bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of deep water and N uptake under varied N and water supply
Authors: Chen Guanying , Rasmussen Camilla Ruø , Dresbøll Dorte Bodin , Smith Abraham George , Thorup-Kristensen Kristian 
Published: October 2021

AbstractAimsEnhanced nitrogen (N) and water uptake from deep soil layers may increase resource use efficiency whilst maintaining yield under stressed conditions. Winter oilseed rape (Brassica napusL.) can develop deep roots and access deep-stored resources such as N and water, while this potential has large uncertainties in variable environments. In this study, we aimed to evaluate the effects of reduced N and water supply on deep N and water uptake.MethodsOilseed rape plants grown in outdoor rhizotrons were supplied with 240 and 80 kg N ha-1respectively in 2019 whereas a well-watered and a water-deficit treatment were established in 2020. To track deep water and N uptake, a mixture of2H2O and Ca(15NO3)2was injected into the soil column at 0.5 and 1.7 m depths. δ2H in transpiration water and δ15N in leaves were measured after injection. δ15N in biomass samples were also measured.ResultsDifferences in N or water supply had little effect on root growth. The low N treatment reduced water uptake throughout the soil profile, but caused a non-significant increment in15N uptake efficiency at both 0.5 and 1.7 m. Water deficit in the upper soil layers led to compensatory deep water, while N uptake was not altered by soil water status.ConclusionOur findings demonstrate that for winter oilseed rape, high N application and water deficiency in shallow layers increases deep water uptake, and that the efficiency of deep N uptake is mainly sensitive to N supply rather than water supply.
Clonal hematopoiesis is associated with increased toxicity in large B-cell lymphoma patients treated with chimeric antigen receptor T cell therapy
Authors: Saini Neeraj Y. , Swoboda David M. , Greenbaum Uri , Ma Jungsheng , Patel Romil , Devashish Kartik , Das Kaberi , Tanner Mark R. , Strati Paolo , Nair Ranjit , Fayad Luis E. , Ahmed Sairah , Lee Hun Ju , Iyer Swaminathan , Steiner Raphael , Jain Nitin , Nastoupil Loretta , Loghavi Sanam , Tang Guilin , Jain Preetesh , Wang Michael , Westin Jason , Green Michael R. , Sallman David , Padron Eric , Davila Marco , Locke Frederick L. , Champlin Richard , Shpall Elizabeth , Kebriaei Partow , Flowers Christopher R. , Jain Michael , Wang Feng , Futreal Andrew , Gillis Nancy , Neelapu Sattva S. , Takahashi Koichi 
Published: October 2021

AbstractTo explore the role of clonal hematopoiesis (CH) on chimeric antigen receptor (CAR) T-cell therapy outcomes, we performed targeted deep-sequencing on 114 large B-cell lymphoma patients treated with anti-CD19 CAR T-cells. We detected CH in 42 (36.8%) pre-treatment patient samples, most frequently in PPM1D (19/114) and TP53 (13/114) genes. The incidence of grade ≥3 immune-effector cell-associated neurotoxicity syndrome (ICANS) was higher in CH-positive patients compared to CH-negative patients (45.2% vs. 25.0%, p=0.038). Higher toxicities with CH were primarily driven by three CH genes, DNMT3A, TET2 and ASXL1 (DTA mutations). The incidence of grade ≥3 ICANS [58.9% vs. 25%, p=0.02] and grade ≥3 cytokine release syndrome [17.7% vs. 4.2%, p=0.08] were higher in patients with DTA mutations than those without CH. The estimated 24-month cumulative incidence of therapy-related myeloid neoplasms after CAR-T therapy was higher in patients with CH than those without CH (19% [95%CI: 5.5-38.7] vs. 4.2% [95%CI: 0.3-18.4], p=0.028).Statement of SignificanceOur study reveals that clonal hematopoiesis mutations, especially those associated with inflammation (DNMT3A, TET2, ASXL1), are associated with severe grade toxicities in lymphoma patients receiving anti-CD19 chimeric antigen receptor therapy. Further studies to investigate the mechanisms and interventions to improve toxicities in the context of CH are warranted.
Occlusion of lip movements impairs reconstruction of acoustic speech features and higher-level segmentational features in the presence of a distractor speaker
Authors: Haider Chandra Leon , Suess Nina , Hauswald Anne , Park Hyojin , Weisz Nathan 
Published: October 2021

