bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ionospheric Scale Index Map Based on TEC Data During the Saint Patrick Magnetic Storm and EPBs
Authors: Denardini C. M. , Picanço G. A. S. , Barbosa Neto P. F. , Nogueira P. A. B. , Carmo C. S. , Resende L. C. A. , Moro J. , Chen S. S. , Romero‐Hernandez E. , Silva R. P. , Bilibio A. V. 
Published: August 2020

AbstractThis study examines the variability of the ionospheric content during the period around the 2015 Saint Patrick magnetic storm and when equatorial plasma bubbles (EPBs) are observed during the quiet time over South America during two other events. It uses the ionospheric scales index map based on the disturbance ionospheric index (DIX). The results are compared to the traces of the ionograms obtained at three different ionospheric stations (Fortaleza, Campo Grande, and Cachoeira Paulista) in Brazil acquired in the same period and at the same time rate. The index is based on the TEC map developed at the “Brazilian Studies and Monitoring of Space Weather” (Embrace/INPE). It covers the whole South America (latitudes from 20°N to 60°S and longitudes from 90°W to 30°W) with 0.5° × 0.5° resolution cells (60 × 60 km2). Among the results, the DIX map revealed some patches of “Disturbed” and “Weakly Disturbed” ionospheric conditions during the magnetically quiet time before the storm, which were associated with range and frequency Spread‐F over the same area as observed in ionograms. Also, the information from the southern portion of the dip equator showed a transition from occurrences of Spread‐F prior to sunrise to a condition favorable enough to develop a F3 layer after sunrise.
Tidal Resonance in the Adriatic Sea: Observational Evidence
Authors: Medvedev Igor P. , Vilibić Ivica , Rabinovich Alexander B. 
Published: August 2020

AbstractTides in the Adriatic Sea are anomalously strong in comparison with most of other parts of the Mediterranean Sea. Consequently, tides play a fundamental role in the hydrodynamics of this sea and in the formation of destructive floods in its northernmost part. The resonant character of the Adriatic tides is evident, but the exact mechanism of their formation has never been thoroughly examined. In the present study, we used multidecadal tide gauge data from 10 stations located along the basin's coastline to examine the spectral properties of the Adriatic Sea and to provide high‐resolution tidal analysis. Our results demonstrate that both diurnal and semidiurnal tidal harmonics are resonantly amplified due to the proximity of tidal periods to the periods of the fundamental (21.5 hr) and first (10.9 hr) Adriatic eigen modes, respectively. The constructed resonance models were found to closely describe specific features of the observed tides in the Adriatic Sea, including both major and minor harmonics, and therefore help to explain the dominant physical mechanism driving the floods in the northernmost part of the basin, including the Venice Lagoon.
Variability of the Canary Current Diagnosed by Inverse Box Models
Authors: Casanova‐Masjoan M. , Pérez‐Hernández M. D. , Vélez‐Belchí P. , Cana L. , Hernández‐Guerra A. 
Published: August 2020

AbstractFour hydrographic cruises carried out between ~26.5 and 31°N in the eastern North Atlantic Subtropical Gyre in fall (2016 and 2017) and spring (2017 and 2018) are used to identify water masses and infer oceanic circulation. Geostrophic velocities are initially adjusted by referencing them to data from a Lower Acoustic Doppler Current Profiler (LADCP) and later to velocities estimated with an inverse box model. The distribution of the intermediate water masses (700 to 1,400 m depth) varies seasonally. Antarctic Intermediate Water (AAIW) comprises the largest contributor to the seasonal cycle in the intermediate water masses. Circulation of the Canary Current (CC) differs in fall and spring. In fall, the CC flows southward through the western islands and recirculates south of the archipelago, subsequently flowing northward through the passage between the eastern islands and Africa. North of Lanzarote, the recirculated CC intensified as it is joined by a southeasterly branch of the CC north of Lanzarote. In spring, the net transport of the CC is southward. High interannual variability in mass transport is evident in both spring and fall as a result of the position of the current, with its easternmost (westernmost) position found in spring (fall) 2018 (2016). At intermediate levels, highly variable northward/southward transport is apparent in fall over the African slope, with the Intermediate Poleward Under Current (IPUC) only present in 2017.
Evaluation of Total Electron Content Prediction Using Three Ionosphere‐Thermosphere Models
Authors: Verkhoglyadova O. , Meng X. , Mannucci A. J. , Shim J.‐S. , McGranaghan R. 
Published: August 2020

