biased signaling in PAR2 using the concept of existence of multiple ligand-stabilized receptor conformations. The results of our in silico study suggest that PAR2 may show biased signaling mainly with agonists of serotonin type 1, β-adrenergic type 1,3 and antagonists of substance K (NK1), serotonin type 2, dopamine type 4, and thromboxane receptors. Further, this study also throws light on the putative ligand-specific conformations of PAR2. Thus, the results of this study provide structural insights to putative conformations of PAR2 and also gives initial clues to medicinal chemists for rational drug design targeting this challenging receptor.
DOI: 10.6084/m9.figshare.1568471.v2
title: Biased signaling: potential agonist and antagonist of PAR2

description: Protease activated receptor 2 (PAR2) has emerged as one of the promising therapeutic targets to inhibit rapidly metastasizing breast cancer cells. However, its elusive molecular mechanism of activation and signaling has made it a difficult target for drug development. In this study, in silico methods were used to unfold PAR2 molecular mechanism of signaling based on the concept of GPCR receptor plasticity. Although, there are no conclusive evidences of the presence of specific endogenous ligands for PAR2, the efficacy of synthetic agonist and antagonist in PAR2 signaling has opened up the possibilities of ligand-mediated signaling. Furthermore, it has been proved that ligands specific for one GPCR can induce signaling in GPCRs belonging to other subfamilies. Therefore, the aim of this study was to identify potential agonists and antagonists from the GPCR ligand library (GLL), which may induce biased signaling in PAR2 using the concept of existence of multiple ligand-stabilized receptor conformations. The results of our in silico study suggest that PAR2 may show biased signaling mainly with agonists of serotonin type 1, β-adrenergic type 1,3 and antagonists of substance K (NK1), serotonin type 2, dopamine type 4, and thromboxane receptors. Further, this study also throws light on the putative ligand-specific conformations of PAR2. Thus, the results of this study provide structural insights to putative conformations of PAR2 and also gives initial clues to medicinal chemists for rational drug design targeting this challenging receptor.
DOI: 10.6084/m9.figshare.1568474.v1
title: Phylogenetic revision of the South American notopithecines (Mammalia: Notoungulata)

description: A phylogenetic analysis of all Eocene taxa assigned to Notopithecinae has been conducted, evaluating relationships amongst notopithecines, basal interatheriids and Interatheriinae. Other groups of native ungulates were also included. New dental and postcranial characters are considered with respect to previously published data; some characters are evaluated in notoungulates for the first time. Two different searches were performed under parsimony and equal weights. The inclusion of postcranial characters strongly influenced tree topology. The most significant result of the phylogenetic analysis was the identification of a novel monophyletic group, including species traditionally grouped as Patagonian Notopithecinae. The ‘notopithecid’ name is linked to the new clade defined as the clade stemming from the most recent common ancestor of the species <i>Notopithecus adapinus</i>, <i>Antepithecus brachystephanus</i>, <i>Transpithecus obtentus</i> and <i>Guilielmoscottia plicifera</i>. This phylogeny supports the main morphological differences of the new clade with respect to Interatheriinae Interatheriidae. In consequence, a diagnosis is proposed based on phylogenetic results, to which some other morphological characters are added. The Chilean basal interatheriids <i>Johnbell</i> and <i>Ignigena</i> as well as <i>Punapithecus</i> (Argentinean Puna) are excluded from the notopithecid clade, implying biostratigraphical and biogeographical changes. Notopithecid distribution now becomes restricted to the middle–late Eocene part of the Sarmiento Formation outcropping in central Chubut and north-east Santa Cruz provinces, Argentina. Other extra-Patagonian records of notopithecids are not confirmed. The resulting phylogeny resolves some relationships within basal interatheriids differently from previous analyses. Interatheriinae is not recovered as a monophyletic group, and Oldfieldthomasiidae and Henricosborniid are paraphyletic. The position of the Archaeopithecidae <i>Acropithecus rigidus</i> is controversial; it appears at the base of the Typotheria lineage or in the notopithecid clade, but systematic taxonomy and phylogenetic relationships amongst members of Archaeopithecidae remain to be established.
DOI: 10.6084/m9.figshare.1568470.v1
title: Spatial and temporal variation of bird dawn chorus and successive acoustic morning activity in a Mediterranean landscape

