bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deformation Analysis in the Barents Sea in Relation to Paleogene Transpression Along the Greenland‐Eurasia Plate Boundary
Authors: Gac Sébastien , Minakov Alexander , Shephard Grace E. , Faleide Jan Inge , Planke Sverre 
Published: October 2020

AbstractLate Cretaceous‐Cenozoic contractional structures are widespread in the Barents Sea. While the exact dating of the deformation is unclear, it can only be inferred that the contraction is younger than the early Cretaceous. One likely contractional mechanism is related to Greenland Plate kinematics at Paleogene times. We use a thin sheet finite element modeling approach to compute deformation within the Barents Sea in response to the Greenland‐Eurasia relative motions during the Paleogene. The analytical solution for the 3‐D folding of sediments above basement faults is used to assess possibilities for folding. Two existing Greenland Plate kinematic models, differing slightly in the timing, magnitude, and direction of motion, are tested. Results show that the Greenland Plate's general northward motion promotes growing anticlines in the entire Barents Sea shelf. Our numerical models suggest that the fan‐shaped pattern of cylindrical anticlines in the Barents Sea can be associated with the Eurekan deformation concurrent to the initial rifting and early seafloor spreading in the northeast Atlantic. The main contraction phase in the SW Barents Sea coincides with the timing of continental breakup, whereas the peak of deformation predicted for the NW Barents Sea occurred at later times. Svalbard has experienced a prolonged period of compressional deformation. We conclude that Paleogene Greenland Plate kinematics are a likely candidate to explain contractional structures in the Barents Sea.
From Caledonian Collapse to North Sea Rift: The Extended History of a Metamorphic Core Complex
Authors: Wiest J. D. , Wrona T. , Bauck M. S. , Fossen H. , Gawthorpe R. L. , Osmundsen P. T. , Faleide J. I. 
Published: October 2020

AbstractExtensional systems evolve through different stages due to changes in the rheological state of the lithosphere. It is crucial to distinguish ductile structures formed before and during rifting, as both cases have important but contrasting bearings on the structural evolution. To address this issue, we present the illustrative ductile‐to‐brittle structural history of a metamorphic core complex (MCC) onshore and offshore western Norway. Combining geological field mapping with newly acquired 3‐D seismic reflection data, we correlate two distinct onshore basement units (BU1 and BU2) to corresponding offshore basement seismic facies (SF1 and SF2). Our interpretation reveals two 40 km wide domes (one onshore and one offshore), which both show characteristic kilometer‐scale, westward plunging upright folds. The gneiss domes fill antiformal culminations in the footwall of a >100 km long, shallowly west dipping, extensional detachment. Overlying Caledonian nappes and Devonian supradetachment basins occupy saddles of the hyperbolic detachment surface. Devonian collapse of the Caledonian orogen formed dome and detachment geometries. During North Sea rifting, brittle reactivation of the MCC resulted in complex fault patterns deviating from N‐S strike dominant at the eastern margin of the rift. Around 61°N, only minor N‐S faults (<100 m throw) cut through the core of the MCC. Major rift faults (≤5 km throw), on the other hand, reactivated the detachment and follow the steep flanks of the MCC. This highlights that inherited ductile structures can locally alter the orientation of brittle faults formed during rifting.
A first-in-human phase 1 and pharmacological study of TAS-119, a novel selective Aurora A kinase inhibitor in patients with advanced solid tumours
Authors: Robbrecht Debbie G. J. , Lopez Juanita , Calvo Emiliano , He Xiaomin , Hiroshi Hirai , Soni Nital , Cook Natalie , Dowlati Afshin , Fasolo Angelica , Moreno Victor , Eskens Ferry A. L. M. , de Bono Johann S. 
Published: October 2020