AbstractPrediction of ionospheric state is a critical space weather problem. We expand on our previous research of medium‐range ionospheric forecasts and present new results on evaluating prediction capabilities of three physics‐based ionosphere‐thermosphere models (Thermosphere Ionosphere Electrodynamics General Circulation Model, TIE‐GCM; Coupled Thermosphere Ionosphere Plasmasphere Electrodynamics Model, CTIPe; and Global Ionosphere Thermosphere Model, GITM). The focus of our study is understanding how current modeling approaches may predict the global ionosphere for geomagnetic storms (as studied through 35 storms during 2000–2016). Prediction approach uses physics‐based modeling without any manual model adjustment, quality control, or selection of the results. Our goal is to understand to what extent current physics‐based modeling can be used in total electron content (TEC) prediction and explore uncertainties of these prediction efforts with multiday lead times. The ionosphere‐thermosphere model runs are driven by actual interplanetary conditions, whether those data come from real‐time measurements or predicted values themselves. These model runs were performed by the Community Coordinated Modeling Center (CCMC). Jet Propulsion Laboratory (JPL)‐produced global ionospheric maps (GIMs) were used to validate model TEC estimates. We utilize the True Skill Statistic (TSS) metric for the TEC prediction evaluation, noting that this is but one metric to assess predictive skill and that complete evaluations require combinations of such metrics. The meanings of contingency table elements for the prediction performance are analyzed in the context of ionosphere modeling. Prediction success is between about 0.2 and 0.5 for weak ionospheric disturbances and decreases for strong disturbances. We evaluate the prediction of TEC decreases and increases. Our results indicate that physics‐based modeling during storms shows promise in TEC prediction with multiday lead time.
The impact of donor type on the outcome of pediatric patients with very high risk acute lymphoblastic leukemia. A study of the ALL SCT 2003 BFM-SG and 2007-BFM-International SG
Authors: Dalle Jean-Hugues , Balduzzi Adriana , Bader Peter , Pieczonka Anna , Yaniv Isaac , Lankester Arjan , Bierings Marc , Yesilipek Akif , Sedlacek Petr , Ifversen Marianne , Svec Peter , Toporski Jacek , Gungor Taifun , Wachowiak Jacek , Glogova Evgenia , Poetschger Ulrike , Peters Christina 
Published: August 2020

AbstractAllogeneic HSCT represents the only potentially curative treatment for very high risk (VHR) ALL. Two consecutive international prospective studies, ALL-SCT-(I)BFM 2003 and 2007 were conducted in 1150 pediatric patients. 569 presented with VHR disease leading to any kind of HSCT. All patients >2 year old were transplanted after TBI-based MAC. The median follow-up was 5 years. 463 patients were transplanted from matched donor (MD) and 106 from mismatched donor (MMD). 214 were in CR1. Stem cell source was unmanipulated BM for 330 patients, unmanipulated PBSC for 135, ex vivo T-cell depleted PBSC for 62 and cord-blood for 26. There were more advanced disease, more ex vivo T-cell depletion, and more chemotherapy based conditioning regimen for patients transplanted from MMD as compared to those transplanted from MSD or MD. Median follow up (reversed Kaplan Meier estimator) was 4.99 years, median follow up of survivals was 4.88, range (0.01–11.72) years. The 4-year CI of extensive cGvHD was 13 ± 2% and 17 ± 4% (p = NS) for the patients transplanted from MD and MMD, respectively. 4-year EFS was statistically better for patients transplanted from MD (60 ± 2% vs. 42 ± 5%, p < 0.001) for the whole cohort. This difference does not exist if considering separately patients treated in the most recent study. There was no difference in 4-year CI of relapse. The 4-year NRM was lower for patients transplanted from MD (9 ± 1% vs. 23 ± 4%, p < 0.001). In multivariate analysis, donor-type appears as a negative risk-factor for OS, EFS, and NRM. This paper demonstrates the impact of donor type on overall results of allogeneic stem cell transplantation for very-high risk pediatric acute lymphoblastic leukemia with worse results when using MMD stem cell source.
Emergence and significance of carbohydrate-specific antibodies
Authors: Kappler Katharina , Hennet Thierry 
Published: August 2020

