bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adolescents’ neural reactivity to acute psychosocial stress: dysfunctional regulation habits are linked to temporal gyrus response
Authors: Golde Sabrina , Gleich Tobias , Romund Lydia , Stippl Anna , Pelz Patricia , Raufelder Diana , Lorenz Robert C. , Beck Anne 
Published: August 2021

AbstractMid-adolescence is a critical time for the development of stress-related disorders and it is associated with significant social vulnerability. However, little is known about normative neural processes accompanying psychosocial stress at this time. Previous research found that emotion regulation strategies critically influence the relationship between stress and the development of psychiatric symptoms during adolescence. Using functional magnetic resonance imaging (fMRI), we examined neural responses to acute stress and analyzed whether the tendency to use adaptive or maladaptive emotion regulation strategies is related to neural and autonomic stress responses. Results show large linear activation increases from low to medium to high stress levels mainly in medial prefrontal, insulae and temporal areas. Caudate and subgenual anterior cingulate cortex, neural areas related to reward and affective valuations, showed linearly decreasing activation. In line with our hypothesis, the current adolescent neural stress profile resembled social rejection and was characterized by pronounced activation in insula, angular and temporal cortices. Moreover, results point to an intriguing role of the anterior temporal gyrus. Stress-related activity in the anterior temporal gyrus was positively related to maladaptive regulation strategies and stress-induced autonomic activity. Maladaptive coping might increase the social threat and reappraisal load of a stressor, relating to higher stress sensitivity of anterior temporal cortices.
Compositional matrix-space models of language: Definitions, properties, and learning methods
Authors: Asaadi Shima , Giesbrecht Eugenie , Rudolph Sebastian 
Published: August 2021

AbstractWe give an in-depth account of compositional matrix-space models (CMSMs), a type of generic models for natural language, wherein compositionality is realized via matrix multiplication. We argue for the structural plausibility of this model and show that it is able to cover and combine various common compositional natural language processing approaches. Then, we consider efficient task-specific learning methods for training CMSMs and evaluate their performance in compositionality prediction and sentiment analysis.
Health behaviours as predictors of the Mediterranean diet adherence: a decision tree approach
Authors: Bôto Joana Margarida , Marreiros Ana , Diogo Patrícia , Pinto Ezequiel , Mateus Maria Palma 
Published: August 2021

AbstractObjective:This study aimed to identify health behaviours that determine adolescent’s adherence to the Mediterranean diet (MD) through a decision tree statistical approach.Design:Cross-sectional study, with data collected through a self-fulfilment questionnaire with five sections: (1) eating habits; (2) adherence to the MD (KIDMED index); (3) physical activity; (4) health habits and (5) socio-demographic characteristics. Anthropometric and blood pressure data were collected by a trained research team. The Automatic Chi-square Interaction Detection (CHAID) method was used to identify health behaviours that contribute to a better adherence to the MD.Setting:Eight public secondary schools, in Algarve, Portugal.Participants:Adolescents with ages between 15 and 19 years (n325).Results:According to the KIDMED index, we found a low adherence to MD in 9·0 % of the participants, an intermediate adherence in 45·5 % and a high adherence in 45·5 %. Participants that regularly have breakfast, eat vegetable soup, have a second piece of fruit/d, eat fresh or cooked vegetables 1 or more times a day, eat oleaginous fruits at least 2 to 3 times a week, and practice sports and leisure physical activities outside school show higher adherence to the MD (P< 0·001).Conclusions:The daily intake of two pieces of fruit and vegetables proved to be a determinant health behaviour for high adherence to MD. Strategies to promote the intake of these foods among adolescents must be developed and implemented.
Effects of Transition to Water‐Efficient Solutions on Existing Centralized Sewer Systems—An Integrated Biophysical Modeling Approach
Authors: Penn Roni , Maurer Max 
Published: August 2021