AbstractMultisensory integration enables stimulus representation even when the sensory input in a single modality is weak. In the context of speech, when confronted with a degraded acoustic signal, congruent visual inputs promote comprehension. When this input is occluded speech comprehension consequently becomes more difficult. But it still remains inconclusive which levels of speech processing are affected under which circumstances by occlusion of the mouth area. To answer this question, we conducted an audiovisual (AV) multi-speaker experiment using naturalistic speech. In half of the trials, the target speaker wore a (surgical) face mask, while we measured the brain activity of normal hearing participants via magnetoencephalography (MEG). We additionally added a distractor speaker in half of the trials in order to create an ecologic difficult listening situation. A decoding model on the clear AV speech was trained and used to reconstruct crucial speech features in each condition. We found significant main effects of face masks on the reconstruction of acoustic features, such as the speech envelope and spectral speech features (i.e. pitch and formant frequencies), while reconstruction of higher level features of speech segmentation (phoneme and word onsets) were especially impaired through masks in difficult listening situations. As we used surgical face masks in our study, which only show mild effects on speech acoustics, we interpret our findings as the result of the occluded lip movements. This idea is in line with recent research showing that visual cortical regions track spectral modulations. Our findings extend previous behavioural results, by demonstrating the complex contextual effects of occluding relevant visual information on speech processing.HighlightsSurgical face masks impair neural tracking of speech featuresTracking of acoustic features is generally impaired, while higher level segmentational features show their effects especially in challenging listening situationsAn explanation is the prevention of a visuo-phonological transformation contributing to audiovisual multisensory integration
Prediction of Inefficient BCI Users based on Cognitive Skills and Personality Traits
Authors: Hagedorn Laura J. , Leeuwis Nikki , Alimardani Maryam 
Published: October 2021

AbstractBCI inefficiency is one of the major challenges of motor imagery brain-computer interfaces (MI-BCI). Past research suggests that certain cognitive skills and personality traits correlate with MI-BCI real-time performance. Other studies have examined sensorimotor rhythm changes (also known as μ suppression) as a valuable indicator of successful execution of the MI task. This research aims to combine these insights by investigating whether cognitive factors and personality traits can make predictions of a user’s ability to modulate μ rhythms during a MI-BCI task. Data containing 55 subjects who completed a MI task was employed, and a stepwise linear regression model was implemented to select the most relevant features for μ suppression prediction. The most accurate model was based on these factors: Spatial Ability, Visuospatial Memory, Autonomy, and Vividness of Visual Imagery. Further correlation analyses showed that a novice user’s μ suppression during a MI-BCI task can be predicted based on their visuospatial memory ability, as measured by the Design Organization Test (DOT).
Biotechnology data analysis training with Jupyter Notebooks
Authors: Liebal Ulf W. , Schimassek Rafael , Broderius Iris , Maaßen Nicole , Vogelgesang Alina , Weyers Philipp , Blank Lars M. 
Published: October 2021

AbstractBiotechnology has experienced innovations in analytics and data processing. As the volume of data and its complexity grows, new computational procedures for extracting information are developed. However, the rate of change outpaces the adaptation of biotechnology curricula, necessitating new teaching methodologies to equip biotechnologists with data analysis abilities. To simulate experimental data, we created a virtual organism simulator (silvio) by combining diverse cellular and sub-cellular microbial models. silvio was utilized to construct a computer-based instructional workflow with important steps during strain characterization and recombinant protein expression. The instructional workflow is provided as a Jupyter Notebook with comprehensive explanatory text of biotechnological facts and experiment simulations using silvio tools. The students conduct data analysis in Python or Excel. This instructional workflow was separately implemented in two distance courses for Master’s students in biology and biotechnology. The concept of using virtual organism simulations that generate coherent results across different experiments can be used to construct consistent and motivating case studies for biotechnological data literacy.
Fast Optoacoustic Mesoscopy of Microvascular Endothelial Dysfunction in Cardiovascular Risk and Disease
Authors: He Hailong , Karlas Angelos , Fasoula Nikolina-Alexia , Kallmayer Michael , Aguirre Juan , Eckstein Hans-Henning , Ntziachristos Vasilis 
Published: October 2021

