cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4565293.v1
title: Early cretaceous ophiolites of the Yarlung Zangbo Suture Zone: insights from dolerites and peridotites from the Baer upper mantle suite, SW Tibet (China)

description: The Baer ophiolitic massif is located in the northern sub-belt of the western segment of the Yarlung Zangbo Suture Zone (YZSZ) and mainly consists of a lherzolite-dominant mantle suite, dolerite intrusions and limited crustal outcrops. The dolerites show sub-ophitic texture and light rare earth element-depleted chondrite-normalized rare earth element patterns similar to normal-mid-ocean ridge basalts (N-MORB); though, they display enrichments in fluid-mobile elements (Rb, Ba, and Sr) and marked depletions in Th and Nb. The U–Pb ages of several magmatic zircon grains recovered from two dolerite samples indicate that the intrusion of the dikes into the Baer lherzolitic mantle occurred at 125.6–126.3 Ma, consistent with the widespread mafic magmatism between 120 and 130 Ma in the Yarlung Zangbo ophiolites. The dolerites have slightly more radiogenic <sup>87</sup>Sr/<sup>86</sup>Sr ratios (0.7043–0.7054) in comparison to N-MORB, whereas they show <sup>143</sup>Nd/<sup>144</sup>Nd values (0.513067–0.513114) similar to N-MORB and high zircon Hf-isotope compositions. They have a limited range of Nd-isotope (<i>ε</i><sub>Nd</sub>(<i>t</i>) values: +8.2 to +9.1) and juvenile Hf-isotope compositions (<i>ε</i><sub>Hf</sub>(<i>t</i>) values: +8.4 to +14.2 and +10.0 to +15.1) indicating derivation from mantle melts. The moderate spread in the <i>ε</i><sub>Hf</sub> (<i>t</i>) values of zircons indicates derivation of the dolerites parental magma from a weakly contaminated spinel-bearing mantle source. This is also corroborated by the geochemical signatures of the Baer dolerites (enrichment in LILE and depletion in HFSE) suggesting minor slab input to the mantle source of the dike-filling melt. We suggest that the genesis of the dolerite dike-forming melt happened at a stage of subduction initiation in a sub-oceanic mantle domain mildly affected by fluids emanating from the downgoing slab. Our data combined with literature data allow us to presume that the intrusion of the dolerites into the Baer mantle corresponds to an early phase of subduction initiation beneath a developing forearc basin.
DOI: 10.6084/m9.figshare.4565293
title: Early cretaceous ophiolites of the Yarlung Zangbo Suture Zone: insights from dolerites and peridotites from the Baer upper mantle suite, SW Tibet (China)

description: The Baer ophiolitic massif is located in the northern sub-belt of the western segment of the Yarlung Zangbo Suture Zone (YZSZ) and mainly consists of a lherzolite-dominant mantle suite, dolerite intrusions and limited crustal outcrops. The dolerites show sub-ophitic texture and light rare earth element-depleted chondrite-normalized rare earth element patterns similar to normal-mid-ocean ridge basalts (N-MORB); though, they display enrichments in fluid-mobile elements (Rb, Ba, and Sr) and marked depletions in Th and Nb. The U–Pb ages of several magmatic zircon grains recovered from two dolerite samples indicate that the intrusion of the dikes into the Baer lherzolitic mantle occurred at 125.6–126.3 Ma, consistent with the widespread mafic magmatism between 120 and 130 Ma in the Yarlung Zangbo ophiolites. The dolerites have slightly more radiogenic <sup>87</sup>Sr/<sup>86</sup>Sr ratios (0.7043–0.7054) in comparison to N-MORB, whereas they show <sup>143</sup>Nd/<sup>144</sup>Nd values (0.513067–0.513114) similar to N-MORB and high zircon Hf-isotope compositions. They have a limited range of Nd-isotope (<i>ε</i><sub>Nd</sub>(<i>t</i>) values: +8.2 to +9.1) and juvenile Hf-isotope compositions (<i>ε</i><sub>Hf</sub>(<i>t</i>) values: +8.4 to +14.2 and +10.0 to +15.1) indicating derivation from mantle melts. The moderate spread in the <i>ε</i><sub>Hf</sub> (<i>t</i>) values of zircons indicates derivation of the dolerites parental magma from a weakly contaminated spinel-bearing mantle source. This is also corroborated by the geochemical signatures of the Baer dolerites (enrichment in LILE and depletion in HFSE) suggesting minor slab input to the mantle source of the dike-filling melt. We suggest that the genesis of the dolerite dike-forming melt happened at a stage of subduction initiation in a sub-oceanic mantle domain mildly affected by fluids emanating from the downgoing slab. Our data combined with literature data allow us to presume that the intrusion of the dolerites into the Baer mantle corresponds to an early phase of subduction initiation beneath a developing forearc basin.
DOI: 10.6084/m9.figshare.4567924.v1
title: PARK2-dependent mitophagy induced by acidic postconditioning protects against focal cerebral ischemia and extends the reperfusion window

