bluuebunny/crossref_metadata_2025_split huggingface dataset:
ProSelfLC: Progressive Self Label Correction Towards A Low-Temperature Entropy State
Authors: Wang Xinshao , Hua Yang , Kodirov Elyor , Mukherjee Sankha Subhra , Clifton David A. , Robertson Neil M. 
Published: July 2022

AbstractTo train robust deep neural networks (DNNs), we systematically study several target modification approaches, which include output regularisation, self and non-self label correction (LC). Three key issues are discovered: (1) Self LC is the most appealing as it exploits its own knowledge and requires no extra models. However, how to automatically decide the trust degree of a learner as training goes is not well answered in the literature. (2) Some methods penalise while the others reward low-entropy predictions, prompting us to ask which one is better. (3) Using the standard training setting, a trained network is of low confidence when severe noise exists, making it hard to leverage its high-entropy self knowledge.To resolve the issue (1), taking two well-accepted propositions–deep neural networks learn meaningful patterns before fitting noise and minimum entropy regularisation principle–we propose a novel end-to-end method named ProSelfLC, which is designed according to learning time and entropy. Specifically, given a data point, we progressively increase trust in its predicted label distribution versus its annotated one if a model has been trained for enough time and the prediction is of low entropy (high confidence). For the issue (2), according to ProSelfLC, we empirically prove that it is better to redefine a meaningful low-entropy status and optimise the learner toward it. This serves as a defence of entropy minimisation. To address the issue (3), we decrease the entropy of self knowledge using a low temperature before exploiting it to correct labels, so that the revised labels redefine a low-entropy target state.We demonstrate the effectiveness of ProSelfLC through extensive experiments in both clean and noisy settings, and on both image and protein datasets. Furthermore, our source code is available athttps://github.com/XinshaoAmosWang/ProSelfLC-AT.
EasyGuide plasmids support in vivo assembly of gRNAs for CRISPR/Cas9 applications in Saccharomyces cerevisiae
Authors: Jacobus Ana P. , Barreto Joneclei A. , de Bem Lucas S. , Menegon Yasmine A. , Fier Ícaro , Bueno João G.R. , dos Santos Leandro V. , Gross Jeferson 
Published: July 2022

ABSTRACTMost CRISPR/Cas9 applications in yeast rely on a plasmid-based expression of Cas9 and its guide RNA (gRNA) containing a 20-nucleotides (nts) spacer tailored to each genomic target. The lengthy assembly of this customized gRNA requires at least 3–5 days for its pre-cloning in Escherichia coli, purification, validation, and co-transformation with Cas9 into a yeast strain. Here, we constructed a series of 12 EasyGuide plasmids to simplify CRISPR/Cas9 applications in Saccharomyces cerevisiae. The new vectors provide templates for generating PCR fragments that can assemble up to six functional gRNAs directly into yeasts via homologous recombination between the 20-nts spacers. By dispensing pre-cloning in E. coli, yeast in vivo gRNA assembly significantly reduces the CRISPR/Cas9 experimental workload. A highly efficient yeast genome editing procedure, involving PCR amplification of gRNAs and donors, followed by their transformation into a Cas9-expressing strain, can be easily accomplished in a single day.
pH Effect on Ligand Binding to an Enzyme Active Site
Authors: Singh Kushal , Muttathukattil Aswathy N. , Singh Prashant Chandra , Reddy Govardhan 
Published: July 2022

