bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Surface to Exosphere Non‐Orographic Gravity Wave Parameterization for the Mars Planetary Climate Model
Authors: Liu Jiandong , Millour Ehouarn , Forget François , Gilli Gabriella , Lott François , Bardet Deborah , González Galindo Francisco , Bierjon Antoine , Naar Joseph , Martinez Antoine , Lebonnois Sébastien , Fan Siteng , Pierron Thomas , Vandemeulebrouck Romain 
Published: July 2023

AbstractIn this paper, the non‐orographic gravity waves (GW) parameterization of the Mars Planetary Climate Model (PCM) previously implemented by Gilli et al. (2020, https://doi.org/10.1029/2018JE005873) is revisited and extended to the exobase (∼250 km). The simulations performed with the new scheme correct some known biases in the modeled thermal tide amplitudes and polar warming, improving the agreement with Mars Climate Sounder (MCS) observed thermal structures and tides below ∼100 km. Additionally, we find that the simulated densities above 150 km are compatible with NGIMS (Neutral Gas and Ion Mass Spectrometer) measured abundances. Large drag depositions ranging up to >∼950 m s−1 sol−1 are induced at altitude of 90–170 km due to the wave saturation (breaking) and depletion, leading to winds damped to magnitudes of ∼150–225 and ∼80 m s−1 in the zonal and meridional directions, respectively. Resulting temperature variations are ∼±10–30 K or 5%–10% at most latitudes except in the polar regions (where they can reach ∼±30–60 K). The results indicate that non‐orographic GW play a significant role in the dynamics of the middle‐upper atmosphere of Mars via the induced transfer of momentum and energy from the lower atmosphere.
Multi‐Objective Optimization Models for the Design of Water Distribution Networks by Exploring Scenario‐Based Approaches
Authors: Cunha M. C. , Magini R. , Marques J. 
Published: July 2023

AbstractDemand in a water distribution network (WDN) is an aleatory variable, owing to the unpredictable behaviors of water users. Therefore, it is one of the main reasons for uncertainty in the design of this infrastructure. The increasing number of water demand data sets offers opportunities to improve the traditional deterministic design approaches of WDNs by combining statistical and optimization methods. Robust optimization (RO) takes demand uncertainty into account by studying solutions that perform well under any possible demand scenario, that is, any possible realizations of this variable in the lifetime of a WDN. The right choice of scenario is therefore essential to ensure the reliability of the designed network. This paper presents a statistical methodology for generating scenarios to be used to solve a robust design optimization problem. It involves three steps: (a) descriptive analytics of historical data to derive the marginal distributions of peak hour demand in each node of the WDN, (b) generation of a very large number of snapshots by stratified sampling from the correlated marginal distributions of nodal peak demand, (c) generation of the peak demand scenarios by reducing the number of snapshots. Two heuristic techniques are proposed to reduce the number of snapshots, and for each of them, two different numbers of scenarios are derived. Two multi‐objective RO models are solved: the first model includes cost minimization and a mean‐variance Generalized Resilience and Failure index maximization objectives, and the second one additionally considers the minimization of the maximum undelivered demand, formalized using a regret function.
Defining the landscape of circular RNAs in neuroblastoma unveils a global suppressive function of MYCN
Authors: Fuchs Steffen , Danßmann Clara , Klironomos Filippos , Winkler Annika , Fallmann Jörg , Kruetzfeldt Louisa-Marie , Szymansky Annabell , Naderi Julian , Bernhart Stephan H. , Grunewald Laura , Helmsauer Konstantin , Rodriguez-Fos Elias , Kirchner Marieluise , Mertins Philipp , Astrahantseff Kathy , Suenkel Christin , Toedling Joern , Meggetto Fabienne , Remke Marc , Stadler Peter F. , Hundsdoerfer Patrick , Deubzer Hedwig E. , Künkele Annette , Lang Peter , Fuchs Jörg , Henssen Anton G. , Eggert Angelika , Rajewsky Nikolaus , Hertwig Falk , Schulte Johannes H. 
Published: July 2023

