bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonlinear machine learning pattern recognition and bacteria-metabolite multilayer network analysis of perturbed gastric microbiome
Authors: Durán Claudio , Ciucci Sara , Palladini Alessandra , Ijaz Umer Z. , Zippo Antonio G. , Sterbini Francesco Paroni , Masucci Luca , Cammarota Giovanni , Ianiro Gianluca , Spuul Pirjo , Schroeder Michael , Grill Stephan W. , Parsons Bryony N. , Pritchard D. Mark , Posteraro Brunella , Sanguinetti Maurizio , Gasbarrini Giovanni , Gasbarrini Antonio , Cannistraci Carlo Vittorio 
Published: March 2021

AbstractThe stomach is inhabited by diverse microbial communities, co-existing in a dynamic balance. Long-term use of drugs such as proton pump inhibitors (PPIs), or bacterial infection such as Helicobacter pylori, cause significant microbial alterations. Yet, studies revealing how the commensal bacteria re-organize, due to these perturbations of the gastric environment, are in early phase and rely principally on linear techniques for multivariate analysis. Here we disclose the importance of complementing linear dimensionality reduction techniques with nonlinear ones to unveil hidden patterns that remain unseen by linear embedding. Then, we prove the advantages to complete multivariate pattern analysis with differential network analysis, to reveal mechanisms of bacterial network re-organizations which emerge from perturbations induced by a medical treatment (PPIs) or an infectious state (H. pylori). Finally, we show how to build bacteria-metabolite multilayer networks that can deepen our understanding of the metabolite pathways significantly associated to the perturbed microbial communities.
TDP-43 and PINK1 mediate CHCHD10S59L mutation–induced defects in Drosophila and in vitro
Authors: Baek Minwoo , Choe Yun-Jeong , Bannwarth Sylvie , Kim JiHye , Maitra Swati , Dorn Gerald W. , Taylor J. Paul , Paquis-Flucklinger Veronique , Kim Nam Chul 
Published: March 2021

AbstractMutations in coiled-coil-helix-coiled-coil-helix domain containing 10 (CHCHD10) can cause amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD). However, the underlying mechanisms are unclear. Here, we generateCHCH10S59L-mutantDrosophila melanogasterand HeLa cell lines to modelCHCHD10-associated ALS-FTD. TheCHCHD10S59Lmutation results in cell toxicity in several tissues and mitochondrial defects.CHCHD10S59Lindependently affects the TDP-43 and PINK1 pathways.CHCHD10S59Lexpression increases TDP-43 insolubility and mitochondrial translocation. Blocking TDP-43 mitochondrial translocation with a peptide inhibitor reducedCHCHD10S59L-mediated toxicity. While genetic and pharmacological modulation ofPINK1expression and activity of its substrates rescues and mitigates theCHCHD10S59L-induced phenotypes and mitochondrial defects, respectively, in bothDrosophilaand HeLa cells. Our findings suggest thatCHCHD10S59L-induced TDP-43 mitochondrial translocation and chronic activation of PINK1-mediated pathways result in dominant toxicity, providing a mechanistic insight into theCHCHD10mutations associated with ALS-FTD.
The Burkholderia pseudomallei intracellular ‘TRANSITome’
Authors: Heacock-Kang Yun , McMillan Ian A. , Norris Michael H. , Sun Zhenxin , Zarzycki-Siek Jan , Bluhm Andrew P. , Cabanas Darlene , Norton Robert E. , Ketheesan Natkunam , Miller Jeff F. , Schweizer Herbert P. , Hoang Tung T. 
Published: March 2021

AbstractProkaryotic cell transcriptomics has been limited to mixed or sub-population dynamics and individual cells within heterogeneous populations, which has hampered further understanding of spatiotemporal and stage-specific processes of prokaryotic cells within complex environments. Here we develop a ‘TRANSITomic’ approach to profile transcriptomes of single Burkholderia pseudomallei cells as they transit through host cell infection at defined stages, yielding pathophysiological insights. We find that B. pseudomallei transits through host cells during infection in three observable stages: vacuole entry; cytoplasmic escape and replication; and membrane protrusion, promoting cell-to-cell spread. The B. pseudomallei ‘TRANSITome’ reveals dynamic gene-expression flux during transit in host cells and identifies genes that are required for pathogenesis. We find several hypothetical proteins and assign them to virulence mechanisms, including attachment, cytoskeletal modulation, and autophagy evasion. The B. pseudomallei ‘TRANSITome’ provides prokaryotic single-cell transcriptomics information enabling high-resolution understanding of host-pathogen interactions.
Formation of large low shear velocity provinces through the decomposition of oxidized mantle
Authors: Wang Wenzhong , Liu Jiachao , Zhu Feng , Li Mingming , Dorfman Susannah M. , Li Jie , Wu Zhongqing 
Published: March 2021

