bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linear causal filtering: definition and theory
Authors: Pascual-Marqui Roberto D. , Biscay Rolando J. , Bosch-Bayard Jorge , Achermann Peter , Faber Pascal , Kinoshita Toshihiko , Kochi Kieko 
Published: May 2021

1.AbstractThis work provides a framework based on multivariate autoregressive modeling for linear causal filtering in the sense of Granger. In its bivariate form, the linear causal filter defined here takes as input signals A and B, and it filters out the causal effect of B on A, thus yielding two new signals only containing the Granger-causal effect of A on B. In its general multivariate form for more than two signals, the effect of all indirect causal connections between A and B, mediated by all other signals, are accounted for, partialled out, and filtered out also. The importance of this filter is that it enables the estimation of directional measures of causal information flow from any non-causal, non-directional measure of association. For instance, based on the classic coherence, a directional measure of strength of information flow from A to B is obtained when applied to the linear causal filtered pair containing only A to B connectivity information. This particular case is equivalent to the isolated effective coherence (doi.org/10.3389/fnhum.2014.00448). Of more recent interest are the large family of phase-phase, phase-amplitude, and amplitude-amplitude cross-frequency coupling measures which are non-directional. The linear causal filter makes it now possible to estimate the directional causal versions these measures of association. One important field of application is in brain connectivity analysis based on cortical signals of electric neuronal activity (e.g. estimated sources of EEG and MEG, and invasive intracranial ECoG recordings). The linear causal filter introduced here provides a novel solution to the problem of estimating the direction of information flow from any non-directional measure of association. This work provides definitions, non-ambiguous equations, and clear prescriptions for implementing the linear causal filter in diverse settings.
Embryonic hyperglycemia perturbs the development of specific retinal cell types, including photoreceptors
Authors: Titialii-Torres Kayla F. , Morris Ann C. 
Published: May 2021

AbstractChronic hyperglycemia has been linked to various long-term metabolic disruptions in adults, such as neuropathy, nephropathy, and diabetic retinopathy. According to the 2020 National Diabetes Statistics Report, 10.5% of the US population has diabetes and may be susceptible to long-term complications if blood glucose is not tightly regulated. Further, in 2018, 7.6% of US pregnancies were affected by gestational diabetes, with an average of 1-14% annually [1]. During pregnancy, glucose can pass through the placental barrier, and plays an important role in fetal development and survival. However, excess maternal glucose can also result in diabetic embryopathy. While many studies have examined the teratogenic effects of maternal diabetes on fetal heart development, little is known about the consequences of maternal hyperglycemia on the development of the embryonic retina. To address this question, we investigated retinal cell type differentiation and survival in both a genetic and nutritional model of embryonic hyperglycemia in zebrafish. Strikingly, we found that hyperglycemic larvae displayed a significant reduction in rod and cone photoreceptors and horizontal cells, whereas other retinal neurons were not affected. We also observed signs of reactive gliosis in the retinal Müller cells, as well as increased reactive oxygen species (ROS) production in hyperglycemic retinas. Hyperglycemic larvae displayed altered expression of metabolism related genes and had a slower optokinetic response than normoglycemic larvae, indicating altered visual function. Further analysis of early events in retinogenesis revealed a delay in retinal cell differentiation at 48 hpf in hyperglycemic embryos, that coincided with an increase in reactive oxygen species. Taken together, our results suggest that embryonic hyperglycemia results in abnormal retinal cell development via altered timing of retinal cell differentiation and ROS production, which is accompanied by visual defects. As the population with diabetes continues to grow, it is imperative to pinpoint the effects of embryonic hyperglycemia on retinal development. Further studies using zebrafish models of hyperglycemia will allow us to understand the molecular mechanisms underlying these effects, which could aid in the development of therapeutic strategies.
Evaluation of efficacy of carfentrazone + metsulfuron, sulfosulfuron + metsulfuron and halauxifen againstRumexspp. in wheat (Triticum aestivum) in Western Haryana
Authors: Soni Sunil , Singh Samunder , Garg Rajbir 
Published: May 2021