AbstractTechnical alternatives offering high water efficiency are being developed to complement existing centralized water and wastewater conveyance and treatment systems. Understanding of the negative effects wide‐spread implementation of such alternative systems may have on existing systems is still limited, despite the importance of this inevitable transition. In this study, we present a novel approach to systematically identify these negative impacts. A comprehensive model integrating transport and transformation processes in sewer pipes was set up and simulated for various transition scenarios. A significant finding of this research is that reduced flows and increased chemical oxygen demand (COD) concentrations result in the accumulation of sediments and sulphides in sewer pipes. For the examined sewer system, when reducing the total daily flow by 50%, 30% of the pipes were found to accumulate sediments, and 30% of the pipes experienced effects due to the presence of sulphides in different states depending on the wastewater temperature. It was found that an optimal spatial distribution of these water‐efficient solutions will most likely require compromises between sediment and sulphide accumulation. The product of two design parameters, diameter and bed slope, was found to be a suitable predictor of the potential of a pipe to accumulate sediments. This research provides novel approaches to assessing the feasibility of transition to solutions offering higher water efficiency. The results indicate where the most affected points in the systems are expected to occur and might help in preparing an experimental approach to assess such negative effects, increasing urban water management efficiency.
Projected Changes to Hydroclimate Seasonality in the Continental United States
Authors: Marvel Kate , Cook Benjamin I. , Bonfils Céline , Smerdon Jason E. , Williams A. Park , Liu Haibo 
Published: August 2021

AbstractFuture changes to the hydrological cycle are projected in a warming world, and any shifts in drought risk may prove extremely consequential for natural and human systems. In addition to long‐term moistening, drying, or warming trends, perturbations to the annual cycle of regional hydroclimate variables may also have substantial impacts. We analyze projected changes in several hydroclimate variables across the continental United States, along with shifts in the amplitude and phase of their annual cycles. We find that even in regions where no robust change in the annual mean is expected, coherent changes to the annual cycle are projected. In particular, we identify robust regional phase shifts toward earlier arrival of peak evaporation in the northern regions, and peak runoff and total soil moisture in the western regions. Changes in the amplitude of the annual cycle of total and surface soil moisture are also projected, and reflect changes to the annual cycle in surface water supply and demand. Whether changes become detectable above the background noise of internal variability depends strongly on the future scenario considered, and significant changes to the annual cycle are largely avoided in the lowest‐forcing scenario.
An Arctic Strait of Two Halves: The Changing Dynamics of Nutrient Uptake and Limitation Across the Fram Strait
Authors: Tuerena Robyn E. , Hopkins Jo , Buchanan Pearse J. , Ganeshram Raja S. , Norman Louisa , von Appen Wilken‐Jon , Tagliabue Alessandro , Doncila Antonia , Graeve Martin , Ludwichowski Kai U. , Dodd Paul A. , de la Vega Camille , Salter Ian , Mahaffey Claire 
Published: August 2021

AbstractThe hydrography of the Arctic Seas is being altered by ongoing climate change, with knock‐on effects to nutrient dynamics and primary production. As the major pathway of exchange between the Arctic and the Atlantic, the Fram Strait hosts two distinct water masses in the upper water column, northward flowing warm and saline Atlantic Waters in the east, and southward flowing cold and fresh Polar Surface Water in the west. Here, we assess how physical processes control nutrient dynamics in the Fram Strait using nitrogen isotope data collected during 2016 and 2018. In Atlantic Waters, a weakly stratified water column and a shallow nitracline reduce nitrogen limitation. To the west, in Polar Surface Water, nitrogen limitation is greater because stronger stratification inhibits nutrient resupply from deeper water and lateral nitrate supply from central Arctic waters is low. A historical hindcast simulation of ocean biogeochemistry from 1970 to 2019 corroborates these findings and highlights a strong link between nitrate supply to Atlantic Waters and the depth of winter mixing, which shoaled during the simulation in response to a local reduction in sea‐ice formation. Overall, we find that while the eastern Fram Strait currently experiences seasonal nutrient replenishment and high primary production, the loss of winter sea ice and continued atmospheric warming has the potential to inhibit deep winter mixing and limit primary production in the future.
Advancing the Evidence for Yoga as a Promising Quality of Life Intervention in Pediatric Populations With Chronic Illness: A Call to Action
Authors: Schaefer Megan R. , Frye William S. 
Published: August 2021