AbstractCircular RNAs (circRNAs) are a regulatory RNA class. While cancer-driving functions have been identified for single circRNAs, how they modulate gene expression in cancer is not well understood. We investigate circRNA expression in the pediatric malignancy, neuroblastoma, through deep whole-transcriptome sequencing in 104 primary neuroblastomas covering all risk groups. We demonstrate that MYCN amplification, which defines a subset of high-risk cases, causes globally suppressed circRNA biogenesis directly dependent on the DHX9 RNA helicase. We detect similar mechanisms in shaping circRNA expression in the pediatric cancer medulloblastoma implying a general MYCN effect. Comparisons to other cancers identify 25 circRNAs that are specifically upregulated in neuroblastoma, including circARID1A. Transcribed from the ARID1A tumor suppressor gene, circARID1A promotes cell growth and survival, mediated by direct interaction with the KHSRP RNA-binding protein. Our study highlights the importance of MYCN regulating circRNAs in cancer and identifies molecular mechanisms, which explain their contribution to neuroblastoma pathogenesis.
Real-time environmental surveillance of SARS-CoV-2 aerosols
Authors: Puthussery Joseph V. , Ghumra Dishit P. , McBrearty Kevin R. , Doherty Brookelyn M. , Sumlin Benjamin J. , Sarabandi Amirhossein , Mandal Anushka Garg , Shetty Nishit J. , Gardiner Woodrow D. , Magrecki Jordan P. , Brody David L. , Esparza Thomas J. , Bricker Traci L. , Boon Adrianus C. M. , Yuede Carla M. , Cirrito John R. , Chakrabarty Rajan K. 
Published: July 2023

AbstractReal-time surveillance of airborne SARS-CoV-2 virus is a technological gap that has eluded the scientific community since the beginning of the COVID-19 pandemic. Offline air sampling techniques for SARS-CoV-2 detection suffer from longer turnaround times and require skilled labor. Here, we present a proof-of-concept pathogen Air Quality (pAQ) monitor for real-time (5 min time resolution) direct detection of SARS-CoV-2 aerosols. The system synergistically integrates a high flow (~1000 lpm) wet cyclone air sampler and a nanobody-based ultrasensitive micro-immunoelectrode biosensor. The wet cyclone showed comparable or better virus sampling performance than commercially available samplers. Laboratory experiments demonstrate a device sensitivity of 77–83% and a limit of detection of 7-35 viral RNA copies/m3 of air. Our pAQ monitor is suited for point-of-need surveillance of SARS-CoV-2 variants in indoor environments and can be adapted for multiplexed detection of other respiratory pathogens of interest. Widespread adoption of such technology could assist public health officials with implementing rapid disease control measures.
Combined multidimensional single-cell protein and RNA profiling dissects the cellular and functional heterogeneity of thymic epithelial cells
Authors: Klein Fabian , Veiga-Villauriz Clara , Börsch Anastasiya , Maio Stefano , Palmer Sam , Dhalla Fatima , Handel Adam E. , Zuklys Saulius , Calvo-Asensio Irene , Musette Lucas , Deadman Mary E. , White Andrea J. , Lucas Beth , Anderson Graham , Holländer Georg A. 
Published: July 2023

AbstractThe network of thymic stromal cells provides essential niches with unique molecular cues controlling T cell development and selection. Recent single-cell RNA sequencing studies have uncovered previously unappreciated transcriptional heterogeneity among thymic epithelial cells (TEC). However, there are only very few cell markers that allow a comparable phenotypic identification of TEC. Here, using massively parallel flow cytometry and machine learning, we deconvoluted known TEC phenotypes into novel subpopulations. Using CITEseq, these phenotypes were related to corresponding TEC subtypes defined by the cells’ RNA profiles. This approach allowed the phenotypic identification of perinatal cTEC and their physical localisation within the cortical stromal scaffold. In addition, we demonstrate the dynamic change in the frequency of perinatal cTEC in response to developing thymocytes and reveal their exceptional efficiency in positive selection. Collectively, our study identifies markers that allow for an unprecedented dissection of the thymus stromal complexity, as well as physical isolation of TEC populations and assignment of specific functions to individual TEC subtypes.
Transmission of SARS-CoV-2 in free-ranging white-tailed deer in the United States
Authors: Feng Aijing , Bevins Sarah , Chandler Jeff , DeLiberto Thomas J. , Ghai Ria , Lantz Kristina , Lenoch Julianna , Retchless Adam , Shriner Susan , Tang Cynthia Y. , Tong Suxiang Sue , Torchetti Mia , Uehara Anna , Wan Xiu-Feng 
Published: July 2023