ABSTRACTRumexspp. is most dominating broad-leaf weed of wheat crop. Complaints of poor efficacy of different herbicides againstRumexspp. have reported recently from different locations of Haryana state. Therefore, the present study was carried out under completely randomised design, replicated thrice, using three different herbicides namely carfentrazone + metsulfuron, sulfosulfuron + metsulfuron and halauxifen as treatments applied with three doses against four populations ofRumexspp. Plant height, chlorophyll fluorescence, electrical conductivity, mortality percentage and dry weight were recorded as observations. Results indicated that most of theRumexbiotypes were found resistant against sulfosulfuron + metsulfuron application. Majority of biotypes were moderately controlled by the application of halauxifen. Carfentrazone + metsulfuron effectively controlled theRumexspp. and provided 70-90 % control to all biotypes at double of the recommended dose. As per results of this study, carfentrazone + metsulfuron can be recommended for control ofRumexspp. in wheat.
Principled decision-making workflow with hierarchical Bayesian models of high throughput dose-response measurements
Authors: Ma Eric J. , Kummer Arkadij 
Published: May 2021

AbstractWe present a case study applying hierarchical Bayesian estimation on high throughput protein melting point data measured across the tree of life. We show that the model is able to impute reasonable melting temperatures even in the face of unreasonably noisy data. Additionally, we demonstrate how to use the variance in melting temperature posterior distribution estimates to enable principled decision-making in common high throughput measurement tasks, and contrast the decision-making workflow against simple maximum-likelihood curve fitting. We conclude with a discussion of the relative merits of each workflow.
Acidophilic Micrarchaeon Seems to Maintain a Slightly Alkaline Cytosolic pH
Authors: Winkler Dennis , Gfrerer Sabrina , Gescher Johannes 
Published: May 2021

AbstractDespite several discoveries in recent years, the physiology of acidophilic Micrarchaeota remains largely enigmatic. “CandidatusMicrarchaeum harzensis A_DKE”, for example, highly expresses numerous genes encoding hypothetical proteins and their function is difficult to elucidate due to a lacking genetic system. Still, not even the intracellular pH value of A_DKE is known, and heterologous production attempts are generally missing so far. Hence, A_DKE’s isocitrate dehydrogenase (MhIDH) was recombinantly produced inEscherichia coliand purified for bio-chemical characterisation. MhIDH appeared to be specific for NADP+, yet promiscuous regarding divalent cations as cofactors. Kinetic studies showedKM-values of 53.03±5.63 µM and 1.94±0.12 mM andkcat-values of 38.48±1.62 s-1and 43.99±1.46 s-1for DL-isocitrate and NADP+, respectively.MhIDH’s exceptionally low affinity for NADP+, potentially limiting its reaction rate, can be likely attributed to the presence of a proline residue in the NADP+binding-pocket, which might cause a decrease in hydrogen bonding of the cofactor and a distortion of local secondary structure. Furthermore, a pH optimum of 7.89 implies, that A_DKE applies potent mechanisms of proton homoeostasis, to maintain a slightly alkaline cytosolic milieu in a highly acidic environment.
3D printed pacifier-shaped mouthpiece for fMRI-compatible gustometers
Authors: Munoz Tord David , Coppin Géraldine , Pool Eva R. , Mermoud Christophe , Pataky Zoltan , Sander David , Delplanque Sylvain 
Published: May 2021

AbstractGustometers have allowed the delivery of liquids in fMRI settings for decades and mouthpieces are a critical part of those taste delivery systems. Here we propose an innovative 3D printed mouthpiece inspired by children’s pacifiers that allow participants to swallow while lying down in an MRI scanner. Our results validate the effectiveness of our method by showing significant clusters of activation in the insular and piriform cortex which are regions that have been consistently identified to compute taste processing. We used a large sample (n=85) to validate our method. Our mouthpiece fulfills several criteria guarantying a gustatory stimulus of quality, making the delivery more precise and reliable. Moreover, this new pacifier-shaped design is: simple and cheap to manufacture, hygienic, comfortable to keep in mouth, and flexible to diverse use cases.We hope that this new method will promote and facilitate the study of taste and flavor perception in the context of reward processing in affective neuroscience and thus help provide an integrative approach to the study of the emotional nature of rewards.
Dichaete, a Sox2 homologue, prevents activation of cell death in multiple developmental contexts
Authors: Harding Katherine , Heath Katerina , White Kristin 
Published: May 2021

