bluuebunny/crossref_metadata_2025_split huggingface dataset:
Foliar element distributions in Guadua bamboo, a major forest dominant in southwestern Amazonia
Authors: Kalliola Risto , Linna Ari , Ruokolainen Kalle , Tyystjärvi Esa , Lange Carl 
Published: February 2022

AbstractSilica is the best-known component filling the spaces that form phytoliths in many plants, but phytoliths may also contain other elements. We used scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM–EDX) to map element distributions in the leaves of Guadua bamboo, which is a successful competitor in southwestern Amazonian forests. We emphasize immobile elements that can be mineralized (silicon and calcium) as well as potassium, an abundant mobile nutrient with many vital functions. We discovered high silicon (Si) content with little or no calcium (Ca) or potassium (K) in bulliform cells, bilobate shaped short cells and stomata, all of which can form phytoliths, and moderately high Si content in the bundle sheet, prickle tips and papillae. K often surrounded Si-loaded cells, Si and K had overlapping distributions in the intercostal areas near vein margins, and Ca showed abundant spotted distribution in the intercostal areas. The dark inside content of the costal zones of some samples in light microscopy showed no mineralization but prominently contained sulfur. Adjacent fusoid cells showed different Si, K and Ca combinations, which may suggest potentially variable functions of these cells. Widespread Si deposition strengthens Guadua bamboo leaves and may help it to outcompete tree species during periods of drought.
Effect of Irrigation Water and Organic Fertilizer on Reducing Nitrate Accumulation and Boosting Lettuce Productivity
Authors: Abd–Elrahman Shaimaa Hassan , Saudy Hani Saber , El–Fattah Dalia Ahmed Abd , Hashem Fadl Abd–Elhamid 
Published: February 2022

Abstract
Accumulation of high level of nitrate (NO3−) in leaves is a serious issue for vegetable crops like lettuce (Lactuca sativa L.). Therefore, this study aimed to limit NO3− level by adjusting the balance between fertilization and irrigation program in lettuce. In a strip plot design with three replicates, lettuce plants were grown under four fertilizer treatments and three irrigation regimes. Three organic fertilizers (biochar, compost and vermicompost), in addition to mineral fertilizer, were used. The irrigation regimes were 60, 80 and 100% of crop evapotranspiration, ETc (ETc60, ETc80, and ETc100). Nitrogen (N), phosphorus (P) potassium (K) and organic matter (OM) in soil as well as yield, N, P, K and NO3− of lettuce were estimated. Findings showed that vermicompost or biochar (with any irrigation regime) as well as compost with irrigation by ETc60 were the effective combinations for increasing K content in soil after harvest. Under irrigation by ETc80 or ETc100, vermicompost or biochar were the efficient treatments for increasing lettuce yield equaling the farmer common practice (ETc100 x mineral fertilizer). Under irrigation by ETc60, mineral fertilizer or vermicompost showed the highest lettuce leaf content of K. Moreover, ETc60 or ETc80 x mineral fertilizer recorded the maximum NO3− content of lettuce leaves. The accumulation of nitrate in lettuce leaves owing to mineral fertilizer reached about 1.24 times than that of organic fertilizers. Compost x ETc80 or ETc100 showed the minimal NO3–N accumulation, hence, high relative reductions in NO3–N accumulation as compared to the common practice (ETc100 x mineral fertilizer) were observed. In conclusion, irrigation by 80% instead of 100% of crop evapotranspiration of organically fertilized lettuce (especially with vermicompost) could be adopted since such practice recorded high lettuce productivity with low NO3− content.
Simultaneous Observations of EMIC‐Induced Drifting Electron Holes (EDEHs) in the Earth's Radiation Belt by the Arase Satellite, Van Allen Probes, and THEMIS
Authors: Nakamura S. , Miyoshi Y. , Shiokawa K. , Omura Y. , Mitani T. , Takashima T. , Higashio N. , Shinohara I. , Hori T. , Imajo S. , Matsuoka A. , Tsuchiya F. , Kumamoto A. , Kasahara Y. , Shoji M. , Spence H. , Angelopoulos V. 
Published: February 2022