AbstractUnderstanding the mechanism of ligands binding to their protein targets and the influence of various factors governing the binding thermodynamics is essential for rational drug design. The solution pH is one of the critical factors that can influence ligand binding to a protein cavity, especially in enzymes whose function is sensitive to the pH. Using computer simulations, we studied the pH effect on the binding of a guanidinium ion (Gdm+) to the active site of hen-egg white lysozyme (HEWL). HEWL serves as a model system for enzymes with two acidic residues in the active site and ligands with Gdm+ moieties, which can bind to the active sites of such enzymes and are present in several approved drugs treating various disorders. The computed free energy surface (FES) shows that Gdm+ binds to the HEWL active site using two dominant binding pathways populating multiple intermediates. We show that the residues close to the active site that can anchor the ligand could play a critical role in ligand binding. Using a Markov state model, we quantified the lifetimes and kinetic pathways connecting the different states in the FES. The protonation and deprotonation of the acidic residues in the active site in response to the pH change strongly influence the Gdm+ binding. There is a sharp jump in the ligand-binding rate constant when the pH approaches the largest pKa of the acidic residue present in the active site. The simulations reveal that, at most, three Gdm+ can bind at the active site, with the Gdm+ bound in the cavity of the active site acting as a scaffold for the other two Gdm+ ions binding. This result implies the possibility of designing single large molecules containing multiple Gdm+ moieties that can have high binding affinities to inhibit the function of enzymes with two acidic residues in their active site.
Drug dependence in cancer is exploitable by optimally constructed treatment holidays
Authors: Maltas Jeff , Singleton Katherine R. , Wood Kris C. , Wood Kevin B. 
Published: July 2022

AbstractRecent work in cell culture models, animal models, and human patients indicates that cancers with acquired resistance to a drug can become simultaneously dependent upon the presence of that drug for survival. This drug dependence offers a potential avenue for improving treatments aimed at slowing resistance, yet relatively little is known about the frequency with which drug dependence arises, the mechanisms underlying that dependence, and how drug schedules might be tuned to optimally exploit drug dependence. In this work, we address these open questions using a combination of laboratory evolution, in vitro experiments, and simple mathematical models. First, we used laboratory evolution to select more than 100 resistant BRAF mutant melanoma cell lines with acquired resistance to BRAF, MEK, or ERK inhibitors. We found that nearly half of these lines exhibit drug dependence, and the dependency response is associated with EGFR-driven senescence induction, but not apoptosis, following drug withdrawal. Then, using melanoma populations with evolved resistance to the BRAF inhibitor PLX4720, we showed that drug dependence can be leveraged to dramatically reduce population growth when treatment strategies include optimally chosen drug-free “holidays”. On short timescales, the duration of these holidays depends sensitively on the composition of the population, but for sufficiently long treatments it depends only on a single dimensionless parameter (γ) that describes how the growth rates of each cell type depend on the different treatment environments. Experiments confirm that the optimal holiday duration changes in time–with holidays of different durations leading to optimized treatments on different timescales. Furthermore, we find that the presence of “non-dependent” resistant cells does not change the optimal treatment schedule but leads to a net increase in population size. Finally, we show that even in the absence of detailed information about the composition and growth characteristics of cellular clones within a population, a simple adaptive therapy protocol can produce near-optimal outcomes using only measurements of total population size, at least when these measurements are sufficiently frequent. As a whole, these results may provide a stepping-stone toward the eventual development of evolution-inspired treatment strategies for drug dependent cancers.
Morphological and genetic diversity of maize landraces along an altitudinal gradient in the Southern Andes
Authors: Rivas Juan G. , Gutierrez Angela V. , Defacio Raquel A. , Schimpf Jorge , Vicario Ana L. , Hopp H. Esteban , Paniego Norma B. , Lia Veronica V. 
Published: July 2022