AbstractMicrovascular endothelial dysfunction (ED) precedes the ED in larger arteries and is an early marker of cardiovascular disease (CVD). While precise assessment of microvascular ED could thus be used for the early detection and risk stratification of CVD, detailed interrogation of skin microvascular ED is limited by the technology available. Herein, we applied a novel approach for the non-invasive assessment of skin microvascular ED by developing fast plane raster-scan optoacoustic mesoscopy (FP-RSOM) to visualize and quantify skin microvasculature perfusion changes during post-occlusive hyperemia (PORH) tests. We combined static three-dimensional RSOM imaging with fast dynamic FP-RSOM measurements (1 frame / second) in human skin in vivo, which allowed for the first time to fully visualize the cutaneous microvascular response and further quantify changes of individual vessel diameter, total blood volume and vessel density during the PORH process. We further computed biomarkers from FP-RSOM images to quantify skin endothelial function within different skin layers as a function of skin depth, while conventional approaches mainly measure overall changes within sampled tissue volumes. FP-RSOM applied on smokers and patients with CVD showed clear ED in both groups compared to healthy volunteers. Moreover, FP-RSOM imaging showed higher sensitivity in quantifying the effects of smoking and CVD on skin microvascular endothelial function compared to clinically used laser Doppler flowmetry and tissue spectrometry (O2C). Our study introduces FP-RSOM as a novel tool to visualize and quantify skin microvascular ED as an early marker for the diagnostics and monitoring of cardiovascular risk and disease.
Light regulated SIK1 remodels the synaptic phosphoproteome to induce sleep
Authors: Taylor Lewis , Palumaa Teele , Reardon Paul K , Walsh Steven , Johnson Bradley H , Liberatori Sabrina , Hasan Sibah , Clark Kristopher , Cohen Philip , Vasudevan Sridhar , Peirson Stuart , Mohammed Shabaz , Vyazovskiy Vladyslav , Foster Russell G , Jagannath Aarti 
Published: October 2021

SUMMARYThe sleep and circadian systems act in concert to regulate sleep-wake timing, yet the molecular mechanisms that underpin their interaction to induce sleep remain unknown. Synaptic protein phosphorylation, driven by the kinase SIK3, correlates with sleep pressure, however it is unclear whether these phosphoproteome changes are causally responsible for inducing sleep. Here we show that the light-dependent activity of SIK1 controls the phosphorylation of a subset of the brain phosphoproteome to induce sleep in a manner that is independent of sleep pressure. By uncoupling phosphorylation and sleep induction from sleep pressure, we establish that synaptic protein phosphorylation provides a causal mechanism for the induction of sleep under different environmental contexts. Furthermore, we propose a framework that details how the salt-inducible kinases regulate the synaptic phosphoproteome to integrate exogenous and endogenous stimuli, thereby providing the molecular basis upon which the sleep and circadian systems interact to control the sleep-wake cycle.
A yeast with muscle doesn’t run faster: full humanization of the glycolytic pathway in Saccharomyces cerevisiae
Authors: Boonekamp Francine J. , Knibbe Ewout , Vieira-Lara Marcel A. , Wijsman Melanie , Luttik Marijke A.H. , van Eunen Karen , den Ridder Maxime , Bron Reinier , Almonacid Suarez Ana Maria , van Rijn Patrick , Wolters Justina C. , Pabst Martin , Daran Jean-Marc , Bakker Barbara , Daran-Lapujade Pascale 
Published: October 2021

