bluuebunny/crossref_metadata_2025_split huggingface dataset:
Magnetic Waves Excited by Newborn Pickup H+ Near Jupiter: Neutral Hydrogen Loss by the Planetary System
Authors: Hollick Sophia J. , Smith Charles W. , Pine Zackary B. , Argall Matthew R. , Joyce Colin J. , Isenberg Philip A. , Vasquez Bernard J. , Schwadron Nathan A. , Sokół Justyna M. , Bzowski Maciej , Kubiak Marzena A. , Bagenal F. , Richardson John D. 
Published: July 2022

AbstractWe report here observations of magnetic waves recorded by the Voyager spacecraft in the solar wind near Jupiter that are possibly the result of excitation by newborn pickup H+. Consideration of growth rates due to the known interstellar ion sources strongly disfavor an interstellar source. To determine the likely source of the waves, we compute the minimum ion production rate by equating wave growth to turbulent cascade rates and derive a lower limit for the production of H+ at the times of observations. The only available source of neutral H at these times and at the levels required is the Jovian system, most notably charge exchange between energetic protons and the neutral clouds around Io and Europa's orbits. Further refinement of the source identity is not possible at this time. We provide an estimate for the neutral H source subject to assumptions of the latitudinal extent of the population which is not constrained by observation.
Insights for the Partitioning of Ecosystem Evaporation and Transpiration in Short‐Statured Croplands
Authors: Paul‐Limoges Eugenie , Revill Andrew , Maier Regine , Buchmann Nina , Damm Alexander 
Published: July 2022

AbstractReducing water losses in agriculture needs a solid understanding of when evaporation (E) losses occur and how much water is used through crop transpiration (T). Partitioning ecosystem T is however challenging, and even more so when it comes to short‐statured crops, where many standard methods lead to inaccurate measurements. In this study, we combined biometeorological measurements with a Soil‐Plant‐Atmosphere Crop (SPA‐Crop) model to estimate T and E at a Swiss cropland over two crop seasons with winter cereals. We compared our results with two data‐driven approaches: The Transpiration Estimation Algorithm (TEA) and the underlying Water Use Efficiency (uWUE). Despite large differences in the productivity of both years, the T to evapotranspiration (ET) ratio had relatively similar seasonal and diurnal dynamics, and averaged to 0.72 and 0.73. Our measurements combined with a SPA‐Crop model provided T estimates similar to the TEA method, while the uWUE method produced systematically lower T even when the soil and leaves were dry. T was strongly related to the leaf area index, but additionally varied due to climatic conditions. The most important climatic drivers controlling T were found to be the photosynthetic photon flux density (R2 = 0.84 and 0.87), and vapor pressure deficit (R2 = 0.86 and 0.70). Our results suggest that site‐specific studies can help establish T/ET ratios, as well as identify dominant climatic drivers, which could then be used to partition T from reliable ET measurements. Moreover, our results suggest that the TEA method is a suitable tool for ET partitioning in short‐statured croplands.
Modeled Streamflow Response to Scenarios of Tundra Lake Water Withdrawal and Seasonal Climate Extremes, Arctic Coastal Plain, Alaska
Authors: Gädeke Anne , Arp Christopher D. , Liljedahl Anna K. , Daanen Ronald P. , Cai Lei , Alexeev Vladimir A. , Jones Benjamin M. , Wipfli Mark S. , Schulla Jörg 
Published: July 2022

AbstractOn the Arctic Coastal Plain (ACP) in northern Alaska (USA), permafrost and abundant surface‐water storage define watershed hydrological processes. In the last decades, the ACP landscape experienced extreme climate events and increased lake water withdrawal (LWW) for infrastructure construction, primarily ice roads and industrial operations. However, their potential (combined) effects on streamflow are relatively underexplored. Here, we applied the process‐based, spatially distributed hydrological and thermal Water Balance Simulation Model (10 m spatial resolution) to the 30 km2 Crea Creek watershed located on the ACP. The impacts of documented seasonal climate extremes and LWW were evaluated on seasonal runoff (May–August), including minimum 7‐day mean flow (MQ7), the recovery time of MQ7 to pre‐perturbation conditions, and the duration of streamflow conditions that prevents fish passage. Low‐rainfall scenarios (21% of normal, one to three summers in a row) caused a larger reduction in MQ7 (−56% to −69%) than LWW alone (−44% to −58%). Decadal‐long consecutive LWW under average climate conditions resulted in a new equilibrium in low flow and seasonal runoff after 3 years that included a disconnected stream network, a reduced watershed contributing area (54% of total watershed area), and limited fish passage of 20 days (vs. 6 days under control conditions) throughout summer. Our results highlight that, even under current average climatic conditions, LWW is not offset by same‐year snowmelt as currently assumed in land management regulations. Effective land management would therefore benefit from considering the combined impact of climate change and industrial LWWs.
The hidden link between circadian entropy and mental health disorders
Authors: Alachkar Amal , Lee Justine , Asthana Kalyani , Vakil Monfared Roudabeh , Chen Jiaqi , Alhassen Sammy , Samad Muntaha , Wood Marcelo , Mayer Emeran A. , Baldi Pierre 
Published: July 2022