description: Ecoacoustic techniques using multiple acoustic sensors and two metrics of the acoustic community – the acoustic complexity index (ACI) and the chorus ratio (CR) – were successfully used to describe and characterize the morning acoustic activity of birds according to three equal temporal intervals during spring 2013: Dawn Chorus, Post Chorus 1, and Post Chorus 2.The metrics were applied across five Italian Mediterranean locations (Valenza, Madonna dei Colli, Monte Curto, Virolo, Croce di Tergagliana) that differed by land-cover typologies. Results from the ACI metrics showed a peak during the Dawn Chorus and a visible lull close to sunrise between Dawn Chorus and Post Chorus 1.The lull was evident in all localities except Valenza, where singing activity was relatively constant across the successive morning intervals. Temperature and vegetation structure were confirmed as important factors associated with morning acoustic activities. Vegetation evenness and temperature across the season was negatively correlated with ACI, whereas CR was positively correlated with temperature and vegetation diversity. Of the 33 species of birds identified during the maximum dawn chorus activity, Blackcap, Blackbird, European Robin, and Great Tit were acoustically dominant and their activity was significantly higher before sunrise except for Blackcap, whose acoustic activity showed no significant differences across time intervals. The dawn chorus is one of the most conspicuous behaviours of birds, engendering much speculation but no definitive, univocal explanations. The ecoacoustic approach opens a new perspective for investigating this complex phenomenon.
DOI: 10.6084/m9.figshare.1568474.v3
title: Phylogenetic revision of the South American notopithecines (Mammalia: Notoungulata)

description: A phylogenetic analysis of all Eocene taxa assigned to Notopithecinae has been conducted, evaluating relationships amongst notopithecines, basal interatheriids and Interatheriinae. Other groups of native ungulates were also included. New dental and postcranial characters are considered with respect to previously published data; some characters are evaluated in notoungulates for the first time. Two different searches were performed under parsimony and equal weights. The inclusion of postcranial characters strongly influenced tree topology. The most significant result of the phylogenetic analysis was the identification of a novel monophyletic group, including species traditionally grouped as Patagonian Notopithecinae. The ‘notopithecid’ name is linked to the new clade defined as the clade stemming from the most recent common ancestor of the species <i>Notopithecus adapinus, Antepithecus brachystephanus, Transpithecus obtentus</i> and <i>Guilielmoscottia plicifera</i>. This phylogeny supports the main morphological differences of the new clade with respect to Interatheriinae Interatheriidae. In consequence, a diagnosis is proposed based on phylogenetic results, to which some other morphological characters are added. The Chilean basal interatheriids <i>Johnbell</i> and <i>Ignigena</i> as well as <i>Punapithecus</i> (Argentinean Puna) are excluded from the notopithecid clade, implying biostratigraphical and biogeographical changes. Notopithecid distribution now becomes restricted to the middle–late Eocene part of the Sarmiento Formation outcropping in central Chubut and north-east Santa Cruz provinces, Argentina. Other extra-Patagonian records of notopithecids are not confirmed. The resulting phylogeny resolves some relationships within basal interatheriids differently from previous analyses. Interatheriinae is not recovered as a monophyletic group, and Oldfieldthomasiidae and Henricosborniid are paraphyletic. The position of the Archaeopithecidae <i>Acropithecus rigidus</i> is controversial; it appears at the base of the Typotheria lineage or in the notopithecid clade, but systematic taxonomy and phylogenetic relationships amongst members of Archaeopithecidae remain to be established.
DOI: 10.6084/m9.figshare.1568470.v3
title: Spatial and temporal variation of bird dawn chorus and successive acoustic morning activity in a Mediterranean landscape