description: Prompt reperfusion after cerebral ischemia is critical for neuronal survival. Any strategies that extend the limited reperfusion window will be of great importance. Acidic postconditioning (APC) is a mild acidosis treatment that involves inhaling CO<sub>2</sub> during reperfusion following ischemia. APC attenuates ischemic brain injury although the underlying mechanisms have not been elucidated. Here we report that APC reinforces ischemia-reperfusion-induced mitophagy in middle cortical artery occlusion (MCAO)-treated mice, and in oxygen-glucose deprivation (OGD)-treated brain slices and neurons. Inhibition of mitophagy compromises neuroprotection conferred by APC. Furthermore, mitophagy and neuroprotection are abolished in <i>Park2</i> knockout mice, indicating that APC-induced mitophagy is facilitated by the recruitment of PARK2 to mitochondria. Importantly, in MCAO mice, APC treatment extended the effective reperfusion window from 2 to 4 h, and this window was further extended to 6 h by exogenously expressing PARK2. Taken together, we found that PARK2-dependent APC-induced mitophagy renders the brain resistant to ischemic injury. APC treatment could be a favorable strategy to extend the thrombolytic time window for stroke therapy.
DOI: 10.6084/m9.figshare.4567924
title: PARK2-dependent mitophagy induced by acidic postconditioning protects against focal cerebral ischemia and extends the reperfusion window

description: Prompt reperfusion after cerebral ischemia is critical for neuronal survival. Any strategies that extend the limited reperfusion window will be of great importance. Acidic postconditioning (APC) is a mild acidosis treatment that involves inhaling CO<sub>2</sub> during reperfusion following ischemia. APC attenuates ischemic brain injury although the underlying mechanisms have not been elucidated. Here we report that APC reinforces ischemia-reperfusion-induced mitophagy in middle cortical artery occlusion (MCAO)-treated mice, and in oxygen-glucose deprivation (OGD)-treated brain slices and neurons. Inhibition of mitophagy compromises neuroprotection conferred by APC. Furthermore, mitophagy and neuroprotection are abolished in <i>Park2</i> knockout mice, indicating that APC-induced mitophagy is facilitated by the recruitment of PARK2 to mitochondria. Importantly, in MCAO mice, APC treatment extended the effective reperfusion window from 2 to 4 h, and this window was further extended to 6 h by exogenously expressing PARK2. Taken together, we found that PARK2-dependent APC-induced mitophagy renders the brain resistant to ischemic injury. APC treatment could be a favorable strategy to extend the thrombolytic time window for stroke therapy.
DOI: 10.6084/m9.figshare.4567936.v1
title: PTK2-mediated degradation of ATG3 impedes cancer cells susceptible to DNA damage treatment

description: ATG3 (autophagy-related 3) is an E2-like enzyme essential for autophagy; however, it is unknown whether it has an autophagy-independent function. Here, we report that ATG3 is a relatively stable protein in unstressed cells, but it is degraded in response to DNA-damaging agents such as etoposide or cisplatin. With mass spectrometry and a mutagenesis assay, phosphorylation of tyrosine 203 of ATG3 was identified to be a critical modification for its degradation, which was further confirmed by manipulating ATG3<sup>Y203E</sup> (phosphorylation mimic) or ATG3<sup>Y203F</sup> (phosphorylation-incompetent) in <i>Atg3</i> knockout MEFs. In addition, by using a generated phospho-specific antibody we showed that phosphorylation of Y203 significantly increased upon etoposide treatment. With a specific inhibitor or siRNA, PTK2 (protein tyrosine kinase 2) was confirmed to catalyze the phosphorylation of ATG3 at Y203. Furthermore, a newly identified function of ATG3 was recognized to be associated with the promotion of DNA damage-induced mitotic catastrophe, in which ATG3 interferes with the function of BAG3, a crucial protein in the mitotic process, by binding. Finally, PTK2 inhibition-induced sustained levels of ATG3 were able to sensitize cancer cells to DNA-damaging agents. Our findings strengthen the notion that targeting PTK2 in combination with DNA-damaging agents is a novel strategy for cancer therapy.
DOI: 10.6084/m9.figshare.4567936
title: PTK2-mediated degradation of ATG3 impedes cancer cells susceptible to DNA damage treatment