Objective: Treatment plans for youth with chronic illness are often solely focused on illness symptomatology, resulting in missed opportunities to address other components of the chronic illness experience. Because yoga incorporates physical activity and meditation, this practice has the potential to improve physical and psychosocial health while improving overall quality of life. Thus, this topical review (a) briefly summarizes preliminary evidence for the impact of yoga on quality of life in pediatric populations with chronic medical conditions, (b) evaluates the current feasibility and acceptability of yoga interventions, (c) describes limitations of current research, and (d) provides an agenda for future research and clinical directions. Method: Topical review. Results: The current literature on yoga interventions in pediatric populations with chronic medical conditions is limited by methodological issues, impacting the interpretability of findings. While more rigorous methodology is needed, preliminary findings suggest promise for the feasibility and acceptability of yoga interventions. Further, the current data indicates practicing yoga may positively impact quality of life outcomes in pediatric populations with chronic illness. Conclusion: Yoga interventions may have the potential to improve quality of life in youth with chronic medical conditions. However, further research is warranted to advance the literature and determine whether yoga is an efficacious and effective treatment for pediatric populations with chronic illness. Implications for Impact Statement Beyond addressing illness symptoms, yoga may have the potential to improve overall quality of life in youth with chronic illness, highlighting the importance of integrative medicine. Currently, methodological rigor is limited in this area; thus, future studies involving randomized controlled trials (RCTs) and standardized yoga intervention protocols are needed to advance this line of research.
FcγR engagement reprograms neutrophils into antigen cross-presenting cells that elicit acquired anti-tumor immunity
Authors: Mysore Vijayashree , Cullere Xavier , Mears Joseph , Rosetti Florencia , Okubo Koshu , Liew Pei X. , Zhang Fan , Madera-Salcedo Iris , Rosenbauer Frank , Stone Richard M. , Aster Jon C. , von Andrian Ulrich H. , Lichtman Andrew H. , Raychaudhuri Soumya , Mayadas Tanya N. 
Published: August 2021

AbstractClassical dendritic cells (cDC) are professional antigen-presenting cells (APC) that regulate immunity and tolerance. Neutrophil-derived cells with properties of DCs (nAPC) are observed in human diseases and after culture of neutrophils with cytokines. Here we show that FcγR-mediated endocytosis of antibody-antigen complexes or an anti-FcγRIIIB-antigen conjugate converts neutrophils into nAPCs that, in contrast to those generated with cytokines alone, activate T cells to levels observed with cDCs and elicit CD8+ T cell-dependent anti-tumor immunity in mice. Single cell transcript analyses and validation studies implicate the transcription factor PU.1 in neutrophil to nAPC conversion. In humans, blood nAPC frequency in lupus patients correlates with disease. Moreover, anti-FcγRIIIB-antigen conjugate treatment induces nAPCs that can activate autologous T cells when using neutrophils from individuals with myeloid neoplasms that harbor neoantigens or those vaccinated against bacterial toxins. Thus, anti-FcγRIIIB-antigen conjugate-induced conversion of neutrophils to immunogenic nAPCs may represent a possible immunotherapy for cancer and infectious diseases.
Integrative oncogene-dependency mapping identifies RIT1 vulnerabilities and synergies in lung cancer
Authors: Vichas Athea , Riley Amanda K. , Nkinsi Naomi T. , Kamlapurkar Shriya , Parrish Phoebe C. R. , Lo April , Duke Fujiko , Chen Jennifer , Fung Iris , Watson Jacqueline , Rees Matthew , Gabel Austin M. , Thomas James D. , Bradley Robert K. , Lee John K. , Hatch Emily M. , Baine Marina K. , Rekhtman Natasha , Ladanyi Marc , Piccioni Federica , Berger Alice H. 
Published: August 2021