AbstractBackgroundThis is a first-in-human study with TAS-119, an Aurora A kinase (AurA) inhibitor.MethodsPatients with advanced, refractory, solid tumours were enrolled into 5 dose escalation cohorts (70–300 mg BID, 4 days on/3 days off, 3 out of 4 weeks or 4 out of 4 weeks). The expansion part consisted of patients with small-cell lung cancer, HER2-negative breast cancer,MYC-amplified/β-catenin-mutated (MT) tumours or other (basket cohort).ResultsIn the escalation part (n = 34 patients), dose-limiting toxicities were one grade 3 nausea, two grade 2 and one grade 3 ocular toxicity and a combination of fatigue, ocular toxicity and nausea in one patient (all grade 2) at dose levels of 150, 200, 250 and 300 mg, respectively. Most frequent treatment-related adverse events were fatigue (32%), diarrhoea (24%) and ocular toxicity (24%). Toxicity grade ≥3 in ≥10% of patients were diarrhoea (15%) and increased lipase (12%). The maximum tolerated dose was 250 mg BID. Due to one additional grade 1 ocular toxicity, the RP2D was set at 200 mg BID (4 days on/3 days off, 3 out of 4 weeks), which was further explored in the expansion part (n = 40 patients). Target inhibition in paired skin biopsies was shown.ConclusionsTAS-119 has a favourable and remarkably distinct safety profile from other AurA inhibitors.Clinical trial registrationNCT02448589.
Deep sequencing detects human papillomavirus (HPV) in cervical cancers negative for HPV by PCR
Authors: Arroyo Mühr Laila Sara , Lagheden Camilla , Lei Jiayao , Eklund Carina , Nordqvist Kleppe Sara , Sparén Pär , Sundström Karin , Dillner Joakim 
Published: October 2020

Abstract
Background
Human papillomavirus (HPV) is a necessary cause of cervical cancer, although some invasive cervical cancers may test negative by HPV PCR. We previously requested all invasive cervical cancers in Sweden during 10 years and subjected them to PCR. We also optimised methods for deep sequencing of formalin-fixed paraffin-embedded samples.

Methods
Using Novaseq 6000, we simultaneously sequenced total DNA and cDNA from 392 HPV PCR-negative cervical cancers. Non-human reads were queried against all known HPVs. The complete database now contains PCR and/or deep sequencing data on 2850 invasive cervical cancers.

Results
HPV sequences were detected in 169/392 of HPV PCR-negative cervical cancers. Overall, 30 different HPV types were detected, but only 5 types were present in proportions above 3% of cancers. More than 92% of tumours were HPV-positive in PCR and/or sequencing (95% confidence interval: 91.1–93.1%). Exploring possible reasons for failure to previously detect HPV suggest that more sensitive type-specific PCRs for HPV 31, 33, 45 and 73 targeting retained regions of HPV would have detected most of these (117/392).

Conclusions
Unbiased deep sequencing provides comprehensive data on HPV types in cervical cancers and appears to be an important tool for quality assurance of HPV screening.
EFTUD2 maintains the survival of tumor cells and promotes hepatocellular carcinoma progression via the activation of STAT3
Authors: Tu Mengxian , He Lu , You Yang , Li Jinying , Yao Nan , Qu Chen , Huang Wei , Xu Leibo , Luo Rongcheng , Hong Jian 
Published: October 2020

AbstractElongation factor Tu GTP binding domain containing 2 (EFTUD2), a spliceosomal GTPase, plays a pivotal role in multiple organ development and innate immune. It has been reported that EFTUD2 is a new host factor with activity against HCV infection. However, the role of EFTUD2 in solid tumors, including hepatocellular carcinoma (HCC), remains unexplored. In this study, we investigated the molecular function of EFTUD2 in HCC. Data from The Cancer Genome Atlas (TCGA) indicated an upregulation of EFTUD2 in HCC tissues compared to that in nontumor liver tissues. Immunohistochemical analysis performed on two independent HCC cohorts confirmed the upregulation of EFTUD2 in HCC tissues and further suggested that a high level of EFTUD2 expression predicted shorter overall and recurrence-free survival in HCC patients. Functional studies suggested that siRNA interference with EFTUD2 expression significantly suppressed cell viability, blocked cell cycle progression, facilitated tumor cell apoptosis, and inhibited metastasis, while the enhancement of EFTUD2 expression promoted the proliferation and migration of HCC cells both in vitro and in vivo. Surprisingly, we also found that the stable knockdown of EFTUD2 expression via lentivirus infection was lethal for HCC cells. This finding suggested that EFTUD2 was essential for maintaining the survival of HCC cells. Mechanistically, RNA sequencing and gene set enrichment analysis (GSEA) suggested that the gene sets of epithelial–mesenchymal transition (EMT) and the JAK/STAT3 pathway were enriched in EFTUD2-overexpressing cells. Further verification indicated that EFTUD2-overexpressing cells exhibited an EMT-like phenotype and had enhanced STAT3 activation, while the STAT3 inhibitor S3I-201 partially blocked these pro-malignant effects of EFTUD2 overexpression. In summary, we report EFTUD2 as a novel oncogene that helps to maintain the survival of HCC cells and promotes HCC progression through the activation of STAT3. The high level of expression of EFTUD2 in HCC tissues indicates shorter overall and recurrence-free survival in HCC patients.
Authentic self-expression on social media is associated with greater subjective well-being
Authors: Bailey Erica R. , Matz Sandra C. , Youyou Wu , Iyengar Sheena S. 
Published: October 2020