AbstractLarge Low Shear Velocity Provinces (LLSVPs) in the lowermost mantle are key to understanding the chemical composition and thermal structure of the deep Earth, but their origins have long been debated. Bridgmanite, the most abundant lower-mantle mineral, can incorporate extensive amounts of iron (Fe) with effects on various geophysical properties. Here our high-pressure experiments and ab initio calculations reveal that a ferric-iron-rich bridgmanite coexists with an Fe-poor bridgmanite in the 90 mol% MgSiO3–10 mol% Fe2O3 system, rather than forming a homogeneous single phase. The Fe3+-rich bridgmanite has substantially lower velocities and a higher VP/VS ratio than MgSiO3 bridgmanite under lowermost-mantle conditions. Our modeling shows that the enrichment of Fe3+-rich bridgmanite in a pyrolitic composition can explain the observed features of the LLSVPs. The presence of Fe3+-rich materials within LLSVPs may have profound effects on the deep reservoirs of redox-sensitive elements and their isotopes.
Evaluating the economic impact of water scarcity in a changing world
Authors: Dolan Flannery , Lamontagne Jonathan , Link Robert , Hejazi Mohamad , Reed Patrick , Edmonds Jae 
Published: March 2021

AbstractWater scarcity is dynamic and complex, emerging from the combined influences of climate change, basin-level water resources, and managed systems’ adaptive capacities. Beyond geophysical stressors and responses, it is critical to also consider how multi-sector, multi-scale economic teleconnections mitigate or exacerbate water shortages. Here, we contribute a global-to-basin-scale exploratory analysis of potential water scarcity impacts by linking a global human-Earth system model, a global hydrologic model, and a metric for the loss of economic surplus due to resource shortages. We find that, dependent on scenario assumptions, major hydrologic basins can experience strongly positive or strongly negative economic impacts due to global trade dynamics and market adaptations to regional scarcity. In many cases, market adaptation profoundly magnifies economic uncertainty relative to hydrologic uncertainty. Our analysis finds that impactful scenarios are often combinations of standard scenarios, showcasing that planners cannot presume drivers of uncertainty in complex adaptive systems.
Neural alignment predicts learning outcomes in students taking an introduction to computer science course
Authors: Meshulam Meir , Hasenfratz Liat , Hillman Hanna , Liu Yun-Fei , Nguyen Mai , Norman Kenneth A. , Hasson Uri 
Published: March 2021

AbstractDespite major advances in measuring human brain activity during and after educational experiences, it is unclear how learners internalize new content, especially in real-life and online settings. In this work, we introduce a neural approach to predicting and assessing learning outcomes in a real-life setting. Our approach hinges on the idea that successful learning involves forming the right set of neural representations, which are captured in canonical activity patterns shared across individuals. Specifically, we hypothesized that learning is mirrored in neural alignment: the degree to which an individual learner’s neural representations match those of experts, as well as those of other learners. We tested this hypothesis in a longitudinal functional MRI study that regularly scanned college students enrolled in an introduction to computer science course. We additionally scanned graduate student experts in computer science. We show that alignment among students successfully predicts overall performance in a final exam. Furthermore, within individual students, we find better learning outcomes for concepts that evoke better alignment with experts and with other students, revealing neural patterns associated with specific learned concepts in individuals.
Microwave resonances of magnetic skyrmions in thin film multilayers
Authors: Satywali Bhartendu , Kravchuk Volodymyr P. , Pan Liqing , Raju M. , He Shikun , Ma Fusheng , Petrović A. P. , Garst Markus , Panagopoulos Christos 
Published: March 2021

