bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climatic Controls on Soil Carbon Accumulation and Loss in a Dryland Ecosystems
Authors: Waring Bonnie G. , Smith Kenneth R. , Grote Edmund E. , Howell Armin , Reibold Robin , Tucker Colin L. , Reed Sasha C. 
Published: November 2021

AbstractArid and semiarid ecosystems drive year‐to‐year variability in the strength of the terrestrial carbon (C) sink, yet there is uncertainty about how soil C gains and losses contribute to this variation. To address this knowledge gap, we embedded C‐depleted soil mesocosms, containing litter or biocrust C inputs, within an in situ dryland ecosystem warming experiment. Over the course of one year, changes in microbial biomass and total soil organic C pools were monitored alongside hourly measurements of soil CO2 flux. We also developed a biogeochemical model to explore the mechanisms that gave rise to observed soil C dynamics. Field data and model simulations demonstrated that water exerted much stronger control on soil biogeochemistry than temperature, with precipitation events triggering large CO2 pulses and transport of litter‐ and biocrust‐derived C into the soil profile. We expected leaching of organic matter would result in steady accumulation of C within the mineral soil over time. Instead, the size of the total organic C pool fluctuated throughout the year, largely in response to microbial growth: increases in the size of microbial biomass were negatively correlated with the quantity of C residing in the top 2 cm, where most biogeochemical changes were observed. Our data and models suggest that microbial responses to precipitation events trigger rapid metabolism of dissolved organic C inputs, which strongly limit accumulation of autotroph‐derived C belowground. Accordingly, changes in the magnitude and/or frequency of precipitation events in this dryland ecosystem could have profound impacts on the strength of the soil C sink.
Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate
Authors: Kim Hyungseok , Kimbrel Jeffrey A , Vaiana Christopher A , Wollard Jessica R , Mayali Xavier , Buie Cullen R 
Published: November 2021

Abstract
Photosynthetic microalgae are responsible for 50% of the global atmospheric CO2 fixation into organic matter and hold potential as a renewable bioenergy source. Their metabolic interactions with the surrounding microbial community (the algal microbiome) play critical roles in carbon cycling, but due to methodological limitations, it has been challenging to examine how community development is influenced by spatial proximity to their algal host. Here we introduce a copolymer-based porous microplate to co-culture algae and bacteria, where metabolites are constantly exchanged between the microorganisms while maintaining physical separation. In the microplate, we found that the diatom Phaeodactylum tricornutum accumulated to cell abundances ~20 fold higher than under normal batch conditions due to constant replenishment of nutrients through the porous structure. We also demonstrate that algal-associated bacteria, both single isolates and complex communities, responded to inorganic nutrients away from their host as well as organic nutrients originating from the algae in a spatially predictable manner. These experimental findings coupled with a mathematical model suggest that host proximity and algal culture growth phase impact bacterial community development in a taxon-specific manner through organic and inorganic nutrient availability. Our novel system presents a useful tool to investigate universal metabolic interactions between microbes in aquatic ecosystems.
Fast non-line-of-sight imaging with high-resolution and wide field of view using synthetic wavelength holography
Authors: Willomitzer Florian , Rangarajan Prasanna V. , Li Fengqiang , Balaji Muralidhar M. , Christensen Marc P. , Cossairt Oliver 
Published: November 2021

AbstractThe presence of a scattering medium in the imaging path between an object and an observer is known to severely limit the visual acuity of the imaging system. We present an approach to circumvent the deleterious effects of scattering, by exploiting spectral correlations in scattered wavefronts. Our Synthetic Wavelength Holography (SWH) method is able to recover a holographic representation of hidden targets with sub-mm resolution over a nearly hemispheric angular field of view. The complete object field is recorded within 46 ms, by monitoring the scattered light return in a probe area smaller than 6 cm × 6 cm. This unique combination of attributes opens up a plethora of new Non-Line-of-Sight imaging applications ranging from medical imaging and forensics, to early-warning navigation systems and reconnaissance. Adapting the findings of this work to other wave phenomena will help unlock a wider gamut of applications beyond those envisioned in this paper.
Seasonal mixed layer depth shapes phytoplankton physiology, viral production, and accumulation in the North Atlantic
Authors: Diaz Ben P. , Knowles Ben , Johns Christopher T. , Laber Christien P. , Bondoc Karen Grace V. , Haramaty Liti , Natale Frank , Harvey Elizabeth L. , Kramer Sasha J. , Bolaños Luis M. , Lowenstein Daniel P. , Fredricks Helen F. , Graff Jason , Westberry Toby K. , Mojica Kristina D. A. , Haëntjens Nils , Baetge Nicholas , Gaube Peter , Boss Emmanuel , Carlson Craig A. , Behrenfeld Michael J. , Van Mooy Benjamin A. S. , Bidle Kay D. 
Published: November 2021

