bluuebunny/crossref_metadata_2025_split huggingface dataset:
CRISPR Knock-in Designer: automatic oligonucleotide design software to introduce point mutations using CRISPR/Cas9
Authors: Prykhozhij Sergey V. , Rajan Vinothkumar , Ban Kevin , Berman Jason N. 
Published: April 2021

AbstractKnock-in of precise point mutations into protein-coding genes has been one of the earliest and most important applications of Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/Cas9. The ability to perform such precise gene editing is crucial to interrogate the function of specific protein residues and to create models of human diseases caused by protein amino acid changes. The homologous protein residues can be mutated in model animal species, and the consequences of these mutations can be studied, leading to a better understanding of the disease in question. Design of point mutation knock-in strategies has been a combination of manual steps assisted by several computational tools resulting in a time-consuming process and preventing a single rapid and integrated solution. We have therefore designed CRISPR Knock-in Designer, which can perform rapid and automatic design of point mutation knock-in DNA oligonucleotides upon provision of the mutation, a guide RNA, and essential identifier or sequence information. The tool supports most experimentally established CRISPR types and has multiple options for the resulting oligonucleotides to satisfy the needs of most users. We also provide allele-specific PCR-based and restriction enzyme-based genotyping strategies as part of the program output. CRISPR Knock-in Designer adjusts to the genomic context of any target codon and tries to design knock-in strategies when a codon straddles two exons, a situation we explored in whole genomes of several model species. CRISPR Knock-in Designer output can also be adapted for use with some of the newer Prime Editing design tools to facilitate the introduction of a specific mutation sequence using this advanced technology.
Detection of sleep apnea from single-channel electroencephalogram (EEG) using an explainable convolutional neural network
Authors: Barnes Lachlan D , Lee Kevin , Kempa-Liehr Andreas W , Hallum Luke E 
Published: April 2021

AbstractSleep apnea (SA) is a common disorder involving the cessation of breathing during sleep. It can cause daytime hypersomnia, accidents, and, if allowed to progress, serious, chronic conditions. Continuous positive airway pressure is an effective SA treatment. However, long waitlists impede timely diagnosis; overnight sleep studies involve trained technicians scoring a polysomnograph, which comprises multiple physiological signals including multi-channel electroencephalography (EEG). Therefore, it is important to develop simplified and automated approaches to detect SA. We have developed an explainable convolutional neural network (CNN) to detect SA from single-channel EEG recordings which generalizes across subjects. The network architecture consisted of three convolutional layers. We tuned hyperparameters using the Hyperband algorithm, optimized parameters using Adam, and quantified network performance with subjectwise 10-fold cross-validation. Our CNN performed with an accuracy of 76.7% and a Matthews correlation coefficient (MCC) of 0.54. This performance was reliably above the conservative baselines of 50% (accuracy) and 0.0 (MCC). To explain the mechanisms of our trained network, we used critical-band masking (CBM): after training, we added bandlimited noise to test recordings; we parametrically varied the noise band center frequency and noise intensity, quantifying the deleterious effect on performance. We reconciled the effects of CBM with lesioning, wherein we zeroed the trained network’s 1st-layer filter kernels in turn, quantifying the deleterious effect on performance. These analyses indicated that the network learned frequency-band information consistent with known SA biomarkers, specifically, delta and beta band activity. Our results indicate single-channel EEG may have clinical potential for SA diagnosis.
Single-cell atlas of progressive supranuclear palsy reveals a distinct hybrid glial cell population
Authors: Sharma Abhijeet , Song Won-Min , Farrell Kurt , Whitney Kristen , Zhang Bin , Crary John F. , Pereira Ana C. 
Published: April 2021