AbstractCarbohydrate-specific antibodies are widespread among all classes of immunoglobulins. Despite their broad occurrence, little is known about their formation and biological significance. Carbohydrate-specific antibodies are often classified as natural antibodies under the assumption that they arise without prior exposure to exogenous antigens. On the other hand, various carbohydrate-specific antibodies, including antibodies to ABO blood group antigens, emerge after the contact of immune cells with the intestinal microbiota, which expresses a vast diversity of carbohydrate antigens. Here we explore the development of carbohydrate-specific antibodies in humans, addressing the definition of natural antibodies and the production of carbohydrate-specific antibodies upon antigen stimulation. We focus on the significance of the intestinal microbiota in shaping carbohydrate-specific antibodies not just in the gut, but also in the blood circulation. The structural similarity between bacterial carbohydrate antigens and surface glycoconjugates of protists, fungi and animals leads to the production of carbohydrate-specific antibodies protective against a broad range of pathogens. Mimicry between bacterial and human glycoconjugates, however, can also lead to the generation of carbohydrate-specific antibodies that cross-react with human antigens, thereby contributing to the development of autoimmune disorders.
Homogeneous and heterogeneous catalytic reduction of amides and related compounds using molecular hydrogen
Authors: Cabrero-Antonino Jose R. , Adam Rosa , Papa Veronica , Beller Matthias 
Published: August 2020

AbstractCatalytic hydrogenation of amides is of great interest for chemists working in organic synthesis, as the resulting amines are widely featured in natural products, drugs, agrochemicals, dyes, etc. Compared to traditional reduction of amides using (over)stoichiometric reductants, the direct hydrogenation of amides using molecular hydrogen represents a greener approach. Furthermore, amide hydrogenation is a highly versatile transformation, since not only higher amines (obtained by C–O cleavage), but also lower amines and alcohols, or amino alcohols (obtained by C–N cleavage) can be selectively accessed by fine tuning of reaction conditions. This review describes the most recent advances in the area of amide hydrogenation using H2exclusively and molecularly defined homogeneous as well as nano-structured heterogeneous catalysts, with a special focus on catalyst development and synthetic applications.
Cyclic peptide FXII inhibitor provides safe anticoagulation in a thrombosis model and in artificial lungs
Authors: Wilbs Jonas , Kong Xu-Dong , Middendorp Simon J. , Prince Raja , Cooke Alida , Demarest Caitlin T. , Abdelhafez Mai M. , Roberts Kalliope , Umei Nao , Gonschorek Patrick , Lamers Christina , Deyle Kaycie , Rieben Robert , Cook Keith E. , Angelillo-Scherrer Anne , Heinis Christian 
Published: August 2020

AbstractInhibiting thrombosis without generating bleeding risks is a major challenge in medicine. A promising solution may be the inhibition of coagulation factor XII (FXII), because its knock-out or inhibition in animals reduced thrombosis without causing abnormal bleeding. Herein, we have engineered a macrocyclic peptide inhibitor of activated FXII (FXIIa) with sub-nanomolar activity (Ki = 370 ± 40 pM) and a high stability (t1/2 > 5 days in plasma), allowing for the preclinical evaluation of a first synthetic FXIIa inhibitor. This 1899 Da molecule, termed FXII900, efficiently blocks FXIIa in mice, rabbits, and pigs. We found that it reduces ferric-chloride-induced experimental thrombosis in mice and suppresses blood coagulation in an extracorporeal membrane oxygenation (ECMO) setting in rabbits, all without increasing the bleeding risk. This shows that FXIIa activity is controllable in vivo with a synthetic inhibitor, and that the inhibitor FXII900 is a promising candidate for safe thromboprotection in acute medical conditions.
The inferior temporal cortex is a potential cortical precursor of orthographic processing in untrained monkeys
Authors: Rajalingham Rishi , Kar Kohitij , Sanghavi Sachi , Dehaene Stanislas , DiCarlo James J. 
Published: August 2020

AbstractThe ability to recognize written letter strings is foundational to human reading, but the underlying neuronal mechanisms remain largely unknown. Recent behavioral research in baboons suggests that non-human primates may provide an opportunity to investigate this question. We recorded the activity of hundreds of neurons in V4 and the inferior temporal cortex (IT) while naïve macaque monkeys passively viewed images of letters, English words and non-word strings, and tested the capacity of those neuronal representations to support a battery of orthographic processing tasks. We found that simple linear read-outs of IT (but not V4) population responses achieved high performance on all tested tasks, even matching the performance and error patterns of baboons on word classification. These results show that the IT cortex of untrained primates can serve as a precursor of orthographic processing, suggesting that the acquisition of reading in humans relies on the recycling of a brain network evolved for other visual functions.
Fifth-degree elastic energy for predictive continuum stress–strain relations and elastic instabilities under large strain and complex loading in silicon
Authors: Chen Hao , Zarkevich Nikolai A. , Levitas Valery I. , Johnson Duane D. , Zhang Xiancheng 
Published: August 2020