ABSTRACTPrecisely regulated cell death plays a critical role in normal development and is controlled by the balance of pro-apoptotic and anti-apoptotic signals. InDrosophila, transcription of the clustered cell death activatorsgrimandreaperis turned on in the developing nervous system to eliminate neural stem cells at the end of embryonic development. This transcription is activated by a pulse of the Hox geneabdominal-A. We show here that the Sox2 homologueDichaeteinhibits neural stem cell death when overexpressed, and loss ofDichaetepromotes premature neural stem cell death. The anti-apoptotic activity of Dichaete opposes the pro-apoptotic factorsabdominal-A, as well as the transcription factorgrainyhead. The function of all three genes impinge on an enhancer that regulates the transcription ofgrimandreaper. Furthermore, we find that the balance betweenabdominal-AandDichaeteis likely to regulate the death of other cells during development, including cells in the developing midline, the developing hindgut, and in the early abdominal epidermis. Loss ofDichaeteresults in premature death in these tissues. This death can be rescued by the deletion of the enhancer region betweengrimandreaper. These data suggest thatDichaetefunctions to inhibit cell death activated byabdominal-Ain multiple developmental contexts.
Emu: Species-Level Microbial Community Profiling for Full-Length Nanopore 16S Reads
Authors: Curry Kristen D. , Wang Qi , Nute Michael G. , Tyshaieva Alona , Reeves Elizabeth , Soriano Sirena , Graeber Enid , Finzer Patrick , Mendling Werner , Wu Qinglong , Savidge Tor , Villapol Sonia , Dilthey Alexander , Treangen Todd J. 
Published: May 2021

ABSTRACT16S rRNA based analysis is the established standard for elucidating microbial community composition. While short read 16S analyses are largely confined to genus-level resolution at best since only a portion of the gene is sequenced, full-length 16S sequences have the potential to provide species-level accuracy. However, existing taxonomic identification algorithms are not optimized for the increased read length and error rate of long-read data. Here we present Emu, a novel approach that employs an expectation-maximization (EM) algorithm to generate taxonomic abundance profiles from full-length 16S rRNA reads. Results produced from one simulated data set and two mock communities prove Emu capable of accurate microbial community profiling while obtaining fewer false positives and false negatives than alternative methods. Additionally, we illustrate a real-world application of our new software by comparing clinical sample composition estimates generated by an established whole-genome shotgun sequencing workflow to those returned by full-length 16S sequences processed with Emu.
Homotopic contralesional excitation suppresses spontaneous circuit repair and global network reconnections following ischemic stroke
Authors: Bice Annie R. , Xiao Qingli , Kong Justin , Yan Ping , Rosenthal Zachary P. , Kraft Andrew W. , Smith Karen , Wieloch Tadeusz , Lee Jin-Moo , Culver Joseph P. , Bauer Adam Q. 
Published: May 2021

AbstractUnderstanding circuit-level changes that affect the brain’s capacity for plasticity will inform the design of targeted interventions for treating stroke recovery. We combine optogenetic photostimulation with optical neuroimaging to examine how contralesional excitatory activity affects cortical remodeling after stroke in mice. Following photothrombosis of left primary somatosensory forepaw (S1FP) cortex, mice received chronic excitation of right S1FP, a maneuver mimicking the use of the unaffected limb during recovery. Contralesional excitation suppressed perilesional S1FP remapping and was associated with abnormal patterns of evoked activity in the unaffected limb. Contralesional stimulation prevented the restoration of resting-state functional connectivity (RSFC) within the S1FP network, RSFC in several networks functionally-distinct from somatomotor regions, and resulted in persistent limb-use asymmetry. In stimulated mice, perilesional tissue exhibited suppressed transcriptional changes in several genes important for recovery. These results suggest that contralesional excitation impedes local and global circuit reconnection through suppression of several neuroplasticity-related genes after stroke.
Definitive Hematopoietic Stem Cells Minimally Contribute to Embryonic Hematopoiesis
Authors: Ulloa Bianca A , Habbsa Samima S , Potts Kathryn S. , Lewis Alana , McKinstry Mia , Payne Sara G. , Flores Julio , Nizhnik Anastasia , Norberto Maria Feliz , Mosimann Christian , Bowman Teresa V 
Published: May 2021