AbstractProgressive supranuclear palsy (PSP) is a neurodegenerative disorder whose molecular complexity at a single cell level has not been evaluated. Here we analyzed 45,559 high quality nuclei from the subthalamic nucleus and associated basal ganglia regions from post-mortem human PSP brains with varying degrees of tau pathology compared to controls (n=3 per group). We identified novel astrocyte-oligodendrocyte hybrid cell populations that overexpress neurotropic factors in conjunction with suppression of the unfolded protein response pathway. Notably, trajectory analysis identified subpopulations of hybrid cells with distinct astrocytic, oligodendrocytic and hybrid molecular states that change from a neuroprotective hybrid cell to an astrocytic cell with impaired homeostatic function in PSP. Our single nucleus transcriptomic data provides insights into the cell-type-specific contributions to the disease for investigating the molecular and cellular basis of PSP.
Structural Insights Into the Initiation and Elongation of Ubiquitination by Ubr1
Authors: Pan Man , Zheng Qingyun , Wang Tian , Liang Lujun , Mao Junxiong , Zuo Chong , Ding Ruichao , Ai Huasong , Xie Yuan , Si Dong , Yu Yuanyuan , Liu Lei , Zhao Minglei 
Published: April 2021

AbstractThe N-end rule pathway was one of the first ubiquitin (Ub)-dependent degradation pathways to be identified. Ubr1, a single-chain E3 ligase, targets proteins bearing a destabilizing residue at the N-terminus (N-degron) for rapid K48-linked ubiquitination and proteasome-dependent degradation. How Ubr1 catalyses the initiation of ubiquitination on the substrate and elongation of the Ub chain in a linkage-specific manner through a single E2 ubiquitin-conjugating enzyme (Ubc2) remains unknown. Here, we report the cryo-electron microscopy structures of two complexes representing the initiation and elongation intermediates of Ubr1 captured using chemical approaches. In these two structures, Ubr1 adopts different conformations to facilitate the transfer of Ub from Ubc2 to either an N-degron peptide or a monoubiquitinated degron. These structures not only reveal the architecture of the Ubr1 complex but also provide mechanistic insights into the initiation and elongation steps of ubiquitination catalysed by Ubr1.
Nanoscale 3D DNA tracing in single human cells visualizes loop extrusion directly in situ
Authors: Beckwith K.S. , Ødegård-Fougner Ø. , Morero N.R. , Barton C. , Schueder F. , Tang W. , Alexander S. , Peters J-M. , Jungmann R. , Birney E. , Ellenberg J. 
Published: April 2021

SummaryThe spatial organization of the genome is essential for its functions, including gene expression, DNA replication and repair, as well as chromosome segregation. Biomolecular condensates and loop extrusion have been proposed as the principal driving forces that underlie the formation of chromatin compartments and topologically associating domains, respectively. However, whether the actual 3D-fold of DNA in single cells is consistent with these mechanisms has been difficult to address in situ. Here, we present LoopTrace, a workflow for nanoscale 3D imaging of the genome sequence in structurally well-preserved nuclei in single human cells. Tracing the in situ structure of DNA in thousands of individual cells reveals that genomic DNA folds as a flexible random coil in the absence of loop extruding enzymes such as Cohesin. In the presence of Cohesin and its boundary factor CTCF, reproducibly positioned loop structures dominate the folds, while Cohesin alone leads to randomly positioned loops. The 3D structure and size variability of DNA loops we observe in a large number of single cells allow us to formulate a data-constrained computational model of genomic DNA folding that explains how sparse and dynamic loops in single cells lead to the emergence of compact topological domains in averages of cell populations.
Direct neural evidence for the contrastive roles of the complementary learning systems in adult acquisition of native vocabulary
Authors: Gore Katherine R. , Woollams Anna M. , Bruehl Stefanie , Halai Ajay D. , Lambon Ralph Matthew A. 
Published: April 2021