AbstractMaize (Zea mays ssp. mays) is a major cereal crop worldwide and is traditionally or commercially cultivated almost all over the Americas. The northwestern region of Argentina (NWA) constitutes one of the main diversity hotspots of the Southern Andes, with contrasting landscapes and a large number of landraces. Despite the extensive collections performed by the “Banco Activo de Germoplasma INTA Pergamino, Argentina” (BAP), most of them have not been characterized yet. Here we report the morphological and molecular evaluation of 30 accessions collected from NWA, along an altitudinal gradient between 1120 and 2950 meters above sea level (masl). Assessment of morphological variation in a common garden allowed the discrimination of two groups, which differed mainly in endosperm type and overall plant size. Although the groups retrieved by the molecular analyses were not consistent with morphological clusters, they showed a clear pattern of altitudinal structuring. Affinities among accessions were not in accordance with racial assignments. Overall, our results revealed that there are two maize gene pools co-existing in NWA, probably resulting from various waves of maize introduction in pre-Columbian times as well as from the adoption of modern varieties by local farmers.In conclusion, the NWA maize landraces preserved at the BAP possess high morphological and molecular variability. Our results highlight their potential as a source of diversity for increasing the genetic basis of breeding programs and provide useful information to guide future sampling and conservation efforts.
The mosquito vectors that sustained malaria transmission during the Magude project despite the combined deployment of indoor residual spraying, insecticide-treated nets and mass-drug administration
Authors: Montoya Lucia Fernandez , Martí-Soler Helena , Máquina Mara , Comiche Kiba , Cuamba Inocencia , Alafo Celso , Koekemoer Lizette L. , Sherrard-Smith Ellie , Bassat Quique , Galatas Beatriz , Aide Pedro , Cuamba Nelson , Jotamo Dulcisaria , Saúte Francisco , Paaijmans Krijn P. 
Published: July 2022

AbstractThe “Magude project” aimed but failed to interrupt local malaria transmission in Magude district, southern Mozambique, by using a comprehensive package of interventions, including indoor residual spraying (IRS), pyrethroid-only long-lasting insecticide treated nets (LLINs) and mass-drug administration (MDA). Here we present detailed information on the vector species that sustained malaria transmission, their association with malaria incidence and behaviors, and their amenability to the implemented control interventions. Mosquitoes were collected monthly between May 2015 and October 2017 in six sentinel sites in Magude district, using CDC light traps both indoors and outdoors. Anopheles arabiensis was the main vector during the project, while An. funestus s.s., An. merus, An. parensis and An. squamosus likely played a secondary role. The latter two species have never previously been found positive for Plasmodium falciparum in southern Mozambique. The intervention package successfully reduced vector sporozoite rates in all species throughout the project. IRS was effective in controlling An. funestus s.s. and An. parensis, which virtually disappeared after its first implementation, but less effective at controlling An. arabiensis. Despite suboptimal use, LLINs likely provided significant protection against An. arabiensis and An. merus that sought their host largely indoors when people where in bed. Adding IRS on top of LLINs and MDA likely added value to the control of malaria vectors during the Magude project. Future malaria elimination attempts in the area could benefit from i) increasing the use of LLINs, ii) using longer-lasting IRS products to counteract the increase in vector densities observed towards the end of the high transmission season, and iii) a higher coverage with MDA to reduce the likelihood of human infection. However, additional interventions targeting vectors that survive IRS and LLINs b,y e.g. biting outdoors or indoors before people go to bed, will be likely needed to achieve local malaria elimination.
Retrograde axonal autophagy and endocytic pathways are parallel but separate in neurons
Authors: Kulkarni Vineet Vinay , Stempel Max Henry , Anand Anip , Sidibe David Kader , Maday Sandra 
Published: July 2022