AbstractThe high overlapping nature of various features across multiple mental health disorders suggests the existence of common psychopathology factor(s) (p-factors) that mediate similar phenotypic presentations across distinct but relatable disorders. In this perspective, we argue that circadian rhythm disruption (CRD) is a common underlying p-factor that bridges across mental health disorders within their age and sex contexts. We present and analyze evidence from the literature for the critical roles circadian rhythmicity plays in regulating mental, emotional, and behavioral functions throughout the lifespan. A review of the literature shows that coarse CRD, such as sleep disruption, is prevalent in all mental health disorders at the level of etiological and pathophysiological mechanisms and clinical phenotypical manifestations. Finally, we discuss the subtle interplay of CRD with sex in relation to these disorders across different stages of life. Our perspective highlights the need to shift investigations towards molecular levels, for instance, by using spatiotemporal circadian “omic” studies in animal models to identify the complex and causal relationships between CRD and mental health disorders.
PLOD3 contributes to HER-2 therapy resistance in gastric cancer through FoxO3/Survivin pathway
Authors: Chen Yueda , Ye Botian , Wang Chunyan , Nie Yanyan , Qin Jing , Shen Zhenbin 
Published: July 2022

AbstractHuman epidermal growth factor receptor 2 (HER-2), a famous therapeutic target for breast cancer, is also associated with an increased risk of recurrence and poor outcomes of other malignancies, including gastric cancer. Yet the mechanism of HER-2 therapy resistance remains controversial due to the heterogeneity of gastric adenocarcinoma. We know, Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 3 (PLOD3), a key gene coding enzymes that catalyze the lysyl hydroxylation of extracellular matrix collagen, plays an important contributor to HER-2 targeting agent Trastuzumab resistance in gastric cancer. Herein, we analyzed clinical samples of gastric cancer patients and gastric cancer cell lines and identified PLOD3, unveiled that depletion of PLOD3 leads to decreased cell proliferation, tumor growth and Trastuzumab sensitivity in these Trastuzumab resistant GC cell lines. Clinically, increased PLOD3 expression correlates with decreased Trastuzumab therapy responsiveness in GC patients. Mechanistically, we show that PLOD3 represses tumor suppressor FoxO3 expression, therefore upregulating Survivin protein expression that contributes to Trastuzumab resistance in GC. Therefore, our study identifies a new signaling axis PLOD3-FoxO3- Survivin pathway that may be therapeutically targeted in HER-2 positive gastric cancer.
Accelerated lysine metabolism conveys kidney protection in salt-sensitive hypertension
Authors: Rinschen Markus M. , Palygin Oleg , El-Meanawy Ashraf , Domingo-Almenara Xavier , Palermo Amelia , Dissanayake Lashodya V. , Golosova Daria , Schafroth Michael A. , Guijas Carlos , Demir Fatih , Jaegers Johannes , Gliozzi Megan L. , Xue Jingchuan , Hoehne Martin , Benzing Thomas , Kok Bernard P. , Saez Enrique , Bleich Markus , Himmerkus Nina , Weisz Ora A. , Cravatt Benjamin F. , Krüger Marcus , Benton H. Paul , Siuzdak Gary , Staruschenko Alexander 
Published: July 2022