AbstractThe Complementary Learning Systems (CLS) theory provides a powerful framework for considering the acquisition, consolidation and generalisation of new knowledge. We tested this proposed neural division of labour in adults through an investigation of the consolidation and long-term retention of newly-learned native vocabulary with post-learning functional neuroimaging. Newly-learned items were compared to two conditions: (i) previously known items to highlight the similarities and differences with established vocabulary; and (ii) unknown/untrained items to provide a control for non-specific perceptual and motor-speech output. Consistent with the CLS, retrieval of newly-learned items was supported by a combination of regions associated with episodic memory (including left hippocampus) and the language-semantic areas that support established vocabulary (left inferior frontal gyrus and left anterior temporal lobe). Furthermore, there was a shifting division of labour across these two networks in line with the items’ consolidation status; faster naming was associated with more activation of language-semantic areas and lesser activation of episodic memory regions. Hippocampal activity during naming predicted more than half the variation in naming retention six months later.
Dynein activation in vivo is regulated by the nucleotide states of its AAA3 domain
Authors: Qiu Rongde , Zhang Jun , Rotty Jeremy D. , Xiang Xin 
Published: April 2021

SummaryCytoplasmic dynein is activated by dynactin and cargo adapters in vitro, and the activation also needs LIS1 (Lissencephaly 1) in vivo. How this process is regulated remains unclear. Here we found inAspergillus nidulansthat a dynein AAA4 arginine-finger mutation bypasses the requirement of LIS1 for dynein activation driven by the early endosomal adapter HookA. As the AAA4 arginine-finger is implicated in AAA3 ATP hydrolysis, we examined AAA3 mutants defective in ATP binding and hydrolysis respectively. Astonishingly, blocking AAA3 ATP hydrolysis allows dynein activation by dynactin in the absence of LIS1 or HookA. As a consequence, dynein accumulates at microtubule minus ends while early endosomes stay near the plus ends. On the other hand, blocking AAA3 ATP binding abnormally prevents LIS1 from being dissociated from dynein upon motor activation. Thus, the AAA3 ATPase cycle regulates the coordination between dynein activation and cargo binding as well as the dynamic dynein-LIS1 interaction.
VHL ligand binding increases intracellular level of VHL
Authors: Frost Julianty , Rocha Sonia , Ciulli Alessio 
Published: April 2021

AbstractThe von–Hippel Lindau (VHL) protein is a tumour suppressor protein frequently mutated in the VHL disease, which functions as substrate recognition subunit of a Cul2 E3 ubiquitin ligase (CRL2VHL). CRL2VHLplays an important role in oxygen sensing, by binding and targeting Hypoxia Inducible Factor-alpha subunits (HIF-alpha) for ubiquitination and degradation. VHL is also commonly hijacked by heterobifunctional degrader molecules known as proteolysis-targeting chimeras (PROTACs). In previous work we reported the structure-based design and functional characterisation of VHL inhibitors (VH032 and VH298) that induce the HIF response in cells. Here, we use unbiased quantitative mass spectrometry to identify the proteomic changes elicited by the VHL inhibitor and compare this to hypoxia or broad-spectrum prolyl-hydroxylase domain (PHD) enzyme inhibitor IOX2. Our results demonstrate the VHL inhibitor selectively activates the HIF response that is also present in the hypoxia- and IOX2-induced proteomic changes. Interestingly, VHL inhibitors were found to selectively upregulate a single protein, which is VHL itself. Our analysis revealed that this occurs via protein stabilisation of VHL isoforms and not via changes in transcript levels. Increased VHL levels upon VH298 treatment resulted in turn to reduced levels of HIF-1α protein. Our results demonstrate the high specificity of VHL inhibitors and suggest that use of these inhibitors would not produce overtly side effects due to prolonged HIF stabilisation. They also exemplify the concept that small-molecule binding induced protein stabilisation can increase protein levels inside cells.
Development of the GM(1,1,⊗b) model with a trapezoidal possibility function and its application
Authors: Li Shuliang , Gong Ke , Zeng Bo , Zhou Wenhao , Zhang Zhouyi , Li Aixing , Zhang Li 
Published: April 2021