SUMMARYHematopoietic stem cells (HSCs) are rare cells that arise in the embryo and sustain adult hematopoiesis. Although the functional potential of nascent HSCs is detectable by transplantation, their native contribution during development is unknown, in part due to the overlapping genesis and marker gene expression with other embryonic blood progenitors. Using single cell transcriptomics, we defined gene signatures that distinguish nascent HSCs from embryonic blood progenitors. Applying a new lineage tracing approach, we selectively tracked HSC outputin situand discovered significantly delayed lymphomyeloid contribution. Using a novel inducible HSC injury model, we demonstrated a negligible impact on larval lymphomyelopoiesis following HSC depletion. HSCs are not merely dormant at this developmental stage as they showed robust regeneration after injury. Combined, our findings illuminate that nascent HSCs self-renew but display differentiation latency, while HSC-independent embryonic progenitors sustain developmental hematopoiesis. Understanding the differences among embryonic HSC and progenitor populations will guide improvedde novogeneration and expansion of functional HSCs.
A Coupled Flow-Thermoregulation Lumped Model to Investigate Cardiac Function
Authors: Deyranlou Amin , Revell Alistair , Keshmiri Amir 
Published: May 2021

AbstractLumped (zero-dimensional) technique is a robust and widely used approach to mathematically model and explore bulk behaviour of different physical phenomena in a lower expense. In modelling of cardio/cerebrovascular fluid dynamics, this technique facilitates the assessment of relevant metrics such as flow, pressure, and temperature at different locations over a large network/domain. Furthermore, they can be employed as boundary conditions in multiscale modelling of physiological flows. In this methodology paper, a lumped model for the cardiovascular flow simulation along with a two-node thermoregulation model are employed. The lumped models are built upon previous studies and are amended appropriately to focus on cardiac function. The output of the coupled model can either be used for assessing the cardiac function in different physiological conditions or it can provide the input data for other investigations. Noteworthy to mention that, the present model has been specifically developed for investigation on the effects of atrial fibrillation on cardiac performance.
An Omics Analysis Search and Information System (OASIS) for Enabling Biological Discovery in the Old Order Amish
Authors: Perry James A , Gaynor Brady J , Mitchell Braxton D , O’Connell Jeffrey R 
Published: May 2021

ABSTRACTThe “Omics Analysis Search and Information System” (OASIS), developed at the University of Maryland School of Medicine, enables discovery by allowing researchers to mine results from genome wide association studies (GWAS). When interesting signals are found, the research can immediately ask follow-up questions and get answers in real-time. OASIS provides this unique capability with a web-based, scientist-friendly search system and a variety of real-time analysis tools (linkage disequilibrium calculations, conditional analysis, and direct variant comparison) plus on-demand visualizations (boxplots, histograms, LocusZoom & Haploview plots, and pedigree charts). Because OASIS uses a web-based user interface, an understanding of programming or the UNIX operating system is not required. The OASIS application has been used to enable discovery from whole-exome, whole-genome, metabolome, transcriptome and methylome association results for Old Order Amish studies at the University of Maryland School of Medicine.
Metagenomics and Metatranscriptomics Suggest Pathways of 3-Chloroaniline Degradation in Wastewater Reactors
Authors: Seshan Hari , Santillan Ezequiel , Constancias Florentin , Chandra Segaran Uma Shankari , Williams Rohan B. H. , Wuertz Stefan 
Published: May 2021