AbstractSeasonal shifts in phytoplankton accumulation and loss largely follow changes in mixed layer depth, but the impact of mixed layer depth on cell physiology remains unexplored. Here, we investigate the physiological state of phytoplankton populations associated with distinct bloom phases and mixing regimes in the North Atlantic. Stratification and deep mixing alter community physiology and viral production, effectively shaping accumulation rates. Communities in relatively deep, early-spring mixed layers are characterized by low levels of stress and high accumulation rates, while those in the recently shallowed mixed layers in late-spring have high levels of oxidative stress. Prolonged stratification into early autumn manifests in negative accumulation rates, along with pronounced signatures of compromised membranes, death-related protease activity, virus production, nutrient drawdown, and lipid markers indicative of nutrient stress. Positive accumulation renews during mixed layer deepening with transition into winter, concomitant with enhanced nutrient supply and lessened viral pressure.
Survival of polycyclic aromatic hydrocarbon knockout fragments in the interstellar medium
Authors: Gatchell Michael , Ameixa João , Ji MingChao , Stockett Mark H. , Simonsson Ansgar , Denifl Stephan , Cederquist Henrik , Schmidt Henning T. , Zettergren Henning 
Published: November 2021

AbstractLaboratory studies play a crucial role in understanding the chemical nature of the interstellar medium (ISM), but the disconnect between experimental timescales and the timescales of reactions in space can make a direct comparison between observations, laboratory, and model results difficult. Here we study the survival of reactive fragments of the polycyclic aromatic hydrocarbon (PAH) coronene, where individual C atoms have been knocked out of the molecules in hard collisions with He atoms at stellar wind and supernova shockwave velocities. Ionic fragments are stored in the DESIREE cryogenic ion-beam storage ring where we investigate their decay for up to one second. After 10 ms the initially hot stored ions have cooled enough so that spontaneous dissociation no longer takes place at a measurable rate; a majority of the fragments remain intact and will continue to do so indefinitely in isolation. Our findings show that defective PAHs formed in energetic collisions with heavy particles may survive at thermal equilibrium in the interstellar medium indefinitely, and could play an important role in the chemistry in there, due to their increased reactivity compared to intact or photo-fragmented PAHs.
Efficient biosynthesis of nucleoside cytokinin angustmycin A containing an unusual sugar system
Authors: Yu Le , Zhou Wenting , She Yixuan , Ma Hongmin , Cai You-Sheng , Jiang Ming , Deng Zixin , Price Neil P. J. , Chen Wenqing 
Published: November 2021

