bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rewetting does not return drained fen peatlands to their old selves
Authors: Kreyling J. , Tanneberger F. , Jansen F. , van der Linden S. , Aggenbach C. , Blüml V. , Couwenberg J. , Emsens W-J , Joosten H. , Klimkowska A. , Kotowski W. , Kozub L. , Lennartz B. , Liczner Y. , Liu H. , Michaelis D. , Oehmke C. , Parakenings K. , Pleyl E. , Poyda A. , Raabe S. , Röhl M. , Rücker K. , Schneider A. , Schrautzer J. , Schröder C. , Schug F. , Seeber E. , Thiel F. , Thiele S. , Tiemeyer B. , Timmermann T. , Urich T. , van Diggelen R. , Vegelin K. , Verbruggen E. , Wilmking M. , Wrage-Mönnig N. , Wołejko L. , Zak D. , Jurasinski G. 
Published: October 2021

AbstractPeatlands have been drained for land use for a long time and on a large scale, turning them from carbon and nutrient sinks into respective sources, diminishing water regulation capacity, causing surface height loss and destroying biodiversity. Over the last decades, drained peatlands have been rewetted for biodiversity restoration and, as it strongly decreases greenhouse gas emissions, also for climate protection. We quantify restoration success by comparing 320 rewetted fen peatland sites to 243 near-natural peatland sites of similar origin across temperate Europe, all set into perspective by 10k additional European fen vegetation plots. Results imply that rewetting of drained fen peatlands induces the establishment of tall, graminoid wetland plants (helophytisation) and long-lasting differences to pre-drainage biodiversity (vegetation), ecosystem functioning (geochemistry, hydrology), and land cover characteristics (spectral temporal metrics). The Paris Agreement entails the rewetting of 500,000 km2 of drained peatlands worldwide until 2050-2070. A better understanding of the resulting locally novel ecosystems is required to improve planning and implementation of peatland rewetting and subsequent management.
Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes
Authors: Emerson Joanne B. , Varner Ruth K. , Wik Martin , Parks Donovan H. , Neumann Rebecca B. , Johnson Joel E. , Singleton Caitlin M. , Woodcroft Ben J. , Tollerson Rodney , Owusu-Dommey Akosua , Binder Morgan , Freitas Nancy L. , Crill Patrick M. , Saleska Scott R. , Tyson Gene W. , Rich Virginia I. 
Published: October 2021

AbstractNorthern post-glacial lakes are significant, increasing sources of atmospheric carbon through ebullition (bubbling) of microbially-produced methane (CH4) from sediments. Ebullitive CH4 flux correlates strongly with temperature, reflecting that solar radiation drives emissions. However, here we show that the slope of the temperature-CH4 flux relationship differs spatially across two post-glacial lakes in Sweden. We compared these CH4 emission patterns with sediment microbial (metagenomic and amplicon), isotopic, and geochemical data. The temperature-associated increase in CH4 emissions was greater in lake middles—where methanogens were more abundant—than edges, and sediment communities were distinct between edges and middles. Microbial abundances, including those of CH4-cycling microorganisms and syntrophs, were predictive of porewater CH4 concentrations. Results suggest that deeper lake regions, which currently emit less CH4 than shallower edges, could add substantially to CH4 emissions in a warmer Arctic and that CH4 emission predictions may be improved by accounting for spatial variations in sediment microbiota.
Systematic review and meta-analyses of studies analysing instructions to authors from 1987 to 2017
Authors: Malički Mario , Jerončić Ana , Aalbersberg IJsbrand Jan , Bouter Lex , ter Riet Gerben 
Published: October 2021