PurposeThe purpose of this paper is to overcome the weakness of the traditional model, in which the grey action quantity is a real number and thus leads to a “unique solution” and to build the model with a trapezoidal possibility degree function.Design/methodology/approachUsing the system input and output block diagram of the model, the interval grey action quantity is restored under the condition of insufficient system influencing factors, and the trapezoidal possibility degree function is formed. Based on that, a new model able to output non-unique solutions is constructed.FindingsThe model satisfies the non-unique solution principle of the grey theory under the condition of insufficient information. The model is compatible with the traditional model in structure and modelling results. The validity and practicability of the new model are verified by applying it in simulating the ecological environment water consumption in the Yangtze River basin.Practical implicationsIn this study, the interval grey number form of grey action quantity is restored under the condition of insufficient system influencing factors, and the unique solution to the problem of the traditional model is solved. It is of great value in enriching the theoretical system of grey prediction models.Social implicationsTaking power consumption as an example, the accurate prediction of the future power consumption level is related to the utilization efficiency of the power infrastructure investment. If the prediction of the power consumption level is too low, it will lead to the insufficient construction of the power infrastructure and the frequent occurrence of “power shortage” in the power industry. If the prediction is too high, it will lead to excessive investment in the power infrastructure. As a result, the overall surplus of power supply will lead to relatively low operation efficiency. Therefore, building an appropriate model for the correct interval prediction is a better way to solve such problems. The model proposed in this study is an effective one to solve such problems.Originality/valueA new grey prediction model with its interval grey action quantity based on the trapezoidal possibility degree function is proposed for the first time.
Unpacking the SEC’s new disgorgement powers
Authors: Ryan Russ , Baughman Matthew H. , Lawrence Carmen J. , Lipson Aaron W. , Walker Richard H. , Rapoport Jessica , Barry Katie , Hiers Scott 
Published: April 2021

Purpose
To analyze the impact of recent legislation that amended the Securities Exchange Act of 1934 to expressly empower the U.S. Securities and Exchange Commission (SEC) to seek disgorgement in federal district court proceedings and to codify applicable statutes of limitations.

Design/methodology/approach
This article provides an overview of the authors’ prior work analyzing courts’ treatment of SEC disgorgement and summarizes how the scope of the remedy has evolved since Kokesh v. SEC (2017). Then, the article analyzes the changes to the Securities Exchange Act of 1934 contained in Section 6501 the 2021 National Defense Authorization Act (NDAA), which statutorily empowered the SEC to seek and obtain disgorgement in federal court actions. Finally, the authors discuss the impact of the legislation on the Supreme Court’s decisions in Kokesh and Liu v. SEC (2020).

Findings
The availability and appropriateness of SEC disgorgement have been the subject of vigorous debate. Just as courts began to iron out the contours of SEC disgorgement in the wake of Kokesh and Liu, Congress intervened by granting to the SEC explicit statutory authority to seek a remedy traditionally obtained at equity. In passing this legislation, Congress answered some questions that remained after Liu but also raised many new ones. These new questions will likely take years to resolve through subsequent litigation and potentially additional legislation.

Originality/value
Original, practical analysis and guidance from experienced lawyers in financial services regulatory and enforcement practices, many of whom have previously worked in the SEC’s Division of Enforcement.
Getting critical with disciplinary literacy: a read aloud strategy
Authors: Wrenn Melissa , Gallagher Jennifer L. 
Published: April 2021

PurposeThe purpose of this article is to explain and demonstrate a critical disciplinary read aloud strategy that has both an equity goal and a social studies goal.Design/methodology/approachThe authors begin by explaining background information on read alouds and critical disciplinary literacy. Then, the authors explain the four steps in the critical disciplinary literacy read aloud strategy. As the authors do so, they share important research that supports each of the four steps. Next, the authors offer a sample lesson plan using the informational picture book, Carter Reads the Newspaper.FindingsThe lesson plan uses a 5E template to promote critical disciplinary literacy before, during and after reading in such a way that teachers can foster inquiry through the use of social studies read alouds. After reading this article, teachers will understand more about what critical disciplinary literacy means, what it looks like a lesson plan and how to create their own similar plans using the template and resources provided.Originality/valueThe critical disciplinary literacy strategy offers teachers a way to engage elementary students in work that highlights social justice topics and inquiry.
Adaptation to vector‐based transmission in a honeybee virus
Authors: Norton Amanda M. , Remnant Emily J. , Tom Jolanda , Buchmann Gabriele , Blacquiere Tjeerd , Beekman Madeleine 
Published: April 2021