AbstractWe present an observation of rapid flux depressions in relativistic electrons, which is referred to as “EMIC‐induced drifting electron holes (EDEHs).” The Arase, Van Allen Probes, and THEMIS detected simultaneously electron flux fluctuations. The time variation of flux shows depressions of 1‐min scale with energy dispersion, which appear only in the relativistic energy range and small pitch angles. These characteristics of the flux depression indicate that electromagnetic ion cyclotron waves caused pitch angle scattering on a short time scale in a longitudinally limited region. The Arase satellite detected the local depression of the phase space density of 1,000 MeV/G electron, indicating that EMIC waves cause the true loss of electrons. Tracing the energy dispersion profile of EDEHs, we show that EDEHs are formed at localized region in the dusk side. Multisatellite observations demonstrate that a series of EDEHs eventually cause a substantial depression of the radiation belt on 1‐hr time scale.
The Decadal Variation of Eastward‐Moving Tropical Cyclones in the South China Sea During 1980–2020
Authors: Luo Xi , Yang Lei , Chen Sheng , Liang Dong , Chan Johnny C. L. , Wang Dongxiao 
Published: February 2022

AbstractThe track of tropical cyclones (TCs) formed in the South China Sea (SCS) can be divided into eastward and westward directions. Significant decadal variation during 1980–2020 only exists in the number of eastward‐moving TCs, especially during July–September, with 47% TCs moving eastward during 1994–2004 (Period II), 22% during 1980–1993 (Period I) and only 15% during 2005–2020 (Period III). This decadal change is related to the zonal shift of Western Pacific Subtropical High (WPSH). An eastward‐retreated WPSH during 1994–2004 leads to upward motion and westerly flow anomaly over the northern SCS, and therefore favors TC genesis and eastward motion. The eastward‐retreated WPSH is associated with a warm sea surface temperature anomaly over the tropical western‐central Pacific which induces a cyclonic flow and weakens the WPSH. With the weaker modulation of WPSH, stronger intraseasonal oscillation (ISO) in the SCS during Period II favors eastward‐moving TCs due to the westerly flow associated with the ISO.
A Comprehensive Set of Juno In Situ and Remote Sensing Observations of the Ganymede Auroral Footprint
Authors: Hue V. , Szalay J. R. , Greathouse T. K. , Bonfond B. , Kotsiaros S. , Louis C. K. , Sulaiman A. H. , Clark G. , Allegrini F. , Gladstone G. R. , Paranicas C. , Versteeg M. H. , Mura A. , Moirano A. , Gershman D. J. , Bolton S. J. , Connerney J. E. P. , Davis M. W. , Ebert R. W. , Gérard J.‐C. , Giles R. S. , Grodent D. C. , Imai M. , Kammer J. A. , Kurth W. S. , Lamy L. , Mauk B. H. 
Published: February 2022

AbstractJupiter's satellite auroral footprints are a manifestation of the satellite‐magnetosphere interaction of the Galilean moons. Juno's polar elliptical orbit enables crossing the magnetic flux tubes connecting each Galilean moon with their associated auroral emission. Its payload allows measuring the fields and particle population in the flux tubes while remotely sensing their associated auroral emissions. During its thirtieth perijove, Juno crossed the flux tube directly connected to Ganymede's leading footprint spot, a unique event in the entire Juno prime mission. Juno revealed a highly‐structured precipitating electron flux, up to 316 mW/m2, while measuring both a small perturbation in the magnetic field azimuthal component and small Poynting flux with an estimated total downward current of 4.2 ± 1.2 kA. Based on the evolution of the footprint morphology and the field and particle measurements, Juno transited for the first time through a region connected to the transhemispheric electron beam of the Ganymede footprint.
Multi-omics reveals mitochondrial metabolism proteins susceptible for drug discovery in AML
Authors: Caplan Mika , Wittorf Karli J. , Weber Kasidy K. , Swenson Samantha A. , Gilbreath Tyler J. , Willow Hynes-Smith R. , Amador Catalina , Hyde R. Katherine , Buckley Shannon M. 
Published: February 2022