AbstractTo gain insight into changes of scholarly journals’ recommendations, we conducted a systematic review of studies that analysed journals’ Instructions to Authors (ItAs). We summarised results of 153 studies, and meta-analysed how often ItAs addressed: 1) authorship, 2) conflicts of interest, 3) data sharing, 4) ethics approval, 5) funding disclosure, and 6) International Committee of Medical Journal Editors’ Uniform Requirements for Manuscripts. For each topic we found large between-study heterogeneity. Here, we show six factors that explained most of that heterogeneity: 1) time (addressing of topics generally increased over time), 2) country (large differences found between countries), 3) database indexation (large differences found between databases), 4) impact factor (topics were more often addressed in highest than in lowest impact factor journals), 5) discipline (topics were more often addressed in Health Sciences than in other disciplines), and 6) sub-discipline (topics were more often addressed in general than in sub-disciplinary journals).
Antigen presentation by lung epithelial cells directs CD4+ TRM cell function and regulates barrier immunity
Authors: Shenoy Anukul T. , Lyon De Ana Carolina , Arafa Emad I. , Salwig Isabelle , Barker Kimberly A. , Korkmaz Filiz T. , Ramanujan Aditya , Etesami Neelou S. , Soucy Alicia M. , Martin Ian M. C. , Tilton Brian R. , Hinds Anne , Goltry Wesley N. , Kathuria Hasmeena , Braun Thomas , Jones Matthew R. , Quinton Lee J. , Belkina Anna C. , Mizgerd Joseph P. 
Published: October 2021

AbstractBarrier tissues are populated by functionally plastic CD4+ resident memory T (TRM) cells. Whether the barrier epithelium regulates CD4+ TRM cell locations, plasticity and activities remains unclear. Here we report that lung epithelial cells, including distinct surfactant protein C (SPC)lowMHChigh epithelial cells, function as anatomically-segregated and temporally-dynamic antigen presenting cells. In vivo ablation of lung epithelial MHC-II results in altered localization of CD4+ TRM cells. Recurrent encounters with cognate antigen in the absence of epithelial MHC-II leads CD4+ TRM cells to co-express several classically antagonistic lineage-defining transcription factors, changes their cytokine profiles, and results in dysregulated barrier immunity. In addition, lung epithelial MHC-II is needed for surface expression of PD-L1, which engages its ligand PD-1 to constrain lung CD4+ TRM cell phenotypes. Thus, we establish epithelial antigen presentation as a critical regulator of CD4+ TRM cell function and identify epithelial-CD4+ TRM cell immune interactions as core elements of barrier immunity.
Single-cell analysis of patient-derived PDAC organoids reveals cell state heterogeneity and a conserved developmental hierarchy
Authors: Krieger Teresa G. , Le Blanc Solange , Jabs Julia , Ten Foo Wei , Ishaque Naveed , Jechow Katharina , Debnath Olivia , Leonhardt Carl-Stephan , Giri Anamika , Eils Roland , Strobel Oliver , Conrad Christian 
Published: October 2021

AbstractPancreatic ductal adenocarcinoma (PDAC) is projected to be the second leading cause of cancer mortality by 2030. Bulk transcriptomic analyses have distinguished ‘classical’ from ‘basal-like’ tumors with more aggressive clinical behavior. We derive PDAC organoids from 18 primary tumors and two matched liver metastases, and show that ‘classical’ and ‘basal-like’ cells coexist in individual organoids. By single-cell transcriptome analysis of PDAC organoids and primary PDAC, we identify distinct tumor cell states shared across patients, including a cycling progenitor cell state and a differentiated secretory state. Cell states are connected by a differentiation hierarchy, with ‘classical’ cells concentrated at the endpoint. In an imaging-based drug screen, expression of ‘classical’ subtype genes correlates with better drug response. Our results thus uncover a functional hierarchy of PDAC cell states linked to transcriptional tumor subtypes, and support the use of PDAC organoids as a clinically relevant model for in vitro studies of tumor heterogeneity.
Afucosylated Plasmodium falciparum-specific IgG is induced by infection but not by subunit vaccination
Authors: Larsen Mads Delbo , Lopez-Perez Mary , Dickson Emmanuel Kakra , Ampomah Paulina , Tuikue Ndam Nicaise , Nouta Jan , Koeleman Carolien A. M. , Ederveen Agnes L. Hipgrave , Mordmüller Benjamin , Salanti Ali , Nielsen Morten Agertoug , Massougbodji Achille , van der Schoot C. Ellen , Ofori Michael F. , Wuhrer Manfred , Hviid Lars , Vidarsson Gestur 
Published: October 2021

AbstractPlasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) family members mediate receptor- and tissue-specific sequestration of infected erythrocytes (IEs) in malaria. Antibody responses are a central component of naturally acquired malaria immunity. PfEMP1-specific IgG likely protects by inhibiting IE sequestration and through IgG-Fc Receptor (FcγR) mediated phagocytosis and killing of antibody-opsonized IEs. The affinity of afucosylated IgG to FcγRIIIa is up to 40-fold higher than fucosylated IgG, resulting in enhanced antibody-dependent cellular cytotoxicity. Most IgG in plasma is fully fucosylated, but afucosylated IgG is elicited in response to enveloped viruses and to paternal alloantigens during pregnancy. Here we show that naturally acquired PfEMP1-specific IgG is strongly afucosylated in a stable and exposure-dependent manner, and efficiently induces FcγRIIIa-dependent natural killer (NK) cell degranulation. In contrast, immunization with a subunit PfEMP1 (VAR2CSA) vaccine results in fully fucosylated specific IgG. These results have implications for understanding protective natural- and vaccine-induced immunity to malaria.
Characterization of humoral and SARS-CoV-2 specific T cell responses in people living with HIV
Authors: Alrubayyi Aljawharah , Gea-Mallorquí Ester , Touizer Emma , Hameiri-Bowen Dan , Kopycinski Jakub , Charlton Bethany , Fisher-Pearson Natasha , Muir Luke , Rosa Annachiara , Roustan Chloe , Earl Christopher , Cherepanov Peter , Pellegrino Pierre , Waters Laura , Burns Fiona , Kinloch Sabine , Dong Tao , Dorrell Lucy , Rowland-Jones Sarah , McCoy Laura E. , Peppa Dimitra 
Published: October 2021

AbstractThere is an urgent need to understand the nature of immune responses against SARS-CoV-2, to inform risk-mitigation strategies for people living with HIV (PLWH). Here we show that the majority of PLWH with ART suppressed HIV viral load, mount a detectable adaptive immune response to SARS-CoV-2. Humoral and SARS-CoV-2-specific T cell responses are comparable between HIV-positive and negative subjects and persist 5-7 months following predominately mild COVID-19 disease. T cell responses against Spike, Membrane and Nucleoprotein are the most prominent, with SARS-CoV-2-specific CD4 T cells outnumbering CD8 T cells. We further show that the overall magnitude of SARS-CoV-2-specific T cell responses relates to the size of the naive CD4 T cell pool and the CD4:CD8 ratio in PLWH. These findings suggest that inadequate immune reconstitution on ART, could hinder immune responses to SARS-CoV-2 with implications for the individual management and vaccine effectiveness in PLWH.
Ganitumab and metformin plus standard neoadjuvant therapy in stage 2/3 breast cancer
Authors: Yee Douglas , Isaacs Claudine , Wolf Denise M. , Yau Christina , Haluska Paul , Giridhar Karthik V. , Forero-Torres Andres , Jo Chien A. , Wallace Anne M. , Pusztai Lajos , Albain Kathy S. , Ellis Erin D. , Beckwith Heather , Haley Barbara B. , Elias Anthony D. , Boughey Judy C. , Kemmer Kathleen , Yung Rachel L. , Pohlmann Paula R. , Tripathy Debu , Clark Amy S. , Han Hyo S. , Nanda Rita , Khan Qamar J. , Edmiston Kristen K. , Petricoin Emanuel F. , Stringer-Reasor Erica , Falkson Carla I. , Majure Melanie , Mukhtar Rita A. , Helsten Teresa L. , Moulder Stacy L. , Robinson Patricia A. , Wulfkuhle Julia D. , Brown-Swigart Lamorna , Buxton Meredith , Clennell Julia L. , Paoloni Melissa , Sanil Ashish , Berry Scott , Asare Smita M. , Wilson Amy , Hirst Gillian L. , Singhrao Ruby , Asare Adam L. , Matthews Jeffrey B. , Hylton Nola M. , DeMichele Angela , Melisko Michelle , Perlmutter Jane , Rugo Hope S. , Fraser Symmans W. , van‘t Veer Laura J. , Berry Donald A. , Esserman Laura J. 
Published: October 2021