AbstractHypertension and kidney disease have been repeatedly associated with genomic variants and alterations of lysine metabolism. Here, we combined stable isotope labeling with untargeted metabolomics to investigate lysine’s metabolic fate in vivo. Dietary 13C6 labeled lysine was tracked to lysine metabolites across various organs. Globally, lysine reacts rapidly with molecules of the central carbon metabolism, but incorporates slowly into proteins and acylcarnitines. Lysine metabolism is accelerated in a rat model of hypertension and kidney damage, chiefly through N-alpha-mediated degradation. Lysine administration diminished development of hypertension and kidney injury. Protective mechanisms include diuresis, further acceleration of lysine conjugate formation, and inhibition of tubular albumin uptake. Lysine also conjugates with malonyl-CoA to form a novel metabolite Nε-malonyl-lysine to deplete malonyl-CoA from fatty acid synthesis. Through conjugate formation and excretion as fructoselysine, saccharopine, and Nε-acetyllysine, lysine lead to depletion of central carbon metabolites from the organism and kidney. Consistently, lysine administration to patients at risk for hypertension and kidney disease inhibited tubular albumin uptake, increased lysine conjugate formation, and reduced tricarboxylic acid (TCA) cycle metabolites, compared to kidney-healthy volunteers. In conclusion, lysine isotope tracing mapped an accelerated metabolism in hypertension, and lysine administration could protect kidneys in hypertensive kidney disease.
Development of vanadium-based polyanion positive electrode active materials for high-voltage sodium-based batteries
Authors: Shraer Semyon D. , Luchinin Nikita D. , Trussov Ivan A. , Aksyonov Dmitry A. , Morozov Anatoly V. , Ryazantsev Sergey V. , Iarchuk Anna R. , Morozova Polina A. , Nikitina Victoria A. , Stevenson Keith J. , Antipov Evgeny V. , Abakumov Artem M. , Fedotov Stanislav S. 
Published: July 2022

AbstractPolyanion compounds offer a playground for designing prospective electrode active materials for sodium-ion storage due to their structural diversity and chemical variety. Here, by combining a NaVPO4F composition and KTiOPO4-type framework via a low-temperature (e.g., 190 °C) ion-exchange synthesis approach, we develop a high-capacity and high-voltage positive electrode active material. When tested in a coin cell configuration in combination with a Na metal negative electrode and a NaPF6-based non-aqueous electrolyte solution, this cathode active material enables a discharge capacity of 136 mAh g−1 at 14.3 mA g−1 with an average cell discharge voltage of about 4.0 V. Furthermore, a specific discharge capacity of 123 mAh g−1 at 5.7 A g−1 is also reported for the same cell configuration. Through ex situ and operando structural characterizations, we also demonstrate that the reversible Na-ion storage at the positive electrode occurs mostly via a solid-solution de/insertion mechanism.
The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution
Authors: Shi Tao , Huneau Cécile , Zhang Yue , Li Yan , Chen Jinming , Salse Jérôme , Wang Qingfeng 
Published: July 2022

AbstractMonocots are one of the most diverse groups of flowering plants, and tracing the evolution of their ancestral genome into modern species is essential for understanding their evolutionary success. Here, we report a high-quality assembly of the Acorus tatarinowii genome, a species that diverged early from all the other monocots. Genome-wide comparisons with a range of representative monocots characterized Acorus as a slowly evolved genome with one whole-genome duplication. Our inference of the ancestral monocot karyotypes provides new insights into the chromosomal evolutionary history assigned to modern species and reveals the probable molecular functions and processes related to the early adaptation of monocots to wetland or aquatic habitats (that is, low levels of inorganic phosphate, parallel leaf venation and ephemeral primary roots). The evolution of ancestral gene order in monocots is constrained by gene structural and functional features. The newly obtained Acorus genome offers crucial evidence for delineating the origin and diversification of monocots, including grasses.
In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus
Authors: Oyama Linda B. , Olleik Hamza , Teixeira Ana Carolina Nery , Guidini Matheus M. , Pickup James A. , Hui Brandon Yeo Pei , Vidal Nicolas , Cookson Alan R. , Vallin Hannah , Wilkinson Toby , Bazzolli Denise M. S. , Richards Jennifer , Wootton Mandy , Mikut Ralf , Hilpert Kai , Maresca Marc , Perrier Josette , Hess Matthias , Mantovani Hilario C. , Fernandez-Fuentes Narcis , Creevey Christopher J. , Huws Sharon A. 
Published: July 2022

AbstractHere we report two antimicrobial peptides (AMPs), HG2 and HG4 identified from a rumen microbiome metagenomic dataset, with activity against multidrug-resistant (MDR) bacteria, especially methicillin-resistant Staphylococcus aureus (MRSA) strains, a major hospital and community-acquired pathogen. We employed the classifier model design to analyse, visualise, and interpret AMP activities. This approach allowed in silico discrimination of promising lead AMP candidates for experimental evaluation. The lead AMPs, HG2 and HG4, are fast-acting and show anti-biofilm and anti-inflammatory activities in vitro and demonstrated little toxicity to human primary cell lines. The peptides were effective in vivo within a Galleria mellonella model of MRSA USA300 infection. In terms of mechanism of action, HG2 and HG4 appear to interact with the cytoplasmic membrane of target cells and may inhibit other cellular processes, whilst preferentially binding to bacterial lipids over human cell lipids. Therefore, these AMPs may offer additional therapeutic templates for MDR bacterial infections.
Mortality after second malignancy in breast cancer survivors compared to a first primary cancer: a nationwide longitudinal cohort study
Authors: Deng Zhengyi , Jones Miranda R. , Wang Mei-Cheng , Visvanathan Kala 
Published: July 2022