description: ATG3 (autophagy-related 3) is an E2-like enzyme essential for autophagy; however, it is unknown whether it has an autophagy-independent function. Here, we report that ATG3 is a relatively stable protein in unstressed cells, but it is degraded in response to DNA-damaging agents such as etoposide or cisplatin. With mass spectrometry and a mutagenesis assay, phosphorylation of tyrosine 203 of ATG3 was identified to be a critical modification for its degradation, which was further confirmed by manipulating ATG3<sup>Y203E</sup> (phosphorylation mimic) or ATG3<sup>Y203F</sup> (phosphorylation-incompetent) in <i>Atg3</i> knockout MEFs. In addition, by using a generated phospho-specific antibody we showed that phosphorylation of Y203 significantly increased upon etoposide treatment. With a specific inhibitor or siRNA, PTK2 (protein tyrosine kinase 2) was confirmed to catalyze the phosphorylation of ATG3 at Y203. Furthermore, a newly identified function of ATG3 was recognized to be associated with the promotion of DNA damage-induced mitotic catastrophe, in which ATG3 interferes with the function of BAG3, a crucial protein in the mitotic process, by binding. Finally, PTK2 inhibition-induced sustained levels of ATG3 were able to sensitize cancer cells to DNA-damaging agents. Our findings strengthen the notion that targeting PTK2 in combination with DNA-damaging agents is a novel strategy for cancer therapy.
DOI: 10.6084/m9.figshare.4578721
title: A new otter of giant size, <i>Siamogale melilutra</i> sp. nov. (Lutrinae: Mustelidae: Carnivora), from the latest Miocene Shuitangba site in north-eastern Yunnan, south-western China, and a total-evidence phylogeny of lutrines

description: Otters (subfamily Lutrinae) are semi-aquatic predators in the family Mustelidae. Modern otters have a worldwide distribution but their fossil record is poor, often consisting of fragmentary jaws and teeth. Multiple lineages have developed bunodont dentitions with enlargements of molars, usually for cracking molluscs or other hard foods. Some lineages have evolved badger-like teeth and, as a result, were often confused with melines (Old World badger clade). <i>Siamogale thailandica</i> Ginsburg, Invagat, & Tassy, 1983 from the middle Miocene basin of Mae Moh in northern Thailand is one such species, whose fragmentary dental remains have thus far impeded our understanding. A new species of fossil otter, <i>Siamogale melilutra</i> sp. nov., represented by a nearly complete cranium, mandible and partial skeletons of at least three individuals, was recovered from the latest Miocene (∼6.2 Ma) lignite beds of the Shuitangba Site in north-eastern Yunnan Province, south-western China. Computed tomography (CT) restoration of the crushed skull reveals a combination of otter-like and badger-like cranial and dental characteristics. The new species belongs to the Lutrinae because of its possession of a large infraorbital canal and ventral expansion of the mastoid process, among other traits. A distally expanded M1, however, gives a badger-like appearance. In overall morphology the Shuitangba otter is closest to <i>Siamogale thailandica</i>. A previously described jaw (‘<i>Lutra</i>’ <i>aonychoides</i>) from the early Pliocene of the Yushe Basin in north China is also here referred to <i>S. melilutra</i>. No previous attempt has been made to provide a global phylogenetic framework for otters. We present the first combined morphological and molecular (nuclear and mitochondrial DNAs) character matrices of five extant (<i>Pteronura</i>, <i>Lontra</i>, <i>Enhydra</i>, <i>Aonyx</i>, <i>Lutra</i>) and eight extinct genera (<i>Tyrrhenolutra</i>, <i>Paralutra</i>, <i>Paludolutra</i>, <i>Enhydritherium</i>, <i>Siamogale</i>, <i>Vishnuonyx</i>, <i>Sivaonyx</i>, <i>Enhydriodon</i>) to better understand the evolution of bunodont otters. Parsimony and Bayesian analyses consistently recover an eastern Asian clade that includes forms from Shuitangba, Yushe and Mae Moh, all of which are referred to <i>Siamogale</i>. http://zoobank.org/urn:lsid:zoobank.org:pub:5C637018-0772-4C78-AA4B-783B71085D9D
DOI: 10.6084/m9.figshare.4578721.v1
title: A new otter of giant size, <i>Siamogale melilutra</i> sp. nov. (Lutrinae: Mustelidae: Carnivora), from the latest Miocene Shuitangba site in north-eastern Yunnan, south-western China, and a total-evidence phylogeny of lutrines