AbstractAngustmycin A has anti-mycobacterial and cytokinin activities, and contains an intriguing structure in which an unusual sugar with C5′-C6′ dehydration is linked to adenine via an N-glycosidic bond. However, the logic underlying the biosynthesis of this molecule has long remained obscure. Here, we address angustmycin A biosynthesis by the full deciphering of its pathway. We demonstrate that AgmD, C, A, E, and B function as d-allulose 6-phosphate 3-epimerase, d-allulose 6-phosphate pyrophosphokinase, adenine phosphoallulosyltransferase, phosphoribohydrolase, and phosphatase, respectively, and that these collaboratively catalyze the relay reactions to biosynthesize angustmycin C. Additionally, we provide evidence that AgmF is a noncanonical dehydratase for the final step to angustmycin A via a self-sufficient strategy for cofactor recycling. Finally, we have reconstituted the entire six-enzyme pathway in vitro and in E. coli leading to angustmycin A production. These results expand the enzymatic repertoire regarding natural product biosynthesis, and also open the way for rational and rapid discovery of other angustmycin related antibiotics.
DHX15-independent roles for TFIP11 in U6 snRNA modification, U4/U6.U5 tri-snRNP assembly and pre-mRNA splicing fidelity
Authors: Duchemin Amandine , O’Grady Tina , Hanache Sarah , Mereau Agnès , Thiry Marc , Wacheul Ludivine , Michaux Catherine , Perpète Eric , Hervouet Eric , Peixoto Paul , Ernst Felix G. M. , Audic Yann , Dequiedt Franck , Lafontaine Denis L. J. , Mottet Denis 
Published: November 2021

AbstractThe U6 snRNA, the core catalytic component of the spliceosome, is extensively modified post-transcriptionally, with 2’-O-methylation being most common. However, how U6 2’-O-methylation is regulated remains largely unknown. Here we report that TFIP11, the human homolog of the yeast spliceosome disassembly factor Ntr1, localizes to nucleoli and Cajal Bodies and is essential for the 2’-O-methylation of U6. Mechanistically, we demonstrate that TFIP11 knockdown reduces the association of U6 snRNA with fibrillarin and associated snoRNAs, therefore altering U6 2′-O-methylation. We show U6 snRNA hypomethylation is associated with changes in assembly of the U4/U6.U5 tri-snRNP leading to defects in spliceosome assembly and alterations in splicing fidelity. Strikingly, this function of TFIP11 is independent of the RNA helicase DHX15, its known partner in yeast. In sum, our study demonstrates an unrecognized function for TFIP11 in U6 snRNP modification and U4/U6.U5 tri-snRNP assembly, identifying TFIP11 as a critical spliceosome assembly regulator.
Deep learning for the prediction of early on-treatment response in metastatic colorectal cancer from serial medical imaging
Authors: Lu Lin , Dercle Laurent , Zhao Binsheng , Schwartz Lawrence H. 
Published: November 2021

AbstractIn current clinical practice, tumor response assessment is usually based on tumor size change on serial computerized tomography (CT) scan images. However, evaluation of tumor response to anti-vascular endothelial growth factor therapies in metastatic colorectal cancer (mCRC) is limited because morphological change in tumor may occur earlier than tumor size change. Here we present an analysis utilizing a deep learning (DL) network to characterize tumor morphological change for response assessment in mCRC patients. We retrospectively analyzed 1,028 mCRC patients who were prospectively included in the VELOUR trial (NCT00561470). We found that DL network was able to predict early on-treatment response in mCRC and showed better performance than its size-based counterpart with C-Index: 0.649 (95% CI: 0.619,0.679) vs. 0.627 (95% CI: 0.567,0.638), p = 0.009, z-test. The integration of DL network with size-based methodology could further improve the prediction performance to C-Index: 0.694 (95% CI: 0.661,0.720), which was superior to size/DL-based-only models (all p < 0.001, z-test). Our study suggests that DL network could provide a noninvasive mean for quantitative and comprehensive characterization of tumor morphological change, which may potentially benefit personalized early on-treatment decision making.
Fast spin-valley-based quantum gates in Si with micromagnets
Authors: Huang Peihao , Hu Xuedong 
Published: November 2021

