bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases
Authors: Wang Sean K. , Nair Surag , Li Rui , Kraft Katerina , Pampari Anusri , Patel Aman , Kang Joyce B. , Luong Christy , Kundaje Anshul , Chang Howard Y. 
Published: March 2022

ABSTRACTGenome-wide association studies (GWAS) of eye disorders have identified hundreds of genetic variants associated with ocular disease. However, the vast majority of these variants are noncoding, making it challenging to interpret their function. Here, we present a joint single-cell atlas of gene expression and chromatin accessibility of the adult human retina with >50,000 cells, which we used to analyze noncoding single-nucleotide polymorphisms (SNPs) implicated by GWAS of age-related macular degeneration, glaucoma, diabetic retinopathy, myopia, and type 2 macular telangiectasia. We integrate this atlas with a HiChIP enhancer connectome, expression quantitative trait loci (eQTL) data, and base-resolution deep learning models to predict noncoding SNPs with causal roles in eye disease, assess SNP impact on transcription factor binding, and define their known and novel target genes. Our efforts nominate pathogenic SNP-target gene interactions for multiple vision disorders and provide a potentially powerful resource for interpreting noncoding variation in the eye.
AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures
Authors: Tejero Roberto , Huang Yuanpeng J. , Ramelot Theresa A. , Montelione Gaetano T. 
Published: March 2022

AbstractRecent advances in molecular modeling using deep learning have the potential to revolutionize the field of structural biology. In particular, AlphaFold has been observed to provide models of protein structures with accuracy rivaling medium-resolution X-ray crystal structures, and with excellent atomic coordinate matches to experimental protein NMR and cryo-electron microscopy structures. Here we assess the hypothesis that AlphaFold models of small, relatively rigid proteins have accuracies (based on comparison against experimental data) similar to experimental solution NMR structures. We selected six representative small proteins with structures determined by both NMR and X-ray crystallography, and modeled each of them using AlphaFold. Using several structure validation tools integrated under the Protein Structure Validation Software suite (PSVS), we then assessed how well these models fit to experimental NMR data, including NOESY peak lists (RPF-DP scores), comparisons between predicted rigidity and chemical shift data (ANSURR scores), and 15N-1H residual dipolar coupling data (RDC Q factors) analyzed by software tools integrated in the PSVS suite. Remarkably, the fits to NMR data for the protein structure models predicted with AlphaFold are generally similar, or better, than for the corresponding experimental NMR or X-ray crystal structures. Similar conclusions were reached in comparing AlphaFold2 predictions and NMR structures for three targets from the Critical Assessment of Protein Structure Prediction (CASP). These results contradict the widely held misperception that AlphaFold cannot accurately model solution NMR structures. They also document the value of PSVS for model vs. data assessment of protein NMR structures, and the potential for using AlphaFold models for guiding analysis of experimental NMR data and more generally in structural biology.
DNA Double Strand Breaks cause chromosome loss through sister chromatid tethering in human embryos
Authors: Turocy Jenna , Marin Diego , Xu Shuangyi , Xu Jia , Robles Alex , Treff Nathan , Egli Dieter 
Published: March 2022

Summary paragraphGenome editing by DNA double-strand breaks (DSB) is currently being investigated as a tool to treat or even prevent heritable diseases1. However, DNA repair mechanisms in the human embryo remain poorly understood and DSBs may result in chromosome loss 2,3. Here we provide evidence of whole and segmental chromosome loss in over one third of chromosomes 16, 17 and X targeted by CRISPR/Cas9-induced DNA DSB, including pericentromeric and mid-arm sites. Chromosomal changes were asymmetric relative to the Cas9 cut site: segmental losses occurred on both centric as well as acentric chromosome arms, while gains were exclusively found on acentric arms, suggesting that centromeres in broken chromosomes continued to mediate sister chromatid separation. Using this pattern of chromosomal errors, we were able to define new genomic coordinates of the active centromere on chromosome 16. Asymmetry was also found in the attrition of gDNA at the break site: attrition occurred centromeric of the DSB, while telomeric to the break, chromosomal ends were protected. Thus, spindle forces at centromeres and end tethering and protection at DSBs are antagonistic forces that interfere with accurate segregation of sister chromatids. Thereby, a single DSB is sufficient to result in the loss of a chromosome from the embryo. These results highlight the risks of aneuploidy in CRISPR/Cas9 genome editing, while also providing a mechanism for mitotically acquired aneuploidy caused by DNA breaks in human embryos.
Altered DNA repair pathway engagement by engineered CRISPR-Cas9 nucleases
Authors: Chauhan Vikash P. , Sharp Phillip A. , Langer Robert 
Published: March 2022

AbstractCRISPR-Cas9 introduces targeted DNA breaks that engage competing DNA repair pathways, producing a spectrum of imprecise insertion/deletion mutations (indels) and precise templated mutations (precise edits). The relative frequencies of these pathways are thought to primarily depend on genomic sequence and cell state contexts, limiting control over mutational outcomes. Here we report that engineered Cas9 nucleases that create different DNA break structures engage competing repair pathways at dramatically altered frequencies. We accordingly designed a Cas9 variant (vCas9) that produces breaks which suppress otherwise dominant nonhomologous end-joining (NHEJ) repair. Instead, breaks created by vCas9 are predominantly repaired by pathways utilizing homologous sequences, specifically microhomology-mediated end-joining (MMEJ) and homology-directed repair (HDR). Consequently, vCas9 enables efficient precise editing through HDR or MMEJ while suppressing indels caused by NHEJ in dividing and non-dividing cells. These findings establish a new paradigm of targeted nucleases custom-designed for specific mutational applications.TeaserCRISPR-Cas9 can be designed to make otherwise infrequent precise editing pathways dominant in dividing and non-dividing cells
Structural consequences of deproteinating the 50S ribosome
Authors: Larsson Daniel S. D. , Sandesh Kanchugal P , Selmer Maria 
Published: March 2022