AbstractNon-collinear magnets exhibit a rich array of dynamic properties at microwave frequencies. They can host nanometre-scale topological textures known as skyrmions, whose spin resonances are expected to be highly sensitive to their local magnetic environment. Here, we report a magnetic resonance study of an [Ir/Fe/Co/Pt] multilayer hosting Néel skyrmions at room temperature. Experiments reveal two distinct resonances of the skyrmion phase during in-plane ac excitation, with frequencies between 6–12 GHz. Complementary micromagnetic simulations indicate that the net magnetic dipole moment rotates counterclockwise (CCW) during both resonances. The magnon probability distribution for the lower-frequency resonance is localised within isolated skyrmions, unlike the higher-frequency mode which principally originates from areas between skyrmions. However, the properties of both modes depend sensitively on the out-of-plane dipolar coupling, which is controlled via the ferromagnetic layer spacing in our heterostructures. The gyrations of stable isolated skyrmions reported in this room temperature study encourage the development of new material platforms and applications based on skyrmion resonances. Moreover, our material architecture enables the resonance spectra to be tuned, thus extending the functionality of such applications over a broadband frequency range.
Brown and beige adipose tissue regulate systemic metabolism through a metabolite interorgan signaling axis
Authors: Whitehead Anna , Krause Fynn N. , Moran Amy , MacCannell Amanda D. V. , Scragg Jason L. , McNally Ben D. , Boateng Edward , Murfitt Steven A. , Virtue Samuel , Wright John , Garnham Jack , Davies Graeme R. , Dodgson James , Schneider Jurgen E. , Murray Andrew J. , Church Christopher , Vidal-Puig Antonio , Witte Klaus K. , Griffin Julian L. , Roberts Lee D. 
Published: March 2021

AbstractBrown and beige adipose tissue are emerging as distinct endocrine organs. These tissues are functionally associated with skeletal muscle, adipose tissue metabolism and systemic energy expenditure, suggesting an interorgan signaling network. Using metabolomics, we identify 3-methyl-2-oxovaleric acid, 5-oxoproline, and β-hydroxyisobutyric acid as small molecule metabokines synthesized in browning adipocytes and secreted via monocarboxylate transporters. 3-methyl-2-oxovaleric acid, 5-oxoproline and β-hydroxyisobutyric acid induce a brown adipocyte-specific phenotype in white adipocytes and mitochondrial oxidative energy metabolism in skeletal myocytes both in vitro and in vivo. 3-methyl-2-oxovaleric acid and 5-oxoproline signal through cAMP-PKA-p38 MAPK and β-hydroxyisobutyric acid via mTOR. In humans, plasma and adipose tissue 3-methyl-2-oxovaleric acid, 5-oxoproline and β-hydroxyisobutyric acid concentrations correlate with markers of adipose browning and inversely associate with body mass index. These metabolites reduce adiposity, increase energy expenditure and improve glucose and insulin homeostasis in mouse models of obesity and diabetes. Our findings identify beige adipose-brown adipose-muscle physiological metabokine crosstalk.
The inherent uncertainty of temporal networks is a true challenge for control
Authors: De Lellis Pietro , Di Meglio Anna , Garofalo Franco , Lo Iudice Francesco 
Published: March 2021

AbstractRecently, it has been suggested that network temporality can be exploited to substantially reduce the energy required to control complex networks. This somewhat counterintuitive finding was explained through an evocative example of the advantage of temporal networks: when navigating a sailboat, we raise the sails when the wind helps us while lowering them when it works against us. Unfortunately, controlling complex networks inherits a further analogy with navigating a sailboat: having to face the inherent uncertainty of future winds. We rarely, if ever, have deterministic knowledge of the evolution of the network we want to control. Here, our challenge is to exploit the potential advantages of temporality when only a probabilistic description of the future is available. We prove that, in this more realistic setting, exploiting temporality is no more a panacea for network control, but rather an asset of a wider toolbox made available by the scientific community. One that can indeed turn out useful, provided that the temporality of the network structure matches the intrinsic time scales of the nodes we want to control.
Microsurgical resection of fronto-temporo-insular gliomas in the non-dominant hemisphere, under general anesthesia using adjunct intraoperative MRI and no cortical and subcortical mapping: a series of 20 consecutive patients
Authors: Leroy Henri-Arthur , Strachowksi Ondine , Tuleasca Constantin , Vannod-Michel Quentin , Le Rhun Emilie , Derre Benoit , Lejeune Jean-Paul , Reyns Nicolas 
Published: March 2021