AbstractSARS-CoV-2 is a zoonotic virus with documented bi-directional transmission between people and animals. Transmission of SARS-CoV-2 from humans to free-ranging white-tailed deer (Odocoileus virginianus) poses a unique public health risk due to the potential for reservoir establishment where variants may persist and evolve. We collected 8,830 respiratory samples from free-ranging white-tailed deer across Washington, D.C. and 26 states in the United States between November 2021 and April 2022. We obtained 391 sequences and identified 34 Pango lineages including the Alpha, Gamma, Delta, and Omicron variants. Evolutionary analyses showed these white-tailed deer viruses originated from at least 109 independent spillovers from humans, which resulted in 39 cases of subsequent local deer-to-deer transmission and three cases of potential spillover from white-tailed deer back to humans. Viruses repeatedly adapted to white-tailed deer with recurring amino acid substitutions across spike and other proteins. Overall, our findings suggest that multiple SARS-CoV-2 lineages were introduced, became enzootic, and co-circulated in white-tailed deer.
Symbiont-host interactome mapping reveals effector-targeted modulation of hormone networks and activation of growth promotion
Authors: Osborne Rory , Rehneke Laura , Lehmann Silke , Roberts Jemma , Altmann Melina , Altmann Stefan , Zhang Yingqi , Köpff Eva , Dominguez-Ferreras Ana , Okechukwu Emeka , Sergaki Chrysi , Rich-Griffin Charlotte , Ntoukakis Vardis , Eichmann Ruth , Shan Weixing , Falter-Braun Pascal , Schäfer Patrick 
Published: July 2023

AbstractPlants have benefited from interactions with symbionts for coping with challenging environments since the colonisation of land. The mechanisms of symbiont-mediated beneficial effects and similarities and differences to pathogen strategies are mostly unknown. Here, we use 106 (effector-) proteins, secreted by the symbiont Serendipita indica (Si) to modulate host physiology, to map interactions with Arabidopsis thaliana host proteins. Using integrative network analysis, we show significant convergence on target-proteins shared with pathogens and exclusive targeting of Arabidopsis proteins in the phytohormone signalling network. Functional in planta screening and phenotyping of Si effectors and interacting proteins reveals previously unknown hormone functions of Arabidopsis proteins and direct beneficial activities mediated by effectors in Arabidopsis. Thus, symbionts and pathogens target a shared molecular microbe-host interface. At the same time Si effectors specifically target the plant hormone network and constitute a powerful resource for elucidating the signalling network function and boosting plant productivity.
The Mediator complex regulates enhancer-promoter interactions
Authors: Ramasamy Shyam , Aljahani Abrar , Karpinska Magdalena A. , Cao T. B. Ngoc , Velychko Taras , Cruz J. Neos , Lidschreiber Michael , Oudelaar A. Marieke 
Published: July 2023

AbstractEnhancer-mediated gene activation generally requires physical proximity between enhancers and their target gene promoters. However, the molecular mechanisms by which interactions between enhancers and promoters are formed are not well understood. Here, we investigate the function of the Mediator complex in the regulation of enhancer-promoter interactions, by combining rapid protein depletion and high-resolution MNase-based chromosome conformation capture approaches. We show that depletion of Mediator leads to reduced enhancer-promoter interaction frequencies, which are associated with a strong decrease in gene expression. In addition, we find increased interactions between CTCF-binding sites upon Mediator depletion. These changes in chromatin architecture are associated with a redistribution of the Cohesin complex on chromatin and a reduction in Cohesin occupancy at enhancers. Together, our results indicate that the Mediator and Cohesin complexes contribute to enhancer-promoter interactions and provide insights into the molecular mechanisms by which communication between enhancers and promoters is regulated.
The cognitive benefits of basketball training compared to a combined endurance and resistance training regimen: a four-month intervention study
Authors: Madinabeitia-Cabrera Iker , Alarcón-López Francisco , Chirosa-Ríos Luis J. , Pelayo-Tejo Ignacio , Cárdenas-Vélez David 
Published: July 2023