SummaryWhile transplantation of single genes in yeast plays a key role in elucidating gene functionality in metazoans, technical challenges hamper the humanization of full pathways and processes. Empowered by advances in synthetic biology, this study demonstrates the feasibility and implementation of full humanization of glycolysis in yeast. Single gene and full pathway transplantation revealed the remarkable conservation of both glycolytic and moonlighting functions and, combined with evolutionary strategies, brought to light novel, context-dependent responses. Remarkably, human hexokinase 1 and 2, but not 4, required mutations in their catalytic or allosteric sites for functionality in yeast, while hexokinase 3 was unable to complement its yeast ortholog. Comparison with human tissues cultures showed the preservation of turnover numbers of human glycolytic enzymes in yeast and human cell cultures. This demonstration of transplantation of an entire, essential pathway paves the way to the establishment of species, tissue and disease-specific metazoan models.One Sentence SummaryThis work demonstrates the successful humanization of an entire pathway in Saccharomyces cerevisiae and establishes an attractive strategy to study (human) glycolysis architecture and regulation.HighlightsThe successful humanization of the entire glycolytic pathway in yeast offers new microbial models for both fundamental and applied studies.Both glycolytic and moonlighting functions and turnover numbers of glycolytic enzymes are highly conserved between yeast and human.Functionality of human hexokinases 1 and 2 in yeast requires mutations in the catalytic or allosteric binding sites.Combination of single gene and full transplantation with laboratory evolution reveals context-dependent activity and evolution of glycolytic enzymes.
Neurofibromin 1 controls metabolic balance and Notch-dependent quiescence of juvenile myogenic progenitors
Authors: Wei Xiaoyan , Lienhard Matthias , Murgai Arunima , Franke Julia , Pöhle-Kronawitter Sophie , Kotsaris Georgios , Wu Hao , Börno Stefan , Timmermann Bernd , Glauben Rainer , Stricker Sigmar 
Published: October 2021

AbstractPatients affected by neurofibromatosis type 1 (NF1) frequently show muscle weakness with unknown etiology. Here we show that Neurofibromin-1 (Nf1) is not required in muscle fibers, but specifically in early postnatal myogenic progenitors (MPs), where Nf1 loss led to cell cycle exit and differentiation blockade, depleting the MP pool resulting in reduced myonuclear accrual as well as reduced muscle stem cell numbers. This was caused by precocious induction of stem cell quiescence coupled to metabolic reprogramming of MPs impinging on glycolytic shutdown, which was conserved in muscle fibers. We show that a Mek/Erk/NOS pathway hypersensitizes Nf1-deficient MPs to Notch signaling, consequently, early postnatal Notch pathway inhibition ameliorated premature quiescence, metabolic reprogramming and muscle growth. This reveals an unexpected role of Ras/Mek/Erk signaling supporting postnatal MP quiescence in concert with Notch signaling, which is controlled by Nf1 safeguarding coordinated muscle growth and muscle stem cell pool establishment. Furthermore, our data suggest transmission of metabolic reprogramming across cellular differentiation, affecting fiber metabolism and function in NF1.
Metrics of High Cofluctuation and Entropy to Describe Control of Cardiac Function in the Stellate Ganglion
Authors: Gurel Nil Z. , Sudarshan Koustubh B. , Hadaya Joseph , Karavos Alex , Temma Taro , Hori Yuichi , Armour J. Andrew , Kember Guy , Ajijola Olujimi A. 
Published: October 2021

AbstractStellate ganglia within the intrathoracic cardiac control system receive and integrate central, peripheral, and cardiopulmonary information to produce postganglionic cardiac sympathetic inputs. Pathological anatomical and structural remodeling occurs within the neurons of the stellate ganglion (SG) in the setting of heart failure. A large proportion of SG neurons function as interneurons whose networking capabilities are largely unknown. Current therapies are limited to targeting sympathetic activity at the cardiac level or surgical interventions such as stellectomy, to treat heart failure. Future therapies that target the stellate ganglion will require understanding of their networking capabilities to modify any pathological remodeling. We observe SG networking by examining cofluctuation and specificity of SG networked activity to cardiac cycle phases. We investigate network processing of cardiopulmonary transduction by SG neuronal populations in porcine with chronic pacing-induced heart failure and control subjects during extended in-vivo extracellular microelectrode recordings. We find that information processing and cardiac control in chronic heart failure by the SG, relative to controls, exhibits: i) more frequent, short-lived, high magnitude cofluctuations, ii) greater variation in neural specificity to cardiac cycles, and iii) neural network activity and cardiac control linkage that depends on disease state and cofluctuation magnitude.
Radical pairs may play a role in microtubule reorganization
Authors: Zadeh-Haghighi Hadi , Simon Christoph 
Published: October 2021