description: Ecoacoustic techniques using multiple acoustic sensors and two metrics of the acoustic community – the acoustic complexity index (ACI) and the chorus ratio (CR) – were successfully used to describe and characterize the morning acoustic activity of birds according to three equal temporal intervals during spring 2013: Dawn Chorus, Post Chorus 1, and Post Chorus 2.The metrics were applied across five Italian Mediterranean locations (Valenza, Madonna dei Colli, Monte Curto, Virolo, Croce di Tergagliana) that differed by land-cover typologies. Results from the ACI metrics showed a peak during the Dawn Chorus and a visible lull close to sunrise between Dawn Chorus and Post Chorus 1.The lull was evident in all localities except Valenza, where singing activity was relatively constant across the successive morning intervals. Temperature and vegetation structure were confirmed as important factors associated with morning acoustic activities. Vegetation evenness and temperature across the season was negatively correlated with ACI, whereas CR was positively correlated with temperature and vegetation diversity. Of the 33 species of birds identified during the maximum dawn chorus activity, Blackcap, Blackbird, European Robin, and Great Tit were acoustically dominant and their activity was significantly higher before sunrise except for Blackcap, whose acoustic activity showed no significant differences across time intervals. The dawn chorus is one of the most conspicuous behaviours of birds, engendering much speculation but no definitive, univocal explanations. The ecoacoustic approach opens a new perspective for investigating this complex phenomenon.
DOI: 10.6084/m9.figshare.1568471.v1
title: Biased signaling; potential agonist and antagonist of PAR2

description: Protease activated receptor 2 (PAR2) has emerged as one of the promising therapeutic targets to inhibit rapidly metastasizing breast cancer cells. However, its elusive molecular mechanism of activation and signaling has made it a difficult target for drug development. In this study, in silico methods were used to unfold PAR2 molecular mechanism of signaling based on the concept of GPCR receptor plasticity. Although, there are no conclusive evidences of the presence of specific endogenous ligands for PAR2, the efficacy of synthetic agonist and antagonist in PAR2 signaling has opened up the possibilities of ligand mediated signaling. Furthermore, it has been proved that ligands specific for one GPCR can induce signaling in receptors belonging to other subfamilies. Therefore, the aim of the present study was to identify potential agonists and antagonists from the GPCR ligand database (GLL), which may induce biased signaling in PAR2 using the concept of existence of multiple ligand stabilized receptor conformations. The results of our in silico study suggest that PAR2 may show biased signaling with agonists of serotonin type1, β adrenergic type 1 and antagonists of substance K (NK1), serotonin type 2, dopamine type 4 and thromboxane receptors. Further, this study could also throw light on the putative ligand specific conformations of PAR2. Thus, the results of this study provide structural insights to putative conformations of PAR2 and also gives initial clues to medicinal chemists for rational drug design targeting this challenging receptor.
DOI: 10.6084/m9.figshare.1568474.v2
title: Phylogenetic revision of the South American notopithecines (Mammalia: Notoungulata)

description: A phylogenetic analysis of all Eocene taxa assigned to Notopithecinae has been conducted, evaluating relationships amongst notopithecines, basal interatheriids and Interatheriinae. Other groups of native ungulates were also included. New dental and postcranial characters are considered with respect to previously published data; some characters are evaluated in notoungulates for the first time. Two different searches were performed under parsimony and equal weights. The inclusion of postcranial characters strongly influenced tree topology. The most significant result of the phylogenetic analysis was the identification of a novel monophyletic group, including species traditionally grouped as Patagonian Notopithecinae. The ‘notopithecid’ name is linked to the new clade defined as the clade stemming from the most recent common ancestor of the species <i>Notopithecus adapinus</i>, <i>Antepithecus brachystephanus</i>, <i>Transpithecus obtentus</i> and <i>Guilielmoscottia plicifera</i>. This phylogeny supports the main morphological differences of the new clade with respect to Interatheriinae Interatheriidae. In consequence, a diagnosis is proposed based on phylogenetic results, to which some other morphological characters are added. The Chilean basal interatheriids <i>Johnbell</i> and <i>Ignigena</i> as well as <i>Punapithecus</i> (Argentinean Puna) are excluded from the notopithecid clade, implying biostratigraphical and biogeographical changes. Notopithecid distribution now becomes restricted to the middle–late Eocene part of the Sarmiento Formation outcropping in central Chubut and north-east Santa Cruz provinces, Argentina. Other extra-Patagonian records of notopithecids are not confirmed. The resulting phylogeny resolves some relationships within basal interatheriids differently from previous analyses. Interatheriinae is not recovered as a monophyletic group, and Oldfieldthomasiidae and Henricosborniid are paraphyletic. The position of the Archaeopithecidae <i>Acropithecus rigidus</i> is controversial; it appears at the base of the Typotheria lineage or in the notopithecid clade, but systematic taxonomy and phylogenetic relationships amongst members of Archaeopithecidae remain to be established.
DOI: 10.6084/m9.figshare.1568465
title: Geochemical and Microbiological Studies of Nitrous Oxide Variations within the New NEEM Greenland Ice Core during the Last Glacial Period