AbstractLimited information exists about survival outcomes after second primary cancers (SPCs) among breast cancer survivors. Studies suggest that mortality after certain SPCs may be higher than mortality after first primary cancers (FPCs) of the same type. A cohort study was conducted among 63,424 US women using the Surveillance, Epidemiology, and End Results 18 database (2000–2016) to compare mortality after a SPC among breast cancer survivors to mortality among women after a FPC using Cox proportional hazard regression. Propensity scores were used to match survivors with SPCs to women with FPCs 1:1 based on cancer type and prognostic factors. During a median follow-up of 42 months, 11,532 cancer deaths occurred after SPCs among survivors compared to 9305 deaths after FPCs. Cumulative cancer mortality was 44.7% for survivors with SPCs and 35.2% for women with FPCs. Survivors with SPCs had higher risk of cancer death (hazard ratio (HR): 1.27, 95% CI: 1.23–1.30) and death overall (HR: 1.18, 95% CI: 1.15–1.21) than women with FPCs. Increased risk of cancer death after SPCs compared to FPCs was observed for cancer in breast, lung, colon and/or rectum, uterus, lymphoma, melanoma, thyroid, and leukemia. Estrogen receptor status and treatment of the prior breast cancer as well as time between prior breast cancer and SPC significantly modified the mortality difference between women with SPC and FPC. A more tailored approach to early detection and treatment could improve outcomes from second cancer in breast cancer survivors.
Allelic overload and its clinical modifier effect in Bardet-Biedl syndrome
Authors: Perea-Romero Irene , Solarat Carlos , Blanco-Kelly Fiona , Sanchez-Navarro Iker , Bea-Mascato Brais , Martin-Salazar Eduardo , Lorda-Sanchez Isabel , Swafiri Saoud Tahsin , Avila-Fernandez Almudena , Martin-Merida Inmaculada , Trujillo-Tiebas Maria Jose , Carreño Ester , Jimenez-Rolando Belen , Garcia-Sandoval Blanca , Minguez Pablo , Corton Marta , Valverde Diana , Ayuso Carmen 
Published: July 2022

AbstractBardet–Biedl syndrome (BBS) is an autosomal recessive ciliopathy characterized by extensive inter- and intra-familial variability, in which oligogenic interactions have been also reported. Our main goal is to elucidate the role of mutational load in the clinical variability of BBS. A cohort of 99 patients from 77 different families with biallelic pathogenic variants in a BBS-associated gene was retrospectively recruited. Human Phenotype Ontology terms were used in the annotation of clinical symptoms. The mutational load in 39 BBS-related genes was studied in index cases using different molecular and next-generation sequencing (NGS) approaches. Candidate allele combinations were analysed using the in silico tools ORVAL and DiGePred. After clinical annotation, 76 out of the 99 cases a priori fulfilled established criteria for diagnosis of BBS or BBS-like. BBS1 alleles, found in 42% of families, were the most represented in our cohort. An increased mutational load was excluded in 41% of the index cases (22/54). Oligogenic inheritance was suspected in 52% of the screened families (23/45), being 40 tested by means of NGS data and 5 only by traditional methods. Together, ORVAL and DiGePred platforms predicted an oligogenic effect in 44% of the triallelic families (10/23). Intrafamilial variable severity could be clinically confirmed in six of the families. Our findings show that the presence of more than two alleles in BBS-associated genes correlated in six families with a more severe phenotype and associated with specific findings, highlighting the role of the mutational load in the management of BBS cases.
Antigenic comparison of the neuraminidases from recent influenza A vaccine viruses and 2019–2020 circulating strains
Authors: Gao Jin , Li Xing , Klenow Laura , Malik Tahir , Wan Hongquan , Ye Zhiping , Daniels Robert 
Published: July 2022