AbstractCRISPR-based cancer dependency maps are accelerating advances in cancer precision medicine, but adequate functional maps are limited to the most common oncogenes. To identify opportunities for therapeutic intervention in other rarer subsets of cancer, we investigate the oncogene-specific dependencies conferred by the lung cancer oncogene, RIT1. Here, genome-wide CRISPR screening in KRAS, EGFR, and RIT1-mutant isogenic lung cancer cells identifies shared and unique vulnerabilities of each oncogene. Combining this genetic data with small-molecule sensitivity profiling, we identify a unique vulnerability of RIT1-mutant cells to loss of spindle assembly checkpoint regulators. Oncogenic RIT1M90I weakens the spindle assembly checkpoint and perturbs mitotic timing, resulting in sensitivity to Aurora A inhibition. In addition, we observe synergy between mutant RIT1 and activation of YAP1 in multiple models and frequent nuclear overexpression of YAP1 in human primary RIT1-mutant lung tumors. These results provide a genome-wide atlas of oncogenic RIT1 functional interactions and identify components of the RAS pathway, spindle assembly checkpoint, and Hippo/YAP1 network as candidate therapeutic targets in RIT1-mutant lung cancer.
An engineered IL-2 reprogrammed for anti-tumor therapy using a semi-synthetic organism
Authors: Ptacin Jerod L. , Caffaro Carolina E. , Ma Lina , San Jose Gall Kristine M. , Aerni Hans R. , Acuff Nicole V. , Herman Rob W. , Pavlova Yelena , Pena Michael J. , Chen David B. , Koriazova Lilia K. , Shawver Laura K. , Joseph Ingrid B. , Milla Marcos E. 
Published: August 2021

AbstractThe implementation of applied engineering principles to create synthetic biological systems promises to revolutionize medicine, but application of fundamentally redesigned organisms has thus far not impacted practical drug development. Here we utilize an engineered microbial organism with a six-letter semi-synthetic DNA code to generate a library of site-specific, click chemistry compatible amino acid substitutions in the human cytokine IL-2. Targeted covalent modification of IL-2 variants with PEG polymers and screening identifies compounds with distinct IL-2 receptor specificities and improved pharmacological properties. One variant, termed THOR-707, selectively engages the IL-2 receptor beta/gamma complex without engagement of the IL-2 receptor alpha. In mice, administration of THOR-707 results in large-scale activation and amplification of CD8+T cells and NK cells, without Treg expansion characteristic of IL-2. In syngeneic B16-F10 tumor-bearing mice, THOR-707 enhances drug accumulation in the tumor tissue, stimulates tumor-infiltrating CD8+T and NK cells, and leads to a dose-dependent reduction of tumor growth. These results support further characterization of the immune modulatory, anti-tumor properties of THOR-707 and represent a fundamental advance in the application of synthetic biology to medicine, leveraging engineered semi-synthetic organisms as cellular factories to facilitate discovery and production of differentiated classes of chemically modified biologics.
Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia
Authors: Ingle Danielle J. , Ambrose Rebecca L. , Baines Sarah L. , Duchene Sebastian , Gonçalves da Silva Anders , Lee Darren Y. J. , Jones Miriam , Valcanis Mary , Taiaroa George , Ballard Susan A. , Kirk Martyn D. , Howden Benjamin P. , Pearson Jaclyn S. , Williamson Deborah A. 
Published: August 2021

AbstractSalmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a monophasic variant of Salmonella Typhimurium that has emerged as a global cause of multidrug resistant salmonellosis. We used Bayesian phylodynamics, genomic epidemiology, and phenotypic characterization to describe the emergence and evolution of Salmonella 4,[5],12:i:- in Australia. We show that the interruption of the genetic region surrounding the phase II flagellin, FljB, causing a monophasic phenotype, represents a stepwise evolutionary event through the accumulation of mobile resistance elements with minimal impairment to bacterial fitness. We identify three lineages with different population dynamics and discrete antimicrobial resistance profiles emerged, likely reflecting differential antimicrobial selection pressures. Two lineages are associated with travel to South-East Asia and the third lineage is endemic to Australia. Moreover antimicrobial-resistant Salmonella 4,[5],12:i- lineages efficiently infected and survived in host phagocytes and epithelial cells without eliciting significant cellular cytotoxicity, suggesting a suppression of host immune response that may facilitate the persistence of Salmonella 4,[5],12:i:-.
IceR improves proteome coverage and data completeness in global and single-cell proteomics
Authors: Kalxdorf Mathias , Müller Torsten , Stegle Oliver , Krijgsveld Jeroen 
Published: August 2021