AbstractAcute myeloid leukemia (AML) is a devastating cancer affecting the hematopoietic system. Previous research has relied on RNA sequencing and microarray techniques to study the downstream effects of genomic alterations. While these studies have proven efficacious, they fail to capture the changes that occur at the proteomic level. To interrogate the effect of protein expression alterations in AML, we performed a quantitative mass spectrometry in parallel with RNAseq analysis using AML mouse models. These combined results identified 34 proteins whose expression was upregulated in AML tumors, but strikingly, were unaltered at the transcriptional level. Here we focus on mitochondrial electron transfer proteins ETFA and ETFB. Silencing of ETFA and ETFB led to increased mitochondrial activity, mitochondrial stress, and apoptosis in AML cells, but had little to no effect on normal human CD34+ cells. These studies identify a set of proteins that have not previously been associated with leukemia and may ultimately serve as potential targets for therapeutic manipulation to hinder AML progression and help contribute to our understanding of the disease.
Epigenome-wide association study of posttraumatic stress disorder identifies novel loci in U.S. military veterans
Authors: Montalvo-Ortiz Janitza L. , Gelernter Joel , Cheng Zhongshan , Girgenti Matthew J. , Xu Ke , Zhang Xinyu , Gopalan Shyamalika , Zhou Hang , Duman Ronald S. , Southwick Steven M. , Krystal John H. ,   Traumatic Stress Brain Research Study Group, Friedman Matthew J. , Duman Ronald S. , Girgenti Matthew J. , Krystal John H. , Montalvo-Ortiz Janitza L. , Pietrzak Robert H. 
Published: February 2022

AbstractPosttraumatic stress disorder (PTSD) is a chronic and disabling psychiatric disorder prevalent in military veterans. Epigenetic mechanisms have been implicated in the etiology of PTSD, with DNA methylation being the most studied to identify novel molecular biomarkers associated with this disorder. We performed one of the largest single-sample epigenome-wide association studies (EWAS) of PTSD to date. Our sample included 1135 male European–American U.S. veterans who participated in the National Health and Resilience in Veterans Study (NHRVS). DNA was collected from saliva samples and the Illumina HumanMethylation EPIC BeadChip was used for the methylation analysis. PTSD was assessed using the PTSD Checklist. An EWAS was conducted using linear regression adjusted for age, cell-type proportions, first 10 principal components, and smoking status. After Bonferroni correction, we identified six genome-wide significant (GWS) CpG sites associated with past-month PTSD and three CpGs with lifetime PTSD (prange = 10−10–10−8). These CpG sites map to genes involved in immune function, transcription regulation, axonal guidance, cell signaling, and protein binding. Among these, SENP7, which is involved in transcription regulation and has been linked to risk-taking behavior and alcohol consumption in genome-wide association studies, replicated in an independent veteran cohort and was downregulated in medial orbitofrontal cortex of PTSD postmortem brain tissue. These findings suggest potential epigenetic biomarkers of PTSD that may help inform the pathophysiology of this disorder in veterans and other trauma-affected populations.
Metabolic effects of the schizophrenia-associated 3q29 deletion
Authors: Pollak Rebecca M. , Purcell Ryan H. , Rutkowski Timothy P. , Malone Tamika , Pachura Kimberly J. , Bassell Gary J. , Epstein Michael P. , Dawson Paul A. , Smith Matthew R. , Jones Dean P. , Zwick Michael E. , Warren Stephen T. , Caspary Tamara , Weinshenker David , Mulle Jennifer G. 
Published: February 2022