AbstractSocial media users face a tension between presenting themselves in an idealized or authentic way. Here, we explore how prioritizing one over the other impacts users’ well-being. We estimate the degree of self-idealized vs. authentic self-expression as the proximity between a user’s self-reported personality and the automated personality judgements made on the basis Facebook Likes and status updates. Analyzing data of 10,560 Facebook users, we find that individuals who are more authentic in their self-expression also report greater Life Satisfaction. This effect appears consistent across different personality profiles, countering the proposition that individuals with socially desirable personalities benefit from authentic self-expression more than others. We extend this finding in a pre-registered, longitudinal experiment, demonstrating the causal relationship between authentic posting and positive affect and mood on a within-person level. Our findings suggest that the extent to which social media use is related to well-being depends on how individuals use it.
Machine learning based early warning system enables accurate mortality risk prediction for COVID-19
Authors: Gao Yue , Cai Guang-Yao , Fang Wei , Li Hua-Yi , Wang Si-Yuan , Chen Lingxi , Yu Yang , Liu Dan , Xu Sen , Cui Peng-Fei , Zeng Shao-Qing , Feng Xin-Xia , Yu Rui-Di , Wang Ya , Yuan Yuan , Jiao Xiao-Fei , Chi Jian-Hua , Liu Jia-Hao , Li Ru-Yuan , Zheng Xu , Song Chun-Yan , Jin Ning , Gong Wen-Jian , Liu Xing-Yu , Huang Lei , Tian Xun , Li Lin , Xing Hui , Ma Ding , Li Chun-Rui , Ye Fei , Gao Qing-Lei 
Published: October 2020

AbstractSoaring cases of coronavirus disease (COVID-19) are pummeling the global health system. Overwhelmed health facilities have endeavored to mitigate the pandemic, but mortality of COVID-19 continues to increase. Here, we present a mortality risk prediction model for COVID-19 (MRPMC) that uses patients’ clinical data on admission to stratify patients by mortality risk, which enables prediction of physiological deterioration and death up to 20 days in advance. This ensemble model is built using four machine learning methods including Logistic Regression, Support Vector Machine, Gradient Boosted Decision Tree, and Neural Network. We validate MRPMC in an internal validation cohort and two external validation cohorts, where it achieves an AUC of 0.9621 (95% CI: 0.9464–0.9778), 0.9760 (0.9613–0.9906), and 0.9246 (0.8763–0.9729), respectively. This model enables expeditious and accurate mortality risk stratification of patients with COVID-19, and potentially facilitates more responsive health systems that are conducive to high risk COVID-19 patients.
Interactions with conspecific outsiders as drivers of cognitive evolution
Authors: Ashton Benjamin J. , Kennedy Patrick , Radford Andrew N. 
Published: October 2020

AbstractThe social intelligence hypothesis (SIH) posits that within-group interactions drive cognitive evolution, but it has received equivocal support. We argue the SIH overlooks a major component of social life: interactions with conspecific outsiders. Competition for vital resources means conspecific outsiders present myriad threats and opportunities in all animal taxa across the social spectrum (from individuals to groups). We detail cognitive challenges generated by conspecific outsiders, arguing these select for ‘Napoleonic’ intelligence; explain potential influences on the SIH; and highlight important considerations when empirically testing these ideas. Including interactions with conspecific outsiders may substantially improve our understanding of cognitive evolution.
Metastable hybridization-based DNA information storage to allow rapid and permanent erasure
Authors: Kim Jangwon , Bae Jin H. , Baym Michael , Zhang David Yu 
Published: October 2020