AbstractI-SPY2 is an adaptively randomized phase 2 clinical trial evaluating novel agents in combination with standard-of-care paclitaxel followed by doxorubicin and cyclophosphamide in the neoadjuvant treatment of breast cancer. Ganitumab is a monoclonal antibody designed to bind and inhibit function of the type I insulin-like growth factor receptor (IGF-1R). Ganitumab was tested in combination with metformin and paclitaxel (PGM) followed by AC compared to standard-of-care alone. While pathologic complete response (pCR) rates were numerically higher in the PGM treatment arm for hormone receptor-negative, HER2-negative breast cancer (32% versus 21%), this small increase did not meet I-SPY’s prespecified threshold for graduation. PGM was associated with increased hyperglycemia and elevated hemoglobin A1c (HbA1c), despite the use of metformin in combination with ganitumab. We evaluated several putative predictive biomarkers of ganitumab response (e.g., IGF-1 ligand score, IGF-1R signature, IGFBP5 expression, baseline HbA1c). None were specific predictors of response to PGM, although several signatures were associated with pCR in both arms. Any further development of anti-IGF-1R therapy will require better control of anti-IGF-1R drug-induced hyperglycemia and the development of more predictive biomarkers.
Evidence for independent domestication of sheep mtDNA lineage A in India and introduction of lineage B through Arabian sea route
Authors: Kamalakkannan Ranganathan , Kumar Satish , Bhavana Karippadakam , Prabhu Vandana R. , Machado Carolina Barros , Singha Hijam Surachandra , Sureshgopi Dhandapani , Vijay Vincy , Nagarajan Muniyandi 
Published: October 2021

AbstractIndia ranks the second in the world in terms of its sheep population with approximately 74.26 million represented by 44 well-described breeds in addition to several non-descript populations. Genetic diversity and phylogeography of Indian sheep breeds remain poorly understood, particularly for south Indian breeds. To have a comprehensive view of the domestication history of Indian sheep, we sequenced the mitochondrial DNA (mtDNA) control region (D-loop) and cytochrome b gene (CYTB) of 16 Indian domestic sheep breeds, most of them (13) from the south India. We analysed these sequences along with published data of domestic and wild sheep from different countries, including India. The haplotype diversity was relatively high in Indian sheep, which were classified into the three known mtDNA lineages, namely A, B and C. Lineage A was predominant among Indian sheep whereas lineages B and C were observed at low frequencies but C was restricted to the breeds of north and east India. The median joining network showed five major expanding haplogroups of lineage A (A1–A5). Out of which, A2, A4 and A5 were more frequent in Indian sheep in contrast to breeds from other parts of the world. Among the 27 Indian sheep breeds analysed, Mandya and Sonadi breeds were significantly different from other Indian breeds in the MDS analyses. This was explained by a very high contribution of lineage B into these two breeds. The Approximate Bayesian Computation (ABC) provided evidence for the domestication of lineage A sheep in the Indian subcontinent. Contrary to the current knowledge, we also found strong support for the introduction of lineage B into Indian subcontinent through sea route rather than from the Mongolian Plateau. The neighbour-joining tree of domestic and wild sheep revealed the close genetic relationship of Indian domestic sheep with Pakistani wild sheep O. vignei blanfordi. Based on our analyses and archaeological evidences, we suggest the Indian subcontinent as one of the domestication centres of the lineage A sheep, while lineage B sheep might have arrived into India from elsewhere via Arabian sea route. To the best of our knowledge, this is the first comprehensive study on Indian sheep where we have analysed more than 740 animals belonging to 27 sheep breeds raised in various regions of India. Our study provides insight into the understanding of the origin and migratory history of Indian sheep.
Global distribution of soapberries (Sapindus L.) habitats under current and future climate scenarios
Authors: Liu Jiming , Wang Lianchun , Sun Caowen , Xi Benye , Li Doudou , Chen Zhong , He Qiuyang , Weng Xuehuang , Jia Liming 
Published: October 2021