AbstractFronto-temporo-insular (FTI) gliomas continue to represent a surgical challenge despite numerous technical advances. Some authors advocate for surgery in awake condition even for non-dominant hemisphere FTI, due to risk of sociocognitive impairment. Here, we report outcomes in a series of patients operated using intraoperative magnetic resonance imaging (IoMRI) guided surgery under general anesthesia, using no cortical or subcortical mapping. We evaluated the extent of resection, functional and neuropsychological outcomes after IoMRI guided surgery under general anesthesia of FTI gliomas located in the non-dominant hemisphere. Twenty patients underwent FTI glioma resection using IoMRI in asleep condition. Seventeen tumors were de novo, three were recurrences. Tumor WHO grades were II:12, III:4, IV:4. Patients were evaluated before and after microsurgical resection, clinically, neuropsychologically (i.e., social cognition) and by volumetric MR measures (T1G+ for enhancing tumors, FLAIR for non-enhancing). Fourteen (70%) patients benefited from a second IoMRI. The median age was 33.5 years (range 24–56). Seizure was the inaugural symptom in 71% of patients. The median preoperative volume was 64.5 cm3 (min 9.9, max 211). Fourteen (70%) patients underwent two IoMRI. The final median EOR was 92% (range 69–100). The median postoperative residual tumor volume (RTV) was 4.3 cm3 (range 0–38.2). A vast majority of residual tumors were located in the posterior part of the insula. Early postoperative clinical events (during hospital stay) were three transient left hemiparesis (which lasted less than 48 h) and one prolonged left brachio-facial hemiparesis. Sixty percent of patients were free of any symptom at discharge. The median Karnofsky Performance Score was of 90 both at discharge and at 3 months. No significant neuropsychological impairment was reported, excepting empathy distinction in less than 40% of patients. After surgery, 45% of patients could go back to work. In our experience and using IoMRI as an adjunct, microsurgical resection of non-dominant FTI gliomas under general anesthesia is safe. Final median EOR was 92%, with a vast majority of residual tumors located in the posterior insular part. Patients experienced minor neurological and neuropsychological morbidity. Moreover, neuropsychological evaluation reported a high preservation of sociocognitive abilities. Solely empathy seemed to be impaired in some patients.
RETRACTED ARTICLE: Noninvasive thrombectomy of graft by nano-magnetic ablating particles
Authors: Moghanizadeh Abbas , Ashrafizadeh Fakhreddin , Varshosaz Jaleh , Kharaziha Mahshid , Ferreira Antoine 
Published: March 2021

AbstractArtificial vascular treatment is an emerging interdisciplinary subject of medicine. Although the use of artificial vessels has led to many successful advancements, blood clotting remains a major challenge, especially in terms of mural clots created along the vessel wall that do not completely block the vessel. The main objective of this study is to present a method for declotting artificial vessels. This research introduces a novel thrombectomy technique in artificial vessels by employing nano-magnetic particles under a rotating magnetic field to remove mural clots in artificial vessels. A mathematical model describes the relationship between process parameters. In vitro tests confirm the feasibility of nano-magnetic thrombectomy in cleaning and declotting artificial vessels. The results show that the clot fragments are nano-sized, which eliminates the risk of distal emboli as a concern of using current atherectomy techniques. Meanwhile, no damage to the artificial vessels is observed. The results show that the frequency of rotating the magnetic field has the greatest effect on clot removal. The conceptual principles stated in this study also have the potential to be used in other vascular depositions, such as the accumulation of lipids, and calcification atherosclerosis.
Glutathione ethyl ester reverses the deleterious effects of fentanyl on ventilation and arterial blood-gas chemistry while prolonging fentanyl-induced analgesia
Authors: Jenkins Michael W. , Khalid Faiza , Baby Santhosh M. , May Walter J. , Young Alex P. , Bates James N. , Cheng Feixiong , Seckler James M. , Lewis Stephen J. 
Published: March 2021

AbstractThere is an urgent need to develop novel compounds that prevent the deleterious effects of opioids such as fentanyl on minute ventilation while, if possible, preserving the analgesic actions of the opioids. We report that L-glutathione ethyl ester (GSHee) may be such a novel compound. In this study, we measured tail flick latency (TFL), arterial blood gas (ABG) chemistry, Alveolar-arterial gradient, and ventilatory parameters by whole body plethysmography to determine the responses elicited by bolus injections of fentanyl (75 μg/kg, IV) in male adult Sprague–Dawley rats that had received a bolus injection of GSHee (100 μmol/kg, IV) 15 min previously. GSHee given alone had minimal effects on TFL, ABG chemistry and A-a gradient whereas it elicited changes in some ventilatory parameters such as an increase in breathing frequency. In vehicle-treated rats, fentanyl elicited (1) an increase in TFL, (2) decreases in pH, pO2and sO2and increases in pCO2(all indicative of ventilatory depression), (3) an increase in Alveolar-arterial gradient (indicative of a mismatch in ventilation-perfusion in the lungs), and (4) changes in ventilatory parameters such as a reduction in tidal volume, that were indicative of pronounced ventilatory depression. In GSHee-pretreated rats, fentanyl elicited a more prolonged analgesia, relatively minor changes in ABG chemistry and Alveolar-arterial gradient, and a substantially milder depression of ventilation. GSHee may represent an effective member of a novel class of thiolester drugs that are able to prevent the ventilatory depressant effects elicited by powerful opioids such as fentanyl and their deleterious effects on gas-exchange in the lungs without compromising opioid analgesia.
Extracellular vesicles are associated with C-reactive protein in sepsis
Authors: Fendl Birgit , Weiss René , Eichhorn Tanja , Linsberger Ingrid , Afonyushkin Taras , Puhm Florian , Binder Christoph J. , Fischer Michael B. , Weber Viktoria 
Published: March 2021