AbstractThe potential of DNA as an information storage medium is rapidly growing due to advances in DNA synthesis and sequencing. However, the chemical stability of DNA challenges the complete erasure of information encoded in DNA sequences. Here, we encode information in a DNA information solution, a mixture of true message- and false message-encoded oligonucleotides, and enables rapid and permanent erasure of information. True messages are differentiated by their hybridization to a "truth marker” oligonucleotide, and only true messages can be read; binding of the truth marker can be effectively randomized even with a brief exposure to the elevated temperature. We show 8 separate bitmap images can be stably encoded and read after storage at 25 °C for 65 days with an average of over 99% correct information recall, which extrapolates to a half-life of over 15 years at 25 °C. Heating to 95 °C for 5 minutes, however, permanently erases the message.
Predicting cell-to-cell communication networks using NATMI
Authors: Hou Rui , Denisenko Elena , Ong Huan Ting , Ramilowski Jordan A. , Forrest Alistair R. R. 
Published: October 2020

AbstractDevelopment of high throughput single-cell sequencing technologies has made it cost-effective to profile thousands of cells from diverse samples containing multiple cell types. To study how these different cell types work together, here we develop NATMI (Network Analysis Toolkit for Multicellular Interactions). NATMI uses connectomeDB2020 (a database of 2293 manually curated ligand-receptor pairs with literature support) to predict and visualise cell-to-cell communication networks from single-cell (or bulk) expression data. Using multiple published single-cell datasets we demonstrate how NATMI can be used to identify (i) the cell-type pairs that are communicating the most (or most specifically) within a network, (ii) the most active (or specific) ligand-receptor pairs active within a network, (iii) putative highly-communicating cellular communities and (iv) differences in intercellular communication when profiling given cell types under different conditions. Furthermore, analysis of the Tabula Muris (organism-wide) atlas confirms our previous prediction that autocrine signalling is a major feature of cell-to-cell communication networks, while also revealing that hundreds of ligands and their cognate receptors are co-expressed in individual cells suggesting a substantial potential for self-signalling.
Upregulation of lipid metabolism genes in the breast prior to cancer diagnosis
Authors: Marino Natascia , German Rana , Rao Xi , Simpson Ed , Liu Sheng , Wan Jun , Liu Yunlong , Sandusky George , Jacobsen Max , Stovall Miranda , Cao Sha , Storniolo Anna Maria V. 
Published: October 2020

AbstractHistologically normal tissue adjacent to the tumor can provide insight of the microenvironmental alterations surrounding the cancerous lesion and affecting the progression of the disease. However, little is known about the molecular changes governing cancer initiation in cancer-free breast tissue. Here, we employed laser microdissection and whole-transcriptome profiling of the breast epithelium prior to and post tumor diagnosis to identify the earliest alterations in breast carcinogenesis. Furthermore, a comprehensive analysis of the three tissue compartments (microdissected epithelium, stroma, and adipose tissue) was performed on the breast donated by either healthy subjects or women prior to the clinical manifestation of cancer (labeled “susceptible normal tissue”). Although both susceptible and healthy breast tissues appeared histologically normal, the susceptible breast epithelium displayed a significant upregulation of genes involved in fatty acid uptake/transport (CD36 and AQP7), lipolysis (LIPE), and lipid peroxidation (AKR1C1). Upregulation of lipid metabolism- and fatty acid transport-related genes was observed also in the microdissected susceptible stromal and adipose tissue compartments, respectively, when compared with the matched healthy controls. Moreover, inter-compartmental co-expression analysis showed increased epithelium-adipose tissue crosstalk in the susceptible breasts as compared with healthy controls. Interestingly, reductions in natural killer (NK)-related gene signature and CD45+/CD20+ cell staining were also observed in the stromal compartment of susceptible breasts. Our study yields new insights into the cancer initiation process in the breast. The data suggest that in the early phase of cancer development, metabolic activation of the breast, together with increased epithelium-adipose tissue crosstalk may create a favorable environment for final cell transformation, proliferation, and survival.
Implementing a context-driven awareness programme addressing household air pollution and tobacco: a FRESH AIR study
Authors: Brakema Evelyn A. , van Gemert Frederik A. , Williams Sian , Sooronbaev Talant , Emilov Berik , Mademilov Maamed , Tabyshova Aizhamal , An Pham Le , Quynh Nguyen Nhat , Hong Le Huynh Thi Cam , Dang Tran Ngoc , van der Kleij Rianne M. J. J. , Chavannes Niels H. , de Jong Corina ,   The FRESH AIR collaborators, Anastasaki Marilena , Akylbekov Azamat , Barton Andy , Bertsias Antonios , Binh Pham Duong Uyen , van Boven Job F. M. , Burges Dennis , Cartwright Lucy , Chatzea Vasiliki E. , Cragg Liza , Dautov Ilyas , Ferarrio Irene , Hedrick Ben , Hopkinson Nick , Isaeva Elvira , Jones Rupert , van Kampen Sanne , Katagira Winceslaus , Kjærgaard Jesper , Kocks Janwillem , Lan Le Thi Tuyet , Linh Tran Thanh Duv , Lionis Christos , Loan Kim Xuan , McEwen Andy , Musinguzi Patrick , Nantanda Rebecca , Ndeezi Grace , Papadakis Sophia , Pinnock Hilary , Pooler Jillian , Poot Charlotte C. , Postma Maarten J. , Poulsen Anja , Powell Pippa , Reventlow Susanne , Sifaki-Pistolla Dimitra , Singh Sally , de Sousa Jaime Correia , Stout James , Østergaard Marianne Stubbe , Tsiligianni Ioanna , Tuan Tran Diep , Tumwine James , Van Le Thanh , Vinh Nguyen Nhu , Walusimbi Simon , Warren Louise 
Published: October 2020