AbstractLabel-free proteomics by data-dependent acquisition enables the unbiased quantification of thousands of proteins, however it notoriously suffers from high rates of missing values, thus prohibiting consistent protein quantification across large sample cohorts. To solve this, we here present IceR (Ion current extraction Re-quantification), an efficient and user-friendly quantification workflow that combines high identification rates of data-dependent acquisition with low missing value rates similar to data-independent acquisition. Specifically, IceR uses ion current information for a hybrid peptide identification propagation approach with superior quantification precision, accuracy, reliability and data completeness compared to other quantitative workflows. Applied to plasma and single-cell proteomics data, IceR enhanced the number of reliably quantified proteins, improved discriminability between single-cell populations, and allowed reconstruction of a developmental trajectory. IceR will be useful to improve performance of large scale global as well as low-input proteomics applications, facilitated by its availability as an easy-to-use R-package.
A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics
Authors: Oftadeh Omid , Salvy Pierre , Masid Maria , Curvat Maxime , Miskovic Ljubisa , Hatzimanikatis Vassily 
Published: August 2021

AbstractEukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of multiple biological networks into a single model for cell analysis and engineering. One of the most accurate models of biological systems include Expression and Thermodynamics FLux (ETFL), which efficiently integrates RNA and protein synthesis with traditional genome-scale metabolic models. However, ETFL is so far only applicable for E. coli. To adapt this model for Saccharomyces cerevisiae, we developed yETFL, in which we augmented the original formulation with additional considerations for biomass composition, the compartmentalized cellular expression system, and the energetic costs of biological processes. We demonstrated the ability of yETFL to predict maximum growth rate, essential genes, and the phenotype of overflow metabolism. We envision that the presented formulation can be extended to a wide range of eukaryotic organisms to the benefit of academic and industrial research.
The cytokines HGF and CXCL13 predict the severity and the mortality in COVID-19 patients
Authors: Perreau Matthieu , Suffiotti Madeleine , Marques-Vidal Pedro , Wiedemann Aurelie , Levy Yves , Laouénan Cédric , Ghosn Jade , Fenwick Craig , Comte Denis , Roger Thierry , Regina Jean , Vollenweider Peter , Waeber Gerard , Oddo Mauro , Calandra Thierry , Pantaleo Giuseppe 
Published: August 2021

AbstractThe objective of the present study was to identify biological signatures of severe coronavirus disease 2019 (COVID-19) predictive of admission in the intensive care unit (ICU). Over 170 immunological markers were investigated in a ‘discovery’ cohort (n = 98 patients) of the Lausanne University Hospital (LUH-1). Here we report that 13 out of 49 cytokines were significantly associated with ICU admission in the three cohorts (P < 0.05 to P < 0.001), while cellular immunological markers lacked power in discriminating between ICU and non-ICU patients. The cytokine results were confirmed in two ‘validation’ cohorts, i.e. the French COVID-19 Study (FCS; n = 62) and a second LUH-2 cohort (n = 47). The combination of hepatocyte growth factor (HGF) and C-X-C motif chemokine ligand 13 (CXCL13) was the best predictor of ICU admission (positive and negative predictive values ranging from 81.8% to 93.1% and 85.2% to 94.4% in the 3 cohorts) and occurrence of death during patient follow-up (8.8 fold higher likelihood of death when both cytokines were increased). Of note, HGF is a pleiotropic cytokine with anti-inflammatory properties playing a fundamental role in lung tissue repair, and CXCL13, a pro-inflammatory chemokine associated with pulmonary fibrosis and regulating the maturation of B cell response. Up-regulation of HGF reflects the most powerful counter-regulatory mechanism of the host immune response to antagonize the pro-inflammatory cytokines including CXCL13 and to prevent lung fibrosis in COVID-19 patients.