ABSTRACTAutophagy and endocytic trafficking are two key pathways that regulate the composition and integrity of the neuronal proteome. Alterations in these pathways are sufficient to cause neurodevelopmental and neurodegenerative disorders. Thus, defining how autophagy and endocytic pathways are organized in neurons remains a key area of investigation. These pathways share many features and converge on lysosomes for cargo degradation, but what remains unclear is the degree to which the identity of each pathway is preserved in each compartment of the neuron. Here, we elucidate the degree of intersection between autophagic and endocytic pathways in axons of primary neurons. Using microfluidic chambers, we labeled newly-generated bulk endosomes and signaling endosomes in the distal axon, and systematically tracked their trajectories, molecular composition, and functional characteristics relative to autophagosomes. We find that newly-formed endosomes and autophagosomes both undergo retrograde transport in the axon, but as distinct organelle populations. Moreover, these pathways differ in their degree of acidification and association with molecular determinants of organelle maturation. These results suggest that the identity of autophagic and newly endocytosed organelles is preserved for the length of the axon. Lastly, we find that expression of a pathogenic form of α-synuclein, a protein enriched in presynaptic terminals, increases merging between autophagic and endocytic pathways. Thus, aberrant merging of these pathways may represent a mechanism contributing to neuronal dysfunction in Parkinson’s disease and related α-synucleinopathies.SIGNIFICANCE STATEMENTAutophagy and endocytic trafficking are retrograde pathways in neuronal axons that fulfill critical degradative and signaling functions. These pathways share many features and converge on lysosomes for cargo degradation, but the extent to which the identity of each pathway is preserved in axons is unclear. We find that autophagosomes and endosomes formed in the distal axon undergo retrograde transport to the soma in parallel but separate pathways. These pathways also have distinct maturation profiles along the mid-axon, further highlighting differences in the potential fate of transported cargo. Strikingly, expression of a pathogenic variant of α-synuclein increases merging between autophagic and endocytic pathways, suggesting that mis-sorting of axonal cargo may contribute to neuronal dysfunction in Parkinson’s disease and related α-synucleinopathies.
In vivo spatiotemporal dynamics of astrocyte reactivity following neural electrode implantation
Authors: Savya Sajishnu P , Li Fan , Lam Stephanie , Wellman Steven M. , Stieger Kevin C. , Chen Keying , Eles James R. , Kozai Takashi D.Y. 
Published: July 2022

AbstractBrain computer interfaces (BCIs), including penetrating microelectrode arrays, enable both recording and stimulation of neuronal cells. However, device implantation inevitably causes injury to brain tissue and induces a foreign body response, leading to reduced recording performance and stimulation efficacy. Astrocytes in the healthy brain play multiple roles including regulating energy metabolism, homeostatic balance, transmission of neural signals, and neurovascular coupling. Following an insult to the brain, they are activated and observed to gather around the site of injury. These reactive astrocytes have been regarded as one of the main contributors to the formation of a glial scar which affects the performance of microelectrode arrays. This study investigates the dynamics of astrocytes within the first 2 weeks after implantation of an intracortical microelectrode into the mouse brain using two-photon microscopy. From our observation astrocytes are highly dynamic during this period, exhibiting patterns of process extension, soma migration, morphological activation, and device encapsulation that are spatiotemporally distinct from other glial cells, such as microglia or oligodendrocyte precursor cells. This detailed characterization of astrocyte reactivity will help to better understand the tissue response to intracortical devices and lead to the development of more effective intervention strategies to improve the functional performance neural interfacing technology.
Responses of thein vitroturtle brain to visual and auditory stimuli during severe hypoxia
Authors: Ariel Michael , Ahuja Shivika , Warren Daniel E. 
Published: July 2022

AbstractNorth American pond turtles (Emydidae) are renowned for their ability to survive extreme hypoxia and anoxia, which enables several species to overwinter in ice-locked, anoxic freshwater ponds and bogs for months. Centrally important for surviving these conditions is a profound metabolic suppression, which enables ATP demands to be met entirely with glycolysis. Despite this, turtles have occasionally been observed exploring their natural and laboratory environments while anoxic and can still respond to sensory stimuli. To better understand whether anoxia limits a special sensory function, we recorded evoked potentials in a reduced brain preparation,in vitro,that was perfused with severely hypoxic artificial cerebral spinal fluid (aCSF). For recordings of visual responses, an LED light was flashed onto retinal eyecups while evoked potentials were recorded from the retina or the optic tectum. For recordings of auditory responses, a piezo motor-controlled glass actuator vibrated the tympanic membrane while evoked potentials were recorded from the cochlear nuclei. We found that visual responses decreased even with moderately hypoxic perfusate (aCSF PO2= 30-60 torr) and completely abolished under severe hypoxia. In contrast, the evoked response within the cochlear nuclei was unattenuated with severe hypoxia (aCSF PO2< 20 torr). These data provide further support that pond turtles have a limited ability to sense visual information in their environment even while moderately hypoxic, but that auditory input may become a principal avenue of sensory perception during extreme diving in this species.Summary StatementSevere hypoxia attenuates the visual, but not auditory responses in a reduced brain preparation from a pond turtle.
A biophysical minimal model to investigate age-related changes in CA1 pyramidal cell electrical activity
Authors: McKiernan Erin C. , Herrera-Valdez Marco A. , Marrone Diano F. 
Published: July 2022