AbstractNeurocognitive function, especially executive functioning, is positively associated with better fitness or higher levels of physical activity (PA). Previous research suggests that combined endurance and resistance (AER+R) training leads to greater improvements than training in either modality separately. Dynamic team sports with cognitive dimensions, such as basketball (BAS), may be an excellent context for improving cognition. This study compared the effects of following a four-month PA training program in BAS versus AER+R on executive functions along with a control group with low PA. Fifty participants completed the training period and were randomly distributed into three groups: BAS (16 participants), AER+R (18), and control (16). Participants in the BAS group showed improved inhibition and working memory and those in the AER+R group showed improved inhibition and cognitive flexibility, while inhibition deteriorated in the control group. There were significant differences between groups only in inhibition. It appears that following a four-month PA training program is enough to enhance executive functioning, and improvements in inhibition are more evident when the program includes an open sport such as BAS.
Delayed surgery and health related quality of life in patients with proximal femoral fracture
Authors: Merchán-Galvis Angela María , Muñoz-García David Andrés , Solano Felipe , Velásquez Julián Camilo , Sotelo Nelson Fernando , Molina David Alejandro , Caicedo Juan Pablo , Concha Juan Manuel , Calvache José Andrés , Martínez-Zapata María José 
Published: July 2023

AbstractThis study aimed to establish factors associated with delayed surgery in patients with proximal femoral fracture and to assess patients’ health-related quality of life (HRQoL) after surgery including all-cause 6-months mortality. This was a single-center, observational, prospective cohort study that included patients with a proximal femur fracture. We described patients’ HRQoL measured by EuroQoL (EQ-5D-5L and EQ-VAS) questionnaire and perioperative complications (including mortality) 6 months after surgery. We included 163 patients with a mean age of 80.5 years, the majority were women and 76.1% reported falling from their own height. The mean time between hospital admission and surgery was 8.3 days (SD 4.9 days) and the mean hospital stay was 13.5 days (SD 10.4 days). After adjustment, the principal factor associated with delayed surgery was adjournment in surgery authorization (3.7 days). EQ-5D-5L index values and the VAS score at 1 month after surgery were 0.489 and 61.1, at 3 months were 0.613 and 65.8, and at 6 months 0.662 and 66.7 respectively. Mortality at 6 months of follow-up was 11% (18 patients). In conclusion, administrative authorization was the strongest associated factor with delayed time from hospital admission to surgery. HRQoL of patients with a proximal femoral fracture improved 6 months after surgery.Trial registration:NCT04217642.
Impacts of gender and lifestyle on the association between depressive symptoms and cardiovascular disease risk in the UK Biobank
Authors: Lee Su Nam , Yun Jae-Seung , Ko Seung-Hyun , Ahn Yu-Bae , Yoo Ki-Dong , Her Sung-Ho , Moon Donggyu , Jung Sang-Hyuk , Won Hong-Hee , Kim Dokyoon 
Published: July 2023

AbstractWe investigated the effects of gender and lifestyle on the association between frequency of depressive symptoms and CVD risk. The UK Biobank is a national prospective cohort study that recruited 502,505 participants aged 40–69 years between 2006 and 2010. Participants without CVD were classified as having low, moderate, high, or very high frequency of depressive symptoms according to the number of days they felt depressed in a 2-week period. UKBB data include self-reported questionnaires covering lifestyle behaviors such as smoking, physical activity, eating habits, and sleep duration. The primary outcomes included incident CVD including coronary artery disease, ischemic stroke, hemorrhagic stroke, peripheral artery disease, atrial fibrillation/flutter, and heart failure. Cox proportional hazard models were used to evaluate the effects of gender and lifestyle on the association of frequency of depressive symptoms and CVD risk. During a median follow-up of 8.9 years, 27,394 (6.3%) developed CVD. The frequency of depressive symptoms increased the risk of CVD according to low, moderate, high, and very high frequency of depressive symptoms (P for trend < 0.001). The adjusted CVD risk was 1.38-fold higher for participants with very high frequency of depressive symptoms compared to those with low frequency of depressive symptoms (HR 1.38, 95% CI 1.24–1.53, P < 0.001). The correlation between frequency of depressive symptoms and CVD risk was more remarkable in females than in males. In participants with high or very high frequency of depressive symptoms, the individual lifestyle factors of no current smoking, non-obesity, non-abdominal obesity, regular physical activity, and appropriate sleep respectively was associated with lower CVD risk by 46% (HR 0.54, 95% CI 0.48–0.60, P < 0.001), 36% (HR 0.64, 95% CI 0.58–0.70, P < 0.001), 31% (HR 0.69, 95% CI 0.62–0.76, P < 0.001), 25% (HR 0.75, 95% CI 0.68–0.83, P < 0.001), and 22% (HR 0.78, 95% CI 0.71–0.86, P < 0.001). In this large prospective cohort study, a higher frequency of depressive symptoms at baseline was significantly associated with increased risk of CVD in the middle-aged population, and this relationship was prominent in women. In the middle-aged population with depressive symptoms, engaging in a healthier lifestyle could prevent CVD risk.
Subgroups of adult-onset diabetes: a data-driven cluster analysis in a Ghanaian population
Authors: Danquah Ina , Mank Isabel , Hampe Christiane S. , Meeks Karlijn A. C. , Agyemang Charles , Owusu-Dabo Ellis , Smeeth Liam , Klipstein-Grobusch Kerstin , Bahendeka Silver , Spranger Joachim , Mockenhaupt Frank P. , Schulze Matthias B. , Rolandsson Olov 
Published: July 2023