ABSTRACTThe exact mechanism behind general anesthesia remains an open question in neuroscience. It has been proposed that anesthetics selectively prevent consciousness and memory via acting on microtubules (MTs). It is known that the magnetic field modulates MT organization. A recent study shows that a radical pair model can explain the isotope effect in xenon-induced anesthesia and predicts magnetic field effects on anesthetic potency. Further, reactive oxygen species are also implicated in MT stability and anesthesia. Based on a simple radical pair mechanism model and a simple mathematical model of MT organization, we show that magnetic fields can modulate spin dynamics of naturally occurring radical pairs in MT. We show that the spin dynamics influence a rate in the reaction cycle, which translates into a change in the MT density. We can reproduce magnetic field effects on the MT concentration that have been observed. Our model also predicts additional effects at slightly higher fields. Our model further predicts that the effect of zinc on the MT density exhibits isotopic dependence. The findings of this work make a connection between microtubule-based and radical pair-based quantum theories of consciousness.
Evaluating the reliability, validity, and utility of overlapping networks: Implications for network theories of cognition
Authors: Cookson Savannah L. , D’Esposito Mark 
Published: October 2021

AbstractBrain network definitions typically assume non- or minimal overlap, ignoring regions’ connections to multiple networks. However, new methods are emerging that emphasize network overlap. Here, we investigated the reliability and validity of one assignment method, the mixed membership algorithm, and explored its potential utility for identifying gaps in existing network models of cognition. We first assessed between-sample reliability of overlapping assignment with a split-half design; a bootstrapped Dice similarity analysis demonstrated good agreement between the networks from the two subgroups. Next, we assessed whether overlapping networks captured expected nonoverlapping topographies; overlapping networks captured portions of one to three nonoverlapping topographies, which aligned with canonical network definitions. Following this, a relative entropy analysis showed that a majority of regions participated in more than one network, as is seen biologically, and many regions did not show preferential connection to any one network. Finally, we explored overlapping network membership in regions of the Dual-Networks model of cognitive control, showing that almost every region was a member of multiple networks. Thus, the mixed membership algorithm produces consistent and biologically plausible networks, which presumably will allow for the development of more complete network models of cognition.
Biomass formation and sugar release efficiency ofPopulusmodified by altered expression of a NAC transcription factor
Authors: Payyavula Raja S , Badmi Raghuram , Jawdy Sara S , Rodriguez Miguel , Gunter Lee , Sykes Robert W , Winkeler Kimberly A. , Collins Cassandra M. , Rottmann William H. , Chen Jin-Gui , Yang Xiaohan , Tuskan Gerald A , Kalluri Udaya C 
Published: October 2021

AbstractWoody biomass is an important feedstock for biofuel production. Manipulation of wood properties that enable efficient conversion of biomass to biofuel reduces cost of biofuel production. Wood cell wall composition is regulated at several levels that involve expression of transcription factors such as wood-/secondary cell wall-associated NAC domains (WND or SND). InArabidopsis thaliana, SND1regulates cell wall composition through activation of its down-stream targets such as MYBs. The functional aspects ofSND1homologs in the woodyPopulushave been studied through transgenic manipulation. In this study, we investigated the role ofPdWND1B, Populus SND1sequence ortholog, in wood formation using transgenic manipulation through over-expression or silencing under the control of a vascular-specific4-coumarate-CoAligase (4CL) promoter. As compared to control plants,PdWND1B-RNAi plants were shorter in height, with significantly reduced stem diameter and dry biomass, whereas there were no significant differences in growth and productivity ofPdWND1Bover-expression plants. Conversely,PdWND1Bover-expression lines showed a significant reduction in cellulose and increase in lignin content, whereas there was no significant impact on lignin content of down-regulated lines. Stem carbohydrate composition analysis revealed a decrease in glucose, mannose, arabinose, and galactose, but an increase in xylose in the over-expression lines. Transcriptome analysis revealed upregulation of several downstream transcription factors and secondary cell wall related structural genes in thePdWND1Bover-expression lines that corresponded to significant phenotypic changes in cell wall chemistry observed inPdWND1Boverexpression lines. Relative to the control, glucose release and ethanol production from stem biomass was significantly reduced in over-expression lines but appeared enhanced in the RNAi lines. Our results show thatPdWND1Bis an important factor determining biomass productivity, cell wall chemistry and its conversion to biofuels inPopulus.