AbstractSapindus (Sapindus L.) is a widely distributed economically important tree genus that provides biodiesel, biomedical and biochemical products. However, with climate change, deforestation, and economic development, the diversity of Sapindus germplasms may face the risk of destruction. Therefore, utilising historical environmental data and future climate projections from the BCC-CSM2-MR global climate database, we simulated the current and future global distributions of suitable habitats for Sapindus using a Maximum Entropy (MaxEnt) model. The estimated ecological thresholds for critical environmental factors were: a minimum temperature of 0–20 °C in the coldest month, soil moisture levels of 40–140 mm, a mean temperature of 2–25 °C in the driest quarter, a mean temperature of 19–28 °C in the wettest quarter, and a soil pH of 5.6–7.6. The total suitable habitat area was 6059.97 × 104 km2, which was unevenly distributed across six continents. As greenhouse gas emissions increased over time, the area of suitable habitats contracted in lower latitudes and expanded in higher latitudes. Consequently, surveys and conservation should be prioritised in southern hemisphere areas which are in danger of becoming unsuitable. In contrast, other areas in northern and central America, China, and India can be used for conservation and large-scale cultivation in the future.
The protective effect of the PDE-4 inhibitor rolipram on intracerebral haemorrhage is associated with the cAMP/AMPK/SIRT1 pathway
Authors: Dong Xiao-Liu , Wang Yan-Hui , Xu Jing , Zhang Nan 
Published: October 2021

AbstractRolipram specifically inhibits phosphodiesterase (PDE) 4, thereby preventing inactivation of the intracellular second messenger cyclic adenosine monophosphate (cAMP). Rolipram has been shown to play a neuroprotective role in some central nervous system (CNS) diseases. However, the role of PDE4 and the potential protective effect of rolipram on the pathophysiological process of intracerebral haemorrhage (ICH) are still not entirely clear. In this study, a mouse model of ICH was established by the collagenase method. Rolipram reduced brain oedema, blood–brain barrier (BBB) leakage, neuronal apoptosis and inflammatory cytokine release and improved neurological function in our mouse model of ICH. Moreover, rolipram increased the levels of cAMP and silent information regulator 1 (SIRT1) and upregulated the phosphorylation of AMP-activated protein kinase (AMPK). Furthermore, these effects of rolipram could be reversed by the SIRT1 inhibitor sirtinol. In conclusion, rolipram can play a neuroprotective role in the pathological process of ICH by activating the cAMP/AMPK/SIRT1 pathway.
Risk factor assessments of temporomandibular disorders via machine learning
Authors: Lee Kwang-Sig , Jha Nayansi , Kim Yoon-Ji 
Published: October 2021