Abstract

Global pollinator declines as a result of emerging infectious diseases are of major concern. Managed honeybees Apis mellifera are susceptible to numerous parasites and pathogens, many of which appear to be transmissible to sympatric non‐Apis taxa. The ectoparasitic mite Varroa destructor is considered to be the most significant threat to honeybees due to its role in vectoring RNA viruses, particularly Deformed wing virus (DWV). Vector transmission of DWV has resulted in the accumulation of high viral loads in honeybees and is often associated with colony death. DWV has two main genotypes, A and B. DWV‐A was more prevalent during the initial phase of V. destructor establishment. In recent years, the global prevalence of DWV‐B has increased, suggesting that DWV‐B is better adapted to vector transmission than DWV‐A.

We aimed to determine the role vector transmission plays in DWV genotype prevalence at a colony level.

We experimentally increased or decreased the number of V. destructor mites in honeybee colonies, and tracked DWV‐A and DWV‐B loads over a period of 10 months.

Our results show that the two DWV genotypes differ in their response to mite numbers. DWV‐A accumulation in honeybees was positively correlated with mite numbers yet DWV‐A was largely undetected in the absence of the mite. In contrast, colonies had high loads of DWV‐B even when mite numbers were low. DWV‐B loads persisted in miticide‐treated colonies, indicating that this genotype has a competitive advantage over DWV‐A irrespective of mite numbers.

Our findings suggest that the global increase in DWV‐B prevalence is not driven by selective pressure by the vector. Rather, DWV‐B is able to persist in colonies at higher viral loads relative to DWV‐A in the presence and absence of V. destructor. The interplay between V. destructor and DWV genotypes within honeybee colonies may have broad consequences upon viral diversity in sympatric taxa as a result of spillover.
Sex‐specific foraging of an apex predator puts females at risk of human–wildlife conflict
Authors: Schultz Hendrik , Chang Kevin , Bury Sarah J. , Gaskett Anne C. , Dennis Todd E. , Ismar‐Rebitz Stefanie M. H. , Southey Ian , Hohnhold Rebecca J. , Millar Craig D. 
Published: April 2021

Abstract

Urbanisation and anthropogenic alteration of ecosystems has led to conflict between humans and wildlife. Such conflict is often observed in apex predators. Although human–wildlife conflict has been extensively studied, male/female differences in behaviour are rarely considered.

We investigated male/female differences in foraging behaviour of the predatory/scavenging brown skua Catharacta antarctica lonnbergi breeding on a New Zealand island nature reserve in proximity to farmland. These skuas are subject to culling, when perceived as a threat to livestock.

As part of a long‐term ecological study, we used high‐resolution Global Positioning System (GPS) devices to characterise the space‐use of foraging brown skuas. We also analysed stable isotopes of carbon (δ13C) and nitrogen (δ15N) from modern and archived blood samples to investigate possible changes in diet over the past ~30 years.

Analysis of 100 GPS tracks collected from 2014 to 2016 demonstrated that males and females consistently visited different habitats. Males spent most of their time close to their breeding territory on the island nature reserve and females frequently visited a farmed island approximately two kilometres away. Consistent with this finding, we show that male and female skuas also differed markedly in their diets: males specialised on burrow‐nesting white‐faced storm petrels Pelagodroma marina (80%) with only a small proportion of sheep remains Ovis aries (<6%) contributing to their diet. In contrast, female diet comprised 27% white‐faced storm petrels, other seabirds (18%) and a relatively large proportion of sheep remains (47%). Further, our data (186 blood samples from 122 individuals) show that this male/female difference in diet has persisted at least since 1987.

Because females fed disproportionally on sheep remains, they may be more vulnerable to being culled by farmers. Importantly, our case study suggests that intersexual differences in diet and foraging patterns can have major implications for the reproduction and survival of apex predators that interact with farming. We strongly suggest that intersexual differences in behaviour should be considered when investigating human–wildlife conflicts.