AbstractBiological wastewater treatment systems are often affected by major shifts in influent quality, including the input of various toxic chemicals. Yet the mechanisms underlying adaptation of activated sludge process performance when challenged with a sustained toxin input are rarely studied in a controlled and replicated experimental setting. Three replicate bench-scale bioreactors were subjected to a chemical disturbance in the form of 3-chloroaniline (3-CA) over 132 days, after an acclimation period of 58 days, while three control reactors received no 3-CA input. Nitrification was initially affected by 3-CA but the microbial communities in all three treatment reactors adapted to biologically degrade 3-CA within three weeks of the experiment, resulting in partial nitrification recovery. Combining process and microbial community data from amplicon sequencing with potential functions gleaned from assembled metagenomics and metatranscriptomics data, two putative degradation pathways for 3-CA were identified. The first pathway proceeds via a phenol monooxygenase followed by ortho-cleavage of the aromatic ring, and the second one involves a benzoate dioxygenase and subsequent meta-cleavage of the aromatic ring. The generaGemmatimonas,OLB8, andTaibaiellacorrelated significantly with 3-CA degradation. Metagenome-assembled genome data also showed the genusOLB8to be differentially enriched in treatment reactors, making it a strong candidate as 3-CA degrader. Using replicated reactors, this study has demonstrated the impact of a sustained stress on the activated sludge community and processes carried out by its members, followed by process recovery. By a combination of techniques, we showed that microbial communities can develop degradative capacity following a sustained xenobiotic input, and that targeted culture-independent approaches can suggest plausible mechanisms for 3-CA degradation and identify the taxa potentially contributing to it.
A DUF1068 protein acts as a pectin biosynthesis scaffold and maintains Golgi morphology and cell adhesion in Arabidopsis
Authors: Lathe Rahul S. , McFarlane Heather E. , Khan Ghazanfar Abbas , Ebert Berit , Ramírez-Rodríguez Eduardo Antonio , Noord Niels , Bhalerao Rishikesh , Persson Staffan 
Published: May 2021

ABSTRACTAdjacent plant cells are connected by specialized cell wall regions, called middle lamellae, which influence critical agricultural characteristics, including fruit ripening and organ abscission. Middle lamellae are enriched in pectin polysaccharides, specifically homogalacturonan (HG). Here, we identify a plant-specific Arabidopsis DUF1068 protein, called NKS1, that is required for middle lamellae integrity and cell adhesion. NKS1 localises to the Golgi apparatus and loss of the protein results in changes to Golgi structure and function. Thenks1mutants also display HG deficient phenotypes, including reduced seedling growth, changes to cell wall composition, and tissue integrity defects. These phenotypes are identical to those of the HG deficient mutantsqua1andqua2. Notably, NKS1 physically interacts with both QUA1 and QUA2, and genetic interaction analyses reveal that they work in the same pathway. Based on these results we propose that NKS1 works as a scaffold for HG synthesis and that such scaffolding is important to support Golgi function and the organization of the pectin synthesis machinery.
Soils and sediments host novel archaea with divergent monooxygenases implicated in ammonia oxidation
Authors: Diamond Spencer , Lavy Adi , Crits-Christoph Alexander , Carnevali Paula B. Matheus , Sharrar Allison , Williams Kenneth H. , Banfield Jillian F. 
Published: May 2021

ABSTRACTCopper membrane monooxygenases (CuMMOs) play critical roles in the global carbon and nitrogen cycles. Organisms harboring these enzymes perform the first, and rate limiting, step in aerobic oxidation of ammonia, methane, or other simple hydrocarbons. Within archaea, only organisms in the order Nitrososphaerales (Thaumarchaeota) encode CuMMOs, which function exclusively as ammonia monooxygenases. From grassland and hillslope soils and aquifer sediments, we identified 20 genomes from distinct archaeal species encoding divergent CuMMO sequences. These archaea are phylogenetically clustered in a previously unnamed Thermoplasmatota order, herein named the Ca. Angelarcheales. The CuMMO proteins in Ca. Angelarcheales are more similar in structure to those in ammonia-oxidizing archaea than those of bacteria, and they contain all functional residues required for activity. Similarly to the Nitrososphaerales, Ca. Angelarcheales genomes are significantly enriched in blue copper proteins (BCPs) relative to sibling lineages, including plastocyanin-like electron carriers and divergent nitrite reductase-like (nirK) 2-domain cupredoxin proteins co-located with electron transport machinery. Angelarcheales do not have identifiable genes for methanol oxidation or carbon fixation, encode significant capacity for peptide/amino acid uptake and degradation, and share numerous electron transport mechanisms with the Nitrososphaerales. In the studied soils and sediments Ca. Angelarcheales were at least as abundant as ammonia-oxidizing Nitrososphaerales. Thus, we predict that Angelarcheales live a mixotrophic lifestyle based on oxidation of ammonia liberated from peptide and amino acid degradation. This work expands the known diversity of Thermoplasmatota and of CuMMO enzymes in archaea and suggests that these organisms are important and previously unaccounted for contributors to nitrogen cycling.