AbstractMost patients with chronic respiratory disease live in low-resource settings, where evidence is scarcest. In Kyrgyzstan and Vietnam, we studied the implementation of a Ugandan programme empowering communities to take action against biomass and tobacco smoke. Together with local stakeholders, we co-created a train-the-trainer implementation design and integrated the programme into existing local health infrastructures. Feasibility and acceptability, evaluated by the modified Conceptual Framework for Implementation Fidelity, were high: we reached ~15,000 Kyrgyz and ~10,000 Vietnamese citizens within budget (~€11,000/country). The right engaged stakeholders, high compatibility with local contexts and flexibility facilitated programme success. Scores on lung health awareness questionnaires increased significantly to an excellent level among all target groups. Behaviour change was moderately successful in Vietnam and highly successful in Kyrgyzstan. We conclude that contextualising the awareness programme to diverse low-resource settings can be feasible, acceptable and effective, and increase its sustainability. This paper provides guidance to translate lung health interventions to new contexts globally.
VOLCORE, a global database of visible tephra layers sampled by ocean drilling
Authors: Mahony Sue H. , Barnard Nicholas H. , Sparks R. Stephen J. , Rougier Jonathan C. 
Published: October 2020

AbstractThe VOLCORE (Volcanic Core Records) database is a collection of 34,696 visible tephra (volcanic ash and lithological or grain size variations) occurrences reported in the initial reports volumes of all of the Deep Sea Drilling Project (DSDP; 1966–1983), the Ocean Drilling Program (ODP; 1983–2003), the Integrated Ocean Drilling Program (IODP; 2003–2013) and the International Ocean Discovery Program (IODP; 2013-present) up to and including IODP Expedition 381. The combined international ocean drilling programmes (OD) have locations with global coverage. Cored tephra layers and tephra-bearing sediments span timescales from recent to ~150 million years in age. This database is a collection of information about reported visible tephra layers entirely or predominantly composed of volcanic ash. Data include the depth below sea floor, tephra thickness, location, and any reported comments. An approximate age was estimated for most (29,493) of the tephra layers using published age-depth models. The database can be used as a starting point for studies of tephrochronology, volcanology, geochemistry, studies of sediment transport and palaeoclimatology.
Thermophoretic analysis of ligand-specific conformational states of the inhibitory glycine receptor embedded in copolymer nanodiscs
Authors: Bernhard Max , Laube Bodo 
Published: October 2020

AbstractThe glycine receptor (GlyR), a member of the pentameric ligand-gated ion channel family (pLGIC), displays remarkable variations in the affinity and efficacy of the full agonist glycine and the partial agonist taurine depending on the cell system used. Despite detailed insights in the GlyR three-dimensional structure and activation mechanism, little is known about conformational rearrangements induced by these agonists. Here, we characterized the conformational states of the α1 GlyR upon binding of glycine and taurine by microscale thermophoresis expressed in HEK293 cells and Xenopus oocytes after solubilization in amphipathic styrene-maleic acid copolymer nanodiscs. Our results show that glycine and taurine induce different conformational transitions of the GlyR upon ligand binding. In contrast, the variability of agonist affinity is not mediated by an altered conformational change. Thus, our data shed light on specific agonist induced conformational features and mechanisms of pLGIC upon ligand binding determining receptor activation in native environments.