description: Deep polar ice cores provide atmospheric records of nitrous oxide (N<sub>2</sub>O) and other trace gases reflecting climate history along with a parallel archive of microbial cells transported with mineral dust, marine and volcanic aerosols from around the globe. Our interdisciplinary study of 32 samples from different depths of the recently drilled NEEM Greenland ice core addressed the question whether the identified microorganisms were capable of post-depositional biological production of N<sub>2</sub>O in situ. We used high-resolution geochemical and microbiological approaches to examine the N<sub>2</sub>O concentrations, the quantitative distributions of dust, Ca<sup>+2</sup>, NH<sub>4</sub><sup>+</sup> and NO<sub>3</sub><sup>−</sup> ions related to N cycle pathways, the microbial abundance and diversity at specific NEEM core depths from 1758 m to 1867.8 m. Results showed varying concentrations of N<sub>2</sub>O (220–271.5 ppb). Microbial abundance fluctuated between 3.3 × 10<sup>4</sup> and 3.3 × 10<sup>6</sup> cells mL<sup>−1</sup> in direct correlation with dust and Ca<sup>2+</sup> concentrations with higher cell numbers deposited during colder periods. The average values of NH<sub>4</sub><sup>+</sup> and NO<sub>3</sub><sup>−</sup> indicated that substrates were available for the microorganisms capable of utilizing them. PCR amplification of selected functional genes involved in bacterial and archaeal nitrification and denitrification was not successful. Sanger and Illumina MiSeq sequence analyses of SSU rRNA genes showed variable representation of A<i>lpha-, Beta- and Gammaproteobacteria, Firmicutes, Actinobacteria</i>, chloroplasts and fungi. The metabolic potential of the dominant genera of <i>Proteobacteria</i> and <i>Firmicutes</i> as possible N<sub>2</sub>O producers suggested that denitrification activity may have led to in-situ production and accumulation of N<sub>2</sub>O.
DOI: 10.6084/m9.figshare.1568470.v2
title: Spatial and temporal variation of bird dawn chorus and successive acoustic morning activity in a Mediterranean landscape

description: Ecoacoustic techniques using multiple acoustic sensors and two metrics of the acoustic community – the acoustic complexity index (ACI) and the chorus ratio (CR) – were successfully used to describe and characterize the morning acoustic activity of birds according to three equal temporal intervals during spring 2013: Dawn Chorus, Post Chorus 1, and Post Chorus 2.The metrics were applied across five Italian Mediterranean locations (Valenza, Madonna dei Colli, Monte Curto, Virolo, Croce di Tergagliana) that differed by land-cover typologies. Results from the ACI metrics showed a peak during the Dawn Chorus and a visible lull close to sunrise between Dawn Chorus and Post Chorus 1.The lull was evident in all localities except Valenza, where singing activity was relatively constant across the successive morning intervals. Temperature and vegetation structure were confirmed as important factors associated with morning acoustic activities. Vegetation evenness and temperature across the season was negatively correlated with ACI, whereas CR was positively correlated with temperature and vegetation diversity. Of the 33 species of birds identified during the maximum dawn chorus activity, Blackcap, Blackbird, European Robin, and Great Tit were acoustically dominant and their activity was significantly higher before sunrise except for Blackcap, whose acoustic activity showed no significant differences across time intervals. The dawn chorus is one of the most conspicuous behaviours of birds, engendering much speculation but no definitive, univocal explanations. The ecoacoustic approach opens a new perspective for investigating this complex phenomenon.