AbstractAdult-onset diabetes mellitus (here: aDM) is not a uniform disease entity. In European populations, five diabetes subgroups have been identified by cluster analysis using simple clinical variables; these may elucidate diabetes aetiology and disease prognosis. We aimed at reproducing these subgroups among Ghanaians with aDM, and establishing their importance for diabetic complications in different health system contexts. We used data of 541 Ghanaians with aDM (age: 25–70 years; male sex: 44%) from the multi-center, cross-sectional Research on Obesity and Diabetes among African Migrants (RODAM) Study. Adult-onset DM was defined as fasting plasma glucose (FPG) ≥ 7.0 mmol/L, documented use of glucose-lowering medication or self-reported diabetes, and age of onset ≥ 18 years. We derived subgroups by cluster analysis using (i) a previously published set of variables: age at diabetes onset, HbA1c, body mass index, HOMA-beta, HOMA-IR, positivity of glutamic acid decarboxylase autoantibodies (GAD65Ab), and (ii) Ghana-specific variables: age at onset, waist circumference, FPG, and fasting insulin. For each subgroup, we calculated the clinical, treatment-related and morphometric characteristics, and the proportions of objectively measured and self-reported diabetic complications. We reproduced the five subgroups: cluster 1 (obesity-related, 73%) and cluster 5 (insulin-resistant, 5%) with no dominant diabetic complication patterns; cluster 2 (age-related, 10%) characterized by the highest proportions of coronary artery disease (CAD, 18%) and stroke (13%); cluster 3 (autoimmune-related, 5%) showing the highest proportions of kidney dysfunction (40%) and peripheral artery disease (PAD, 14%); and cluster 4 (insulin-deficient, 7%) characterized by the highest proportion of retinopathy (14%). The second approach yielded four subgroups: obesity- and age-related (68%) characterized by the highest proportion of CAD (9%); body fat-related and insulin-resistant (18%) showing the highest proportions of PAD (6%) and stroke (5%); malnutrition-related (8%) exhibiting the lowest mean waist circumference and the highest proportion of retinopathy (20%); and ketosis-prone (6%) with the highest proportion of kidney dysfunction (30%) and urinary ketones (6%). With the same set of clinical variables, the previously published aDM subgroups can largely be reproduced by cluster analysis in this Ghanaian population. This method may generate in-depth understanding of the aetiology and prognosis of aDM, particularly when choosing variables that are clinically relevant for the target population.
Spring migration patterns of red knots in the Southeast United States disentangled using automated telemetry
Authors: Smith Adam D. , Sanders Felicia J. , Lefevre Kara L. , Thibault Janet M. , Kalasz Kevin S. , Handmaker Maina C. , Smith Fletcher M. , Keyes Tim S. 
Published: July 2023

AbstractRed Knots use the Southeast United States as a stopover during north and southbound migration and during the winter. We examined northbound red knot migration routes and timing using an automated telemetry network. Our primary goal was to evaluate the relative use of an Atlantic migratory route through Delaware Bay versus an inland route through the Great Lakes en route to Arctic breeding grounds and to identify areas of apparent stopovers. Secondarily, we explored the association of red knot routes and ground speeds with prevailing atmospheric conditions. Most Red Knots migrating north from the Southeast United States skipped or likely skipped Delaware Bay (73%) while 27% of the knots stopped in Delaware Bay for at least 1 day. A few knots used an Atlantic Coast strategy that did not include Delaware Bay, relying instead on the areas around Chesapeake Bay or New York Bay for stopovers. Nearly 80% of migratory trajectories were associated with tailwinds at departure. Most knots tracked in our study traveled north through the eastern Great Lake Basin, without stopping, thus making the Southeast United States the last terminal stopover for some knots before reaching boreal or Arctic stopover sites.