AbstractAlthough viral-based influenza vaccines contain neuraminidase (NA or N) antigens from the recommended seasonal strains, NA is not extensively evaluated like hemagglutinin (H) during the strain selection process. Here, we compared the antigenicity of NAs from recently recommended H1N1 (2010–2021 seasons) and H3N2 (2015–2021 seasons) vaccine strains and viruses that circulated between September 2019 and December 2020. The antigenicity was evaluated by measuring NA ferret antisera titers that provide 50% inhibition of NA activity in an enzyme-linked lectin assay. Our results show that NAs from circulating H1N1 viruses and vaccine strains for the 2017–2021 seasons are all antigenically similar and distinct from the NA in the H1N1 strain recommended for the 2010–2017 seasons. Changes in N1 antigenicity were attributed to the accumulation of substitutions over time, especially the loss of an N-linked glycosylation site (Asn386) in current N1s. The NAs from circulating H3N2 viruses and the 2020–2021 vaccine strains showed similar antigenicity that varied across the N2s in the 2016–2020 vaccine strains and was distinct from the N2 in the 2015–2016 vaccine strain. These data suggest that the recent N1 antigenicity has remained similar since the loss of the head domain N-linked glycosylation site, whereas N2 antigenicity has changed more incrementally each season.
Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b2
Authors: Newman Joseph , Thakur Nazia , Peacock Thomas P. , Bialy Dagmara , Elrefaey Ahmed M. E. , Bogaardt Carlijn , Horton Daniel L. , Ho Sammy , Kankeyan Thivya , Carr Christine , Hoschler Katja , Barclay Wendy S. , Amirthalingam Gayatri , Brown Kevin E. , Charleston Bryan , Bailey Dalan 
Published: July 2022

AbstractSARS-CoV-2 variants may threaten the effectiveness of vaccines and antivirals to mitigate serious COVID-19 disease. This is of most concern in clinically vulnerable groups such as older adults. We analysed 72 sera samples from 37 individuals, aged 70–89 years, vaccinated with two doses of BNT162b2 (Pfizer–BioNTech) 3 weeks apart, for neutralizing antibody responses to wildtype SARS-CoV-2. Between 3 and 20 weeks after the second vaccine dose, neutralizing antibody titres fell 4.9-fold to a median titre of 21.3 (neutralization dose 80%), with 21.6% of individuals having no detectable neutralizing antibodies at the later time point. Next, we examined neutralization of 21 distinct SARS-CoV-2 variant spike proteins with these sera, and confirmed substantial antigenic escape, especially for the Omicron (B.1.1.529, BA.1/BA.2), Beta (B.1.351), Delta (B.1.617.2), Theta (P.3), C.1.2 and B.1.638 spike variants. By combining pseudotype neutralization with specific receptor-binding domain (RBD) enzyme-linked immunosorbent assays, we showed that changes to position 484 in the spike RBD were mainly responsible for SARS-CoV-2 neutralizing antibody escape. Nineteen sera from the same individuals boosted with a third dose of BNT162b2 contained higher neutralizing antibody titres, providing cross-protection against Omicron BA.1 and BA.2. Despite SARS-CoV-2 immunity waning over time in older adults, booster vaccines can elicit broad neutralizing antibodies against a large number of SARS-CoV-2 variants in this clinically vulnerable cohort.
Chromosomal phase improves aneuploidy detection in non-invasive prenatal testing at low fetal DNA fractions
Authors: Genovese Giulio , Mello Curtis J. , Loh Po-Ru , Handsaker Robert E. , Kashin Seva , Whelan Christopher W. , Bayer-Zwirello Lucy A. , McCarroll Steven A. 
Published: July 2022

AbstractNon-invasive prenatal testing (NIPT) to detect fetal aneuploidy by sequencing the cell-free DNA (cfDNA) in maternal plasma is being broadly adopted. To detect fetal aneuploidies from maternal plasma, where fetal DNA is mixed with far-larger amounts of maternal DNA, NIPT requires a minimum fraction of the circulating cfDNA to be of placental origin, a level which is usually attained beginning at 10 weeks gestational age. We present an approach that leverages the arrangement of alleles along homologous chromosomes—also known as chromosomal phase—to make NIPT analyses more conclusive. We validate our approach with in silico simulations, then re-analyze data from a pregnant mother who, due to a fetal DNA fraction of 3.4%, received an inconclusive aneuploidy determination through NIPT. We find that the presence of a trisomy 18 fetus can be conclusively inferred from the patient’s same molecular data when chromosomal phase is incorporated into the analysis. Key to the effectiveness of our approach is the ability of homologous chromosomes to act as natural controls for each other and the ability of chromosomal phase to integrate subtle quantitative signals across very many sequence variants. These results show that chromosomal phase increases the sensitivity of a common laboratory test, an idea that could also advance cfDNA analyses for cancer detection.