AbstractAging is a physiological process that is still poorly understood, especially with respect to effects on the brain. There are open questions about aging that are difficult to answer with an experimental approach. Underlying challenges include the difficulty of recordingin vivosingle cell and network activity simultaneously with submillisecond resolution, and brain compensatory mechanisms triggered by genetic, pharmacologic, or behavioral manipulations. Mathematical modeling can help address some of these questions by allowing us to fix parameters that cannot be controlled experimentally and investigate neural activity under different conditions. We present a biophysical minimal model of CA1 pyramidal cells (PCs) based on general expressions for transmembrane ion transport derived from basic thermodynamical principles. The model allows directly varying the contribution of ion channels by changing their number. By analyzing the dynamics of the model, we find parameter ranges that reproduce the variability in electrical activity seen in PCs. In addition, increasing the L-type Ca2+channel expression in the model reproduces age-related changes in excitability that are qualitatively and quantitatively similar to those observed in PCs from aged animals.
Recombination rate inference via deep learning is limited by sequence diversity
Authors: Johnson Mackenzie M. , Wilke Claus O. 
Published: July 2022

AbstractA common inference task in population genetics is to estimate recombination rate from multiple sequence alignments. Traditionally, recombination rate estimators have been developed from biologically-informed, statistical models, but more recently deep learning models have been employed for this task. While deep learning approaches offer unique advantages, their performance is inconsistent across the range of potential recombination rates. Here, we generate and characterize data sets (genotype alignments with known recombination rates) for use by deep learning estimators and assess how their features limit estimator performance. We find that certain input parameter regimes produce genotype alignments with low sequence diversity, which are inherently information-limited. We next test how estimator performance is impacted by training and evaluating neural networks on data sets with varying degrees of diversity. The inclusion of genotype alignments with low diversity at high frequency results in considerable performance declines across two different network architectures. In aggregate, our results suggest that genotype alignments have inherent information limits when sequence diversity is low, and these limitations need to be considered both when training deep learning recombination rate estimators and when using them in inference applications.
Quantifying trade-offs in the choice of ribosomal barcoding markers for fungal amplicon sequencing: a case study on the grapevine trunk mycobiome
Authors: Monod Vinciane , Hofstetter Valérie , Zufferey Vivian , Viret Olivier , Gindro Katia , Croll Daniel 
Published: July 2022

AbstractThe evolution of sequencing technology and multiplexing has rapidly expanded our ability to characterize fungal diversity in the environment. However, obtaining an unbiased assessment of the fungal community using ribosomal markers remains challenging. Longer amplicons were shown to improve taxonomic resolution and resolve ambiguities by reducing the risk of spurious operational taxonomic units. We examined the implications of barcoding strategies by amplifying and sequencing two ribosomal DNA fragments. We analyzed the performance of the full internal transcribed spacer (ITS) and a longer fragment including also a part of the 28S replicated on 60 grapevine trunk core samples. Grapevine trunks harbor highly diverse fungal communities with implications for disease development. Using identical handling, amplification and sequencing procedures, we obtained higher sequencing depths for the shorter ITS amplicon. Despite the more limited access to polymorphism, the overall diversity in amplified sequence variants was higher for the shorter ITS amplicon. We detected no meaningful bias in the phylogenetic composition due to the amplicon choice across analyzed samples. Despite the increased resolution of the longer ITS-28S amplicon, the higher and more consistent yields of the shorter amplicons produced a clearer resolution of the fungal community of grapevine stem samples. Our study highlights that the choice of ribosomal amplicons should be carefully evaluated and adjusted according to specific goals.