description: Otters (subfamily Lutrinae) are semi-aquatic predators in the family Mustelidae. Modern otters have a worldwide distribution but their fossil record is poor, often consisting of fragmentary jaws and teeth. Multiple lineages have developed bunodont dentitions with enlargements of molars, usually for cracking molluscs or other hard foods. Some lineages have evolved badger-like teeth and, as a result, were often confused with melines (Old World badger clade). <i>Siamogale thailandica</i> Ginsburg, Invagat, & Tassy, 1983 from the middle Miocene basin of Mae Moh in northern Thailand is one such species, whose fragmentary dental remains have thus far impeded our understanding. A new species of fossil otter, <i>Siamogale melilutra</i> sp. nov., represented by a nearly complete cranium, mandible and partial skeletons of at least three individuals, was recovered from the latest Miocene (∼6.2 Ma) lignite beds of the Shuitangba Site in north-eastern Yunnan Province, south-western China. Computed tomography (CT) restoration of the crushed skull reveals a combination of otter-like and badger-like cranial and dental characteristics. The new species belongs to the Lutrinae because of its possession of a large infraorbital canal and ventral expansion of the mastoid process, among other traits. A distally expanded M1, however, gives a badger-like appearance. In overall morphology the Shuitangba otter is closest to <i>Siamogale thailandica</i>. A previously described jaw (‘<i>Lutra</i>’ <i>aonychoides</i>) from the early Pliocene of the Yushe Basin in north China is also here referred to <i>S. melilutra</i>. No previous attempt has been made to provide a global phylogenetic framework for otters. We present the first combined morphological and molecular (nuclear and mitochondrial DNAs) character matrices of five extant (<i>Pteronura</i>, <i>Lontra</i>, <i>Enhydra</i>, <i>Aonyx</i>, <i>Lutra</i>) and eight extinct genera (<i>Tyrrhenolutra</i>, <i>Paralutra</i>, <i>Paludolutra</i>, <i>Enhydritherium</i>, <i>Siamogale</i>, <i>Vishnuonyx</i>, <i>Sivaonyx</i>, <i>Enhydriodon</i>) to better understand the evolution of bunodont otters. Parsimony and Bayesian analyses consistently recover an eastern Asian clade that includes forms from Shuitangba, Yushe and Mae Moh, all of which are referred to <i>Siamogale</i>. http://zoobank.org/urn:lsid:zoobank.org:pub:5C637018-0772-4C78-AA4B-783B71085D9D
DOI: 10.6084/m9.figshare.4585270
title: The ESM zip contains three files. The file fedges.txt are the edges that define the network, the file tedges.txt are the edges between the different layers of the network, while data in the file twitter_foursquare_mapper.dat provides the basic info of each node of the network, as stated in the first row. from Link prediction in multiplex online social networks

description: Online social networks play a major role in modern societies, and they have shaped the way social relationships evolve. Link prediction in social networks has many potential applications such as recommending new items to users, friendship suggestion and discovering spurious connections. Many real social networks evolve the connections in multiple layers (e.g. multiple social networking platforms). In this manuscript, we study the link prediction problem in multiplex networks. As an example, we consider a multiplex network of Twitter (as a microblogging service) and Foursquare (as a location-based social network). We consider social networks of the same users in these two platforms and develop a meta-path-based algorithm for predicting the links. The connectivity information of the two layers is used to predict the links in Foursquare network. Three classical classifiers (naive Bayes, support vector machines (SVM) and K-nearest neighbour) are used for the classification task. Although the networks are not highly correlated in the layers, our experiments show that including the cross-layer information significantly improves the prediction performance. The SVM classifier results in the best performance with an average accuracy of 89%.
DOI: 10.6084/m9.figshare.4585270.v1
title: The ESM zip contains three files. The file fedges.txt are the edges that define the network, the file tedges.txt are the edges between the different layers of the network, while data in the file twitter_foursquare_mapper.dat provides the basic info of each node of the network, as stated in the first row. from Link prediction in multiplex online social networks