AbstractThe 1.6 Mb 3q29 deletion is associated with developmental and psychiatric phenotypes, including a 40-fold increased risk for schizophrenia. Reduced birth weight and a high prevalence of feeding disorders in patients suggest underlying metabolic dysregulation. We investigated 3q29 deletion-induced metabolic changes using our previously generated heterozygous B6.Del16+/Bdh1-Tfrc mouse model. Animals were provided either standard chow (STD) or high-fat diet (HFD). Growth curves were performed on HFD mice to assess weight change (n = 30–50/group). Indirect calorimetry and untargeted metabolomics were performed on STD and HFD mice to evaluate metabolic phenotypes (n = 8–14/group). A behavioral battery was performed on STD and HFD mice to assess behavior change after the HFD challenge (n = 5–13/group). We found that B6.Del16+/Bdh1-Tfrc animals preferentially use dietary lipids as an energy source. Untargeted metabolomics of liver tissue showed a strong sex-dependent effect of the 3q29 deletion on fat metabolism. A HFD partially rescued the 3q29 deletion-associated weight deficit in females, but not males. Untargeted metabolomics of liver tissue after HFD revealed persistent fat metabolism alterations in females. The HFD did not affect B6.Del16+/Bdh1-Tfrc behavioral phenotypes, suggesting that 3q29 deletion-associated metabolic and behavioral outcomes are uncoupled. Our data suggest that dietary interventions to improve weight phenotypes in 3q29 deletion syndrome patients are unlikely to exacerbate behavioral manifestations. Our study also highlights the importance of assessing sex in metabolic studies and suggests that mechanisms underlying 3q29 deletion-associated metabolic phenotypes are sex-specific.
CytofIn enables integrated analysis of public mass cytometry datasets using generalized anchors
Authors: Lo Yu-Chen , Keyes Timothy J. , Jager Astraea , Sarno Jolanda , Domizi Pablo , Majeti Ravindra , Sakamoto Kathleen M. , Lacayo Norman , Mullighan Charles G. , Waters Jeffrey , Sahaf Bita , Bendall Sean C. , Davis Kara L. 
Published: February 2022

AbstractThe increasing use of mass cytometry for analyzing clinical samples offers the possibility to perform comparative analyses across public datasets. However, challenges in batch normalization and data integration limit the comparison of datasets not intended to be analyzed together. Here, we present a data integration strategy, CytofIn, using generalized anchors to integrate mass cytometry datasets from the public domain. We show that low-variance controls, such as healthy samples and stable channels, are inherently homogeneous, robust against stimulation, and can serve as generalized anchors for batch correction. Single-cell quantification comparing mass cytometry data from 989 leukemia files pre- and post normalization with CytofIn demonstrates effective batch correction while recapitulating the gold-standard bead normalization. CytofIn integration of public cancer datasets enabled the comparison of immune features across histologies and treatments. We demonstrate the ability to integrate public datasets without necessitating identical control samples or bead standards for fast and robust analysis using CytofIn.
Charge-noise spectroscopy of Si/SiGe quantum dots via dynamically-decoupled exchange oscillations
Authors: Connors Elliot J. , Nelson J. , Edge Lisa F. , Nichol John M. 
Published: February 2022

AbstractElectron spins in silicon quantum dots are promising qubits due to their long coherence times, scalable fabrication, and potential for all-electrical control. However, charge noise in the host semiconductor presents a major obstacle to achieving high-fidelity single- and two-qubit gates in these devices. In this work, we measure the charge-noise spectrum of a Si/SiGe singlet-triplet qubit over nearly 12 decades in frequency using a combination of methods, including dynamically-decoupled exchange oscillations with up to 512 π pulses during the qubit evolution. The charge noise is colored across the entire frequency range of our measurements, although the spectral exponent changes with frequency. Moreover, the charge-noise spectrum inferred from conductance measurements of a proximal sensor quantum dot agrees with that inferred from coherent oscillations of the singlet-triplet qubit, suggesting that simple transport measurements can accurately characterize the charge noise over a wide frequency range in Si/SiGe quantum dots.
Atomically unveiling the structure-activity relationship of biomacromolecule-metal-organic frameworks symbiotic crystal
Authors: Tong Linjing , Huang Siming , Shen Yujian , Liu Suya , Ma Xiaomin , Zhu Fang , Chen Guosheng , Ouyang Gangfeng 
Published: February 2022

AbstractCrystallization of biomacromolecules-metal-organic frameworks (BMOFs) allows for orderly assemble of symbiotic hybrids with desirable biological and chemical functions in one voxel. The structure-activity relationship of this symbiotic crystal, however, is still blurred. Here, we directly identify the atomic-level structure of BMOFs, using the integrated differential phase contrast-scanning transmission electron microscopy, cryo-electron microscopy and x-ray absorption fine structure techniques. We discover an obvious difference in the nanoarchitecture of BMOFs under different crystallization pathways that was previously not seen. In addition, we find the nanoarchitecture significantly affects the bioactivity of the BMOFs. This work gives an important insight into the structure-activity relationship of BMOFs synthesized in different scenarios, and may act as a guide to engineer next-generation materials with excellent biological and chemical functions.
Protease-controlled secretion and display of intercellular signals
Authors: Vlahos Alexander E. , Kang Jeewoo , Aldrete Carlos A. , Zhu Ronghui , Chong Lucy S. , Elowitz Michael B. , Gao Xiaojing J. 
Published: February 2022