AbstractMaterials under complex loading develop large strains and often phase transformation via an elastic instability, as observed in both simple and complex systems. Here, we represent a material (exemplified for Si I) under large Lagrangian strains within a continuum description by a 5th-order elastic energy found by minimizing error relative to density functional theory (DFT) results. The Cauchy stress—Lagrangian strain curves for arbitrary complex loadings are in excellent correspondence with DFT results, including the elastic instability driving the Si I → II phase transformation (PT) and the shear instabilities. PT conditions for Si I → II under action of cubic axial stresses are linear in Cauchy stresses in agreement with DFT predictions. Such continuum elastic energy permits study of elastic instabilities and orientational dependence leading to different PTs, slip, twinning, or fracture, providing a fundamental basis for continuum physics simulations of crystal behavior under extreme loading.
Linking metabolic phenotypes to pathogenic traits among “Candidatus Liberibacter asiaticus” and its hosts
Authors: Zuñiga Cristal , Peacock Beth , Liang Bo , McCollum Greg , Irigoyen Sonia C. , Tec-Campos Diego , Marotz Clarisse , Weng Nien-Chen , Zepeda Alejandro , Vidalakis Georgios , Mandadi Kranthi K. , Borneman James , Zengler Karsten 
Published: August 2020

AbstractCandidatus Liberibacter asiaticus (CLas) has been associated with Huanglongbing, a lethal vector-borne disease affecting citrus crops worldwide. While comparative genomics has provided preliminary insights into the metabolic capabilities of this uncultured microorganism, a comprehensive functional characterization is currently lacking. Here, we reconstructed and manually curated genome-scale metabolic models for the six CLas strains A4, FL17, gxpsy, Ishi-1, psy62, and YCPsy, in addition to a model of the closest related culturable microorganism, L. crescens BT-1. Predictions about nutrient requirements and changes in growth phenotypes of CLas were confirmed using in vitro hairy root-based assays, while the L. crescens BT-1 model was validated using cultivation assays. Host-dependent metabolic phenotypes were revealed using expression data obtained from CLas-infected citrus trees and from the CLas-harboring psyllid Diaphorina citri Kuwayama. These results identified conserved and unique metabolic traits, as well as strain-specific interactions between CLas and its hosts, laying the foundation for the development of model-driven Huanglongbing management strategies.
Structure-guided covalent stabilization of coronavirus spike glycoprotein trimers in the closed conformation
Authors: McCallum Matthew , Walls Alexandra C. , Bowen John E. , Corti Davide , Veesler David 
Published: August 2020

AbstractSARS-CoV-2 is the causative agent of the COVID-19 pandemic, with 10 million infections and more than 500,000 fatalities by June 2020. To initiate infection, the SARS-CoV-2 spike (S) glycoprotein promotes attachment to the host cell surface and fusion of the viral and host membranes. Prefusion SARS-CoV-2 S is the main target of neutralizing antibodies and the focus of vaccine design. However, its limited stability and conformational dynamics are limiting factors for developing countermeasures against this virus. We report here the design of a construct corresponding to the prefusion SARS-CoV-2 S ectodomain trimer, covalently stabilized by a disulfide bond in the closed conformation. Structural and antigenicity analyses show we successfully shut S in the closed state without otherwise altering its architecture. We demonstrate that this strategy is applicable to other β-coronaviruses, such as SARS-CoV and MERS-CoV, and might become an important tool for structural biology, serology, vaccine design and immunology studies.
Haptoglobin polymorphism and prostate cancer mortality
Authors: Kaiser Melanie , Thurner Eva-Maria , Mangge Harald , Herrmann Markus , Semeraro Maria Donatella , Renner Wilfried , Langsenlehner Tanja 
Published: August 2020