AbstractThis study aimed to use artificial intelligence to determine whether biological and psychosocial factors, such as stress, socioeconomic status, and working conditions, were major risk factors for temporomandibular disorders (TMDs). Data were retrieved from the fourth Korea National Health and Nutritional Examination Survey (2009), with information concerning 4744 participants’ TMDs, demographic factors, socioeconomic status, working conditions, and health-related determinants. Based on variable importance observed from the random forest, the top 20 determinants of self-reported TMDs were body mass index (BMI), household income (monthly), sleep (daily), obesity (subjective), health (subjective), working conditions (control, hygiene, respect, risks, and workload), occupation, education, region (metropolitan), residence type (apartment), stress, smoking status, marital status, and sex. The top 20 determinants of temporomandibular disorders determined via a doctor’s diagnosis were BMI, age, household income (monthly), sleep (daily), obesity (subjective), working conditions (control, hygiene, risks, and workload), household income (subjective), subjective health, education, smoking status, residence type (apartment), region (metropolitan), sex, marital status, and allergic rhinitis. This study supports the hypothesis, highlighting the importance of obesity, general health, stress, socioeconomic status, and working conditions in the management of TMDs.
Relationship between physical activity time and intramuscular adipose tissue content of the thigh muscle groups of younger and older men
Authors: Ogawa Madoka , Tanaka Noriko , Yoshiko Akito , Oshida Yoshiharu , Koike Teruhiko , Akima Hiroshi 
Published: October 2021

AbstractWe investigated the effect of physical activity on muscle tissue size and intramuscular adipose tissue (IntraMAT) content in the thigh muscle groups of younger and older men. Twenty younger and 20 older men participated in this study. The muscle tissue cross-sectional area (CSA) and the IntraMAT content in the quadriceps femoris (QF), hamstrings (HM), hip adductors (AD), and mid-thigh total were measured using magnetic resonance imaging. The physical activity time was measured using a triaxial accelerometer, and four levels of physical activity were determined depending on the metabolic equivalent of task (METs), including sedentary (≤ 1.5 METs), light intensity (≤ 2.9 METs), moderate intensity (3.0–5.9 METs), and vigorous intensity (≥ 6.0 METs). No significant correlation was observed between the physical activity parameters and muscle tissue CSA in both groups. The IntraMAT content of the three muscle groups (QF, AD, and HM) and the total thigh was inversely correlated with the time of moderate-intensity physical activity (rs =  − 0.625 to − 0.489, P < 0.05, for all comparisons) in the young group, but not in the older group. These results indicate that IntraMAT accumulation was associated with the amount of moderate-physical activity in younger men.
The cardiac molecular setting of metabolic syndrome in pigs reveals disease susceptibility and suggests mechanisms that exacerbate COVID-19 outcomes in patients
Authors: Ziegler Olivia , Sriram Nivedita , Gelev Vladimir , Radeva Denitsa , Todorov Kostadin , Feng Jun , Sellke Frank W. , Robson Simon C. , Hiromura Makoto , Alexandrov Boian S. , Usheva Anny 
Published: October 2021

AbstractAlthough metabolic syndrome (MetS) is linked to an elevated risk of cardiovascular disease (CVD), the cardiac-specific risk mechanism is unknown. Obesity, hypertension, and diabetes (all MetS components) are the most common form of CVD and represent risk factors for worse COVID-19 outcomes compared to their non MetS peers. Here, we use obese Yorkshire pigs as a highly relevant animal model of human MetS, where pigs develop the hallmarks of human MetS and reproducibly mimics the myocardial pathophysiology in patients. Myocardium-specific mass spectroscopy-derived metabolomics, proteomics, and transcriptomics enabled the identity and quality of proteins and metabolites to be investigated in the myocardium to greater depth. Myocardium-specific deregulation of pro-inflammatory markers, propensity for arterial thrombosis, and platelet aggregation was revealed by computational analysis of differentially enriched pathways between MetS and control animals. While key components of the complement pathway and the immune response to viruses are under expressed, key N6-methyladenosin RNA methylation enzymes are largely overexpressed in MetS. Blood tests do not capture the entirety of metabolic changes that the myocardium undergoes, making this analysis of greater value than blood component analysis alone. Our findings create data associations to further characterize the MetS myocardium and disease vulnerability, emphasize the need for a multimodal therapeutic approach, and suggests a mechanism for observed worse outcomes in MetS patients with COVID-19 comorbidity.