AbstractTo program intercellular communication for biomedicine, it is crucial to regulate the secretion and surface display of signaling proteins. If such regulations are at the protein level, there are additional advantages, including compact delivery and direct interactions with endogenous signaling pathways. Here we create a modular, generalizable design calledRetainedEndoplasmic CleavableSecretion (RELEASE), with engineered proteins retained in the endoplasmic reticulum and displayed/secreted in response to specific proteases. The design allows functional regulation of multiple synthetic and natural proteins by synthetic protease circuits to realize diverse signal processing capabilities, including logic operation and threshold tuning. By linking RELEASE to additional sensing and processing circuits, we can achieve elevated protein secretion in response to “undruggable” oncogene KRAS mutants. RELEASE should enable the local, programmable delivery of intercellular cues for a broad variety of fields such as neurobiology, cancer immunotherapy and cell transplantation.
Rough and smooth variants of Mycobacterium abscessus are differentially controlled by host immunity during chronic infection of adult zebrafish
Authors: Kam Julia Y. , Hortle Elinor , Krogman Elizabeth , Warner Sherridan E. , Wright Kathryn , Luo Kaiming , Cheng Tina , Manuneedhi Cholan Pradeep , Kikuchi Kazu , Triccas James A. , Britton Warwick J. , Johansen Matt D. , Kremer Laurent , Oehlers Stefan H. 
Published: February 2022

AbstractPrevalence of Mycobacterium abscessus infections is increasing in patients with respiratory comorbidities. After initial colonisation, M. abscessus smooth colony (S) variants can undergo an irreversible genetic switch into highly inflammatory, rough colony (R) variants, often associated with a decline in pulmonary function. Here, we use an adult zebrafish model of chronic infection with R and S variants to study M. abscessus pathogenesis in the context of fully functioning host immunity. We show that infection with an R variant causes an inflammatory immune response that drives necrotic granuloma formation through host TNF signalling, mediated by the tnfa, tnfr1 and tnfr2 gene products. T cell-dependent immunity is stronger against the R variant early in infection, and regulatory T cells associate with R variant granulomas and limit bacterial growth. In comparison, an S variant proliferates to high burdens but appears to be controlled by TNF-dependent innate immunity early during infection, resulting in delayed granuloma formation. Thus, our work demonstrates the applicability of adult zebrafish to model persistent M. abscessus infection, and illustrates differences in the immunopathogenesis induced by R and S variants during granulomatous infection.
Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics
Authors: Schweitzer Hannah D. , Smith Heidi J. , Barnhart Elliott P. , McKay Luke J. , Gerlach Robin , Cunningham Alfred B. , Malmstrom Rex R. , Goudeau Danielle , Fields Matthew W. 
Published: February 2022

AbstractEnvironmentally relevant metagenomes and BONCAT-FACS derived translationally active metagenomes from Powder River Basin coal seams were investigated to elucidate potential genes and functional groups involved in hydrocarbon degradation to methane in coal seams with high- and low-sulfate levels. An advanced subsurface environmental sampler allowed the establishment of coal-associated microbial communities under in situ conditions for metagenomic analyses from environmental and translationally active populations. Metagenomic sequencing demonstrated that biosurfactants, aerobic dioxygenases, and anaerobic phenol degradation pathways were present in active populations across the sampled coal seams. In particular, results suggested the importance of anaerobic degradation pathways under high-sulfate conditions with an emphasis on fumarate addition. Under low-sulfate conditions, a mixture of both aerobic and anaerobic pathways was observed but with a predominance of aerobic dioxygenases. The putative low-molecular-weight biosurfactant, lichysein, appeared to play a more important role compared to rhamnolipids. The methods used in this study—subsurface environmental samplers in combination with metagenomic sequencing of both total and translationally active metagenomes—offer a deeper and environmentally relevant perspective on community genetic potential from coal seams poised at different redox conditions broadening the understanding of degradation strategies for subsurface carbon.