AbstractAn electron spin qubit in silicon quantum dots holds promise for quantum information processing due to the scalability and long coherence. An essential ingredient to recent progress is the employment of micromagnets. They generate a synthetic spin–orbit coupling (SOC), which allows high-fidelity spin manipulation and strong interaction between an electron spin and cavity photons. To scaled-up quantum computing, multiple technical challenges remain to be overcome, including controlling the valley degree of freedom, which is usually considered detrimental to a spin qubit. Here, we show that it is possible to significantly enhance the electrical manipulation of a spin qubit through the effect of constructive interference and the large spin-valley mixing. To characterize the quality of spin control, we also studied spin dephasing due to charge noise through spin-valley mixing. The competition between the increased control strength and spin dephasing produces two sweet-spots, where the quality factor of the spin qubit can be high. Finally, we reveal that the synthetic SOC leads to distinctive spin relaxation in silicon, which explains recent experiments.
Adult spiny mice (Acomys) exhibit endogenous cardiac recovery in response to myocardial infarction
Authors: Peng Hsuan , Shindo Kazuhiro , Donahue Renée R. , Gao Erhe , Ahern Brooke M. , Levitan Bryana M. , Tripathi Himi , Powell David , Noor Ahmed , Elmore Garrett A. , Satin Jonathan , Seifert Ashley W. , Abdel-Latif Ahmed 
Published: November 2021

AbstractComplex tissue regeneration is extremely rare among adult mammals. An exception, however, is the superior tissue healing of multiple organs in spiny mice (Acomys). While Acomys species exhibit the remarkable ability to heal complex tissue with minimal scarring, little is known about their cardiac structure and response to cardiac injury. In this study, we first examined baseline Acomys cardiac anatomy and function in comparison with commonly used inbred and outbred laboratory Mus strains (C57BL6 and CFW). While our results demonstrated comparable cardiac anatomy and function between Acomys and Mus, Acomys exhibited a higher percentage of cardiomyocytes displaying distinct characteristics. In response to myocardial infarction, all animals experienced a comparable level of initial cardiac damage. However, Acomys demonstrated superior ischemic tolerance and cytoprotection in response to injury as evidenced by cardiac functional stabilization, higher survival rate, and smaller scar size 50 days after injury compared to the inbred and outbred mouse strains. This phenomenon correlated with enhanced endothelial cell proliferation, increased angiogenesis, and medium vessel maturation in the peri-infarct and infarct regions. Overall, these findings demonstrate augmented myocardial preservation in spiny mice post-MI and establish Acomys as a new adult mammalian model for cardiac research.
Validity of predictive equations for 24-h urinary sodium excretion at the population and individual levels among Chinese adults aged 18–69 years
Authors: Du Xiaofu , Fang Le , Guo Jing , Chen Xiangyu , Su Shuoci , Zhang Jie 
Published: November 2021

AbstractSpot urine (SU) collection is a convenient method commonly used for sodium estimation, but its validity in predicting 24-h urinary sodium (24-hUNa) excretion has not been thoroughly evaluated among the general population. The aim of this study was to comprehensively assess the validity of eight existing methods in predicting 24-hUNa excretion by using SU samples among Chinese adults. We analyzed 1424 representative individuals aged 18 to 69 years. We compared the measured and estimated measurements of 24-hUNa at the population level by examining bias, the correlation, intraclass correlation coefficients (ICCs), receiver operating characteristic (ROC) curves and Bland–Altman plots and analyzed the relative and absolute differences and misclassification at the individual level. The bias for all methods was significant (allp < 0.001), among which the smallest bias was − 7.9 mmol for the Toft formula and the largest bias was − 53.8 mmol for the Mage formula. Correlation coefficients were all less than 0.380, all formulas exhibited an area under the ROC curve below 0.683, and the Bland–Altman plots indicated slightly high dispersion of the estimation biases at higher sodium levels regardless of the formula. The proportions of relative differences > 40% for the eight methods were all over one-third, the proportions of absolute differences > 51.3 mmol/24 h (3 g/day NaCl) were all over 40%, and the misclassification rates (7, 10, and 13 g/day NaCl as cutoff points) were all over 65%. Caution remains due to poor validity between estimated and actual measurements when using the eight formulas to obtain a plausible estimation for surveillance of the Chinese population sodium excretion, and the results do not support the application of SU to estimate sodium intake at the individual level due to its poor performance with respect to classification.
Light-stimulus intensity modulates startle reflex habituation in larval zebrafish
Authors: Beppi Carolina , Beringer Giorgio , Straumann Dominik , Bögli Stefan Yu 
Published: November 2021