AbstractThere is increasing evidence that C-reactive protein (CRP) can mediate inflammatory reactions following the transformation of functionally inert pentameric CRP (pCRP) into its structural isoform pCRP* and into monomeric CRP (mCRP). This conversion can occur on the membranes of apoptotic or activated cells or on extracellular vesicles (EVs) shed from the cell surface. Here, we characterized the association of CRP with EVs in plasma from sepsis patients using flow cytometry, and found highly elevated levels of total EV counts and CRP+ EVs as compared to healthy individuals. We further assessed the ability of PentraSorb CRP, an extracorporeal device for the adsorption of CRP, to deplete free CRP and CRP+ EVs. Treatment of septic plasma with the adsorbent in vitro resulted in almost complete removal of both, free CRP and CRP+ EVs, while total EV counts remained largely unaffected, indicating the detachment of CRP from the EV surface. EVs from septic plasma elicited a release of interleukin-8 from cultured human monocytes, which was significantly reduced by adsorbent treatment prior to EV isolation. Our findings provide evidence that CRP+ EVs exhibit pro-inflammatory characteristics and can contribute to the spreading of inflammation throughout the circulation on top of their pro-coagulant activity.
Adaptive blind equalization of fast time‐varying channel with frequency estimation in impulsive noise environment
Authors: Zhang Yijiao , Tian Shulin , Pan Huiqing , Zhou Yi 
Published: March 2021

AbstractIn this paper, a novel source signal recovery method for fast time‐varying channels described by complex exponential‐basis expansion model (CE‐BEM) in the impulsive noise environment is proposed. This method consists of two phases. The first phase is the equalization of fast time‐varying channels, in this phase, a novel algorithm FSE‐FLOS‐CMA is proposed. The convergence performance of this newly proposed algorithm is much better than that of existing fractionally spaced equalizer‐constant modulus algorithm (FSE‐CMA) in impulsive noise environment. In the second phase, a novel frequency estimation method is proposed. The estimated frequency in impulsive noise environment is obtained by calculating a specific p‐order fractional low‐order cyclic moment of the equalized signal. Simulation results show that the proposed FSE‐FLOS‐CMA and frequency estimation method can effectively estimate the source signals transmitted through the fast time‐varying channels in impulsive noise environment.
Low latency group‐sorted QR decomposition algorithm for larger‐scale MIMO systems
Authors: Chen Lirui , Wang Yu , Xing Zuocheng , Qiu Shikai , Wang Qinglin , Li Yongzhong 
Published: March 2021

AbstractSorted QR decomposition (SQRD) has been extensively adopted for various multiple‐input‐multiple‐output (MIMO) detectors, in which the sorting process incurs severe latency when it comes to larger‐scale MIMO situations. This paper proposes a group‐SQRD (GSQRD) algorithm to alleviate the latency problem of general SQRD architectures for larger‐scale MIMO systems. Via predictively sorting a group of 4 columns at one stage, the GSQRD could eliminate the processing latency by 41% for decomposing 1616 complex‐valued matrices. Additionally, this percentage even rises up to 68% for decomposing 128128 matrices. To analyse the side effects, the GSQRD is applied in various MIMO detectors in a simulation link, which exhibits a negligible performance degradation for MIMO detection. Moreover, GSQRD is a hardware‐friendly algorithm because the division and square root operations in GSQRD are converted to multiplications for simplifying the hardware implementation. Based on this algorithm, two corresponding hardware architectures, which contains 2 and 4 columns respectively in a sorting group, are also implemented with 65‐nm CMOS technology. These architectures can work at 513 MHz to decompose 1616 complex‐valued matrices. The processing latencies are respectively 0.32 and 0.26 s, superior to the state‐of‐art designs.