description: Online social networks play a major role in modern societies, and they have shaped the way social relationships evolve. Link prediction in social networks has many potential applications such as recommending new items to users, friendship suggestion and discovering spurious connections. Many real social networks evolve the connections in multiple layers (e.g. multiple social networking platforms). In this manuscript, we study the link prediction problem in multiplex networks. As an example, we consider a multiplex network of Twitter (as a microblogging service) and Foursquare (as a location-based social network). We consider social networks of the same users in these two platforms and develop a meta-path-based algorithm for predicting the links. The connectivity information of the two layers is used to predict the links in Foursquare network. Three classical classifiers (naive Bayes, support vector machines (SVM) and K-nearest neighbour) are used for the classification task. Although the networks are not highly correlated in the layers, our experiments show that including the cross-layer information significantly improves the prediction performance. The SVM classifier results in the best performance with an average accuracy of 89%.
DOI: 10.6084/m9.figshare.4585372
title: HPLC determination of domoic acid in shellfish based on magnetic molecularly imprinting polymers

description: A magnetic molecularly imprinting polymer for domoic acid was fabricated. Synthesis conditions were optimized. The polymer particles have high magnetization for rapid magnetic separation. The apparent maximum absorption amount and dissociation constant of the polymer were 1,600 µg g<sup>−1</sup> and 20.6 µg mL<sup>−1</sup>, respectively. The polymer retained 90% of adsorption amount after 5 times of repeated use. It was used as an adsorbent for purification and HPLC detection of domoic acid in shellfish with a detection limit of 0.050 µg g<sup>−1</sup>. Thus, the polymer could be applied to the sample pretreatment of aquatic products.
DOI: 10.6084/m9.figshare.4587127
title: Ubiquitin ligase SYVN1/HRD1 facilitates degradation of the SERPINA1 Z variant/α-1-antitrypsin Z variant via SQSTM1/p62-dependent selective autophagy

description: SERPINA1/AAT/α-1-antitrypsin (serpin family A member 1) deficiency (SERPINA1/ AAT-D) is an autosomal recessive disorder characterized by the retention of misfolded SERPINA1/AAT in the endoplasmic reticulum (ER) of hepatocytes and a significant reduction of serum SERPINA1/AAT level. The Z variant of SERPINA1/AAT, containing a Glu342Lys (E342K) mutation (SERPINA1<sup>E342K</sup>/ATZ), the most common form of SERPINA1/AAT-D, is prone to misfolding and polymerization, which retains it in the ER of hepatocytes and leads to liver injury. Both proteasome and macroautophagy/autophagy pathways are responsible for disposal of SERPINA1<sup>E342K</sup>/ATZ after it accumulates in the ER. However, the mechanisms by which SERPINA1<sup>E342K</sup>/ATZ is selectively degraded by autophagy remain unknown. Here, we showed that ER membrane-spanning ubiquitin ligase (E3) SYVN1/HRD1 enhances the degradation of SERPINA1<sup>E342K</sup>/ATZ through the autophagy-lysosome pathway. We found that SYVN1 promoted SERPINA1<sup>E342K</sup>/ATZ, especially Triton X 100-insoluble SERPINA1<sup>E342K</sup>/ATZ clearance. However, the effect of SYVN1 in SERPINA1<sup>E342K</sup>/ATZ clearance was impaired after autophagy inhibition, as well as in autophagy-related 5 (<i>atg5)</i> knockout cells. On the contrary, autophagy induction enhanced SYVN1-mediated SERPINA1<sup>E342K</sup>/ATZ degradation. Further study showed that SYVN1 mediated SERPINA1<sup>E342K</sup>/ATZ ubiquitination, which is required for autophagic degradation of SERPINA1<sup>E342K</sup>/ATZ by promoting the interaction between SERPINA1<sup>E342K</sup>/ATZ and SQSTM1/p62 for formation of the autophagy complex. Interestingly, SYVN1-mediated lysine 48 (K48)-linked polyubiquitin chains that conjugated onto SERPINA1<sup>E342K</sup>/ATZ might predominantly bind to the ubiquitin-associated (UBA) domain of SQSTM1 and couple the ubiquitinated SERPINA1<sup>E342K</sup>/ATZ to the lysosome for degradation. In addition, autophagy inhibition attenuated the suppressive effect of SYVN1 on SERPINA1<sup>E342K</sup>/ATZ cytotoxicity, and the autophagy inducer rapamycin enhanced the suppressive effect of SYVN1 on SERPINA1<sup>E342K</sup>/ATZ-induced cell apoptosis. Therefore, this study proved that SYVN1 enhances SERPINA1<sup>E342K</sup>/ATZ degradation through SQSTM1-dependent autophagy and attenuates SERPINA1<sup>E342K</sup>/ATZ cytotoxicity.