AbstractThe startle reflex in larval zebrafish describes a C-bend of the body occurring in response to sudden, unexpected, stimuli of different sensory modalities. Alterations in the startle reflex habituation (SRH) have been reported in various human and animal models of neurological and psychiatric conditions and are hence considered an important behavioural marker of neurophysiological function. The amplitude, offset and decay constant of the auditory SRH in larval zebrafish have recently been characterised, revealing that the measures are affected by variation in vibratory frequency, intensity, and interstimulus-interval. Currently, no study provides a model-based analysis of the effect of physical properties of light stimuli on the visual SRH. This study assessed the effect of incremental light-stimulus intensity on the SRH of larval zebrafish through a repeated-measures design. Their total locomotor responses were normalised for the time factor, based on the behaviour of a (non-stimulated) control group. A linear regression indicated that light intensity positively predicts locomotor responses due to larger SRH decay constants and offsets. The conclusions of this study provide important insights as to the effect of light properties on the SRH in larval zebrafish. Our methodology and findings constitute a relevant reference framework for further investigation in translational neurophysiological research.
Epidemiologic potentials and correlational analysis of Vibrio species and virulence toxins from water sources in greater Bushenyi districts, Uganda
Authors: Onohuean Hope , Okoh Anthony I. , Nwodo Uchechukwu U. 
Published: November 2021

AbstractAdequate water supply is one of the public health issues among the population living in low-income settings. Vibriosis remain a significant health challenge drawing the attention of both healthcare planners and researchers in South West districts of Uganda. Intending to clamp down the disease cases in the safest water deprive locality, we investigated the virulent toxins as contaminants and epidemiologic potentials of Vibrio species recovered from surface waters in greater Bushenyi districts, Uganda. Surface water sources within 46 villages located in the study districts were obtained between June and October 2018. Standard microbiological and molecular methods were used to analyse samples. Our results showed that 981 presumptive isolates retrieved cell counts of 10–100 CFU/g, with, with (640) 65% confirmed as Vibrio genus using polymerase chain reaction, which is distributed as follows; V. vulnificus 46/640 (7.2%), V. fluvialis 30/594 (5.1), V. parahaemolyticus 21/564 (3.7), V. cholera 5/543 (0.9), V. alginolyticus 62/538 (11.5) and V. mimicus 20/476 (4.2). The virulence toxins observed were heat-stable enterotoxin (stn) 46 (82.10%), V. vulnificus virulence gene (vcgCPI) 40 (87.00%), extracellular haemolysin gene {vfh 21 (70.00)} and Heme utilization protein gene {hupO 5 (16.70)}. The cluster analysis depicts hupO (4.46% n = 112); vfh (18.75%, n = 112); vcgCPI and stn (35.71%, & 41.07%, n = 112). The principal component analysis revealed the toxins (hupO, vfh) were correlated with the isolate recovered from Bohole water (BW) source, while (vcgCPI, stn) toxins are correlated with natural raw water (NRW) and open springs (OS) water sources isolates. Such observation indicates that surface waters sources are highly contaminated with an odds ratio of 1.00, 95% CI (70.48–90.5), attributed risk of (aR = 64.29) and relative risk of (RR = 73.91). In addition, it also implies that the surface waters sources have > 1 risk of contamination with vfh and > six times of contamination with hupO (aR = 40, − 66). This is a call of utmost importance to the population, which depends on these water sources to undertake appropriate sanitation, personal hygienic practices and potential measures that ensure water quality.
A data-driven approach to increasing the lifetime of IoT sensor nodes
Authors: Suryavansh Shikhar , Benna Abu , Guest Chris , Chaterji Somali 
Published: November 2021

AbstractData transmission accounts for significant energy consumption in wireless sensor networks where streaming data is generated by the sensors. This impedes their use in many settings, including livestock monitoring over large pastures (which forms our target application). We present Ambrosia, a lightweight protocol that utilizes a window-based timeseries forecasting mechanism for data reduction. Ambrosia employs a configurable error threshold to ensure that the accuracy of end applications is unaffected by the data transfer reduction. Experimental evaluations using LoRa and BLE on a real livestock monitoring deployment demonstrate 60% reduction in data transmission and a 2 $$\times$$×increase in battery lifetime.