AbstractProstate cancer is a common malignancy in men worldwide and it is known that oxidative stress is a risk factor for cancer development. A common functional haptoglobin (Hp) polymorphism, originating from a duplication of a gene segment spanning over two exons, results in three distinct phenotypes with different anti-oxidative capacities: Hp1-1, Hp1-2, and Hp2-2. The aim of the study was to investigate the relationship between this Hp polymorphism and prostate cancer mortality. The study was performed on 690 patients with histologically confirmed prostate cancer, recruited between January 2004 and January 2007. Hp genotypes were determined by a TaqMan fluorogenic 5′-exonuclease assay. Hp1-1 was present in 76 (11%), Hp1-2 in 314 (45.5%), and Hp2-2 in 300 (43.5%) patients. During a median follow-up of 149 months, 251 (35.3%) patients died. Hp genotypes were not significantly associated with higher overall mortality (HR 1.10; 95% CI 0.91–1.33; p = 0.34). This remained similar in a multivariate analysis including age at diagnosis, androgen deprivation therapy, and risk group based on PSA level, GS, and T stage (HR 1.11; 95% CI 0.91–1.34; p = 0.30). We conclude that the common Hp polymorphism does not seem to be associated with overall mortality in prostate cancer patients.
Using proximity extension proteomics assay to discover novel biomarkers associated with circulating leptin levels in patients with type 2 diabetes
Authors: Vavruch Camilla , Nowak C. , Feldreich T. , Östgren C. J. , Sundström J. , Söderberg S. , Lind L. , Nyström F. , Ärnlöv J. 
Published: August 2020

AbstractWe aimed to discover novel associations between leptin and circulating proteins which could link leptin to the development of cardiovascular disease in patients with type 2 diabetes (T2DM). In a discovery phase, we investigated associations between 88 plasma proteins, assessed with a proximity extension assay, and plasma leptin in a cohort of middle-aged patients with T2DM. Associations passing the significance threshold of a False discovery rate of 5% (corresponding to p < 0.0017) were replicated in patients with T2DM in an independent cohort. We also investigated if proteins mediated the longitudinal association between plasma leptin and the incidence of major cardiovascular events (MACE). One protein, adipocyte fatty acid binding protein (A-FABP), was significantly associated with leptin in both the discovery phase [95% CI (0.06, 0.17) p = 0.00002] and the replication cohort [95% CI (0.12, 0.39) p = 0.0003]. Multiplicative interaction analyses in the two cohorts suggest a stronger association between A-FABP and leptin in men than in women. In longitudinal analyses, the association between leptin and MACE was slightly attenuated after adding A-FABP to the multivariate model. Our analysis identified a consistent association between leptin and A-FABP in two independent cohorts of patients with T2DM, particularly in men.Trial registration: ClinicalTrials.gov identifier NCT 01049737.
FOSL1 is a novel mediator of endotoxin/lipopolysaccharide-induced pulmonary angiogenic signaling
Authors: Nitkin Christopher R. , Xia Sheng , Menden Heather , Yu Wei , Xiong Min , Heruth Daniel P. , Ye Shui Qing , Sampath Venkatesh 
Published: August 2020

AbstractSystemic sepsis is a known risk factor for bronchopulmonary dysplasia (BPD) in premature infants, a disease characterized by dysregulated angiogenesis and impaired vascular and alveolar development. We have previoulsy reported that systemic endotoxin dysregulates pulmonary angiogenesis resulting in alveolar simplification mimicking BPD in neonatal mice, but the underlying mechanisms remain unclear. We undertook an unbiased discovery approach to identify novel signaling pathways programming sepsis-induced deviant lung angiogenesis. Pulmonary endothelial cells (EC) were isolated for RNA-Seq from newborn C57BL/6 mice treated with intraperitoneal lipopolysaccharide (LPS) to mimic systemic sepsis. LPS significantly differentially-regulated 269 genes after 6 h, and 1,934 genes after 24 h. Using bioinformatics, we linked 6 h genes previously unknown to be modulated by LPS to 24 h genes known to regulate angiogenesis/vasculogenesis to identify pathways programming deviant angiogenesis. An immortalized primary human lung EC (HPMEC-im) line was generated by SV40 transduction to facilitate mechanistic studies. RT-PCR and transcription factor binding analysis identified FOSL1 (FOS like 1) as a transcriptional regulator of LPS-induced downstream angiogenic or vasculogenic genes. Over-expression and silencing studies of FOSL1 in immortalized and primary HPMEC demonstrated that baseline and LPS-induced expression of ADAM8, CXCR2, HPX, LRG1, PROK2, and RNF213 was regulated by FOSL1. FOSL1 silencing impaired LPS-induced in vitro HPMEC angiogenesis. In conclusion, we identified FOSL1 as a novel regulator of sepsis-induced deviant angiogenic signaling in mouse lung EC and human fetal HPMEC.