ABSTRACTRibosomes are complex ribonucleoprotein particles. Purified 50S ribosomes subjected to high-salt wash, removing a subset of ribosomal proteins (r-proteins), were early shown competent for in vitro assembly into functional 50S subunits. We here used cryo-EM to determine the structure of such LiCl core particles derived from E. coli 50S subunits. A wide range of complexes with large variation in extent of ordered 23S rRNA and occupancy of r-proteins could be identified, and resolved to between 2.8 Å and 9 Å resolution. Many of these particles showed high similarity to in vivo and in vitro assembly intermediates, supporting the inherent stability or metastability of these states. Similar to states in early ribosome assembly, the main class showed ordered density for 23S rRNA domains 0, I, II, III, VI and the 5’-half of domain IV. In addition, smaller core particles were discovered, which show that the most stable part of the 50S under high-salt conditions includes parts of domain 0 and most of domains I, III and the 5’-half of domain IV and four to eight r-proteins. Our data support a multi-pathway disassembly process based on independent folding blocks, similar but reverse to the assembly process. The study provides examples of dependencies between complex tertiary RNA structure and RNA-protein interactions where protein extensions dissociate before the globular domains. We observe formation of a non-native RNA structure upon protein dissociation, demonstrating that r-proteins stabilize native RNA structure and prevent non-native interactions also after folding.IMPORTANCERibosome assembly and stability remain only partially understood. Incubation of ribosomes with salts was early shown to induce dissociation of the more loosely bound ribosomal proteins (r-proteins) and formation of so-called core particles. In this work, cryo-EM imaging of 50S LiCl core particles from E. coli for the first time allowed structural characterization of such particles of different size. The smallest particles demonstrate what constitutes the smallest stable core of the 50S ribosomal subunit, and the sequential comparison with larger particles show how the ribosome disassembles and assembles in layers of rRNA structure stabilized by globular domains and extended tails of r-proteins. Major insights are that ribosomes disassemble along different paths, that dissociation of r-proteins can induce misfolding of rRNA and that extended tails of r-proteins dissociate from rRNA before the globular domains. The characterized particles can be used in future mechanistic studies of ribosome biogenesis.
Lamin A/C mediated invaginations in the nuclear surface allow the nucleus to pass unimpeded through a dense array of fiber-like obstacles
Authors: Katiyar Aditya , Zhang Jian , Antani Jyot D. , Yu Yifan , Scott Kelsey L. , Lele Pushkar P. , Reinhart-King Cynthia A. , Sniadecki Nathan J. , Roux Kyle J. , Dickinson Richard B. , Lele Tanmay P. 
Published: March 2022

AbstractMigrating cells must deform their stiff cell nucleus to move through pores and fibers in tissue. Lamin A/C is known to hinder cell migration by limiting nuclear deformation and passage through confining channels, but its role in nuclear deformation and passage through fibrous environments is less clear. We studied cell and nuclear migration through discrete, closely spaced, slender obstacles which mimic the mechanical properties of collagen fibers. Nuclei bypassed slender obstacles while preserving their overall morphology by deforming around them with deep local invaginations of little resisting force. The obstacles did not impede the nuclear trajectory or cause a rupture of the nuclear envelope. Nuclei likewise deformed around single collagen fibers in cells migrating in 3D collagen gels. In contrast to its limiting role in nuclear passage through confining channels, lamin A/C facilitated nuclear deformation and passage through fibrous environments; nuclei in lamin-null (Lmna-/-) cells lost their overall morphology and became entangled on the obstacles. Analogous to surface tension-mediated deformation of a liquid drop, lamin A/C imparts a surface tension on the nucleus that allows nuclear invaginations with little mechanical resistance, preventing nuclear entanglement and allowing nuclear passage through fibrous environments.
A distant global control region is essential for normal expression of anterior HOXA genes during mouse and human craniofacial development
Authors: Wilderman Andrea , D’haene Eva , Baetens Machteld , Yankee Tara N. , Winchester Emma Wentworth , Glidden Nicole , Roets Ellen , Van Dorpe Jo , Vergult Sarah , Cox Timothy C. , Cotney Justin 
Published: March 2022

AbstractDefects in embryonic patterning resulting in craniofacial abnormalities account for approximately 1/3 of birth defects. The regulatory programs that build and shape the face require precisely controlled spatiotemporal gene expression, achieved through tissue-specific enhancers. Large regions with coactivation of enhancer elements and co-regulation of multiple genes, referred to as superenhancers, are important in determining cell identity and perturbation could result in developmental defects. Building upon a previously published epigenomic atlas of human embryonic craniofacial tissue in which we identified over 75,000 putative embryonic craniofacial enhancer regions, we have identified 531 superenhancer regions unique to embryonic craniofacial tissue, including 37 which fall in completely noncoding regions. To demonstrate the utility of this data for the understanding of craniofacial development and the etiology of craniofacial abnormalities, we focused on a craniofacial-specific superenhancer in a ∼600kb noncoding region located between NPVF and NFE2L3. This region harbors over 100 individual putative craniofacial enhancer segments and 7 in vivo validated craniofacial enhancers from primary craniofacial tissue as well as strong enhancer activation signatures in a culture model of cranial neural crest cell (CNCC) development. However, none of the directly adjacent genes have been implicated in neural crest specification, craniofacial development, or abnormalities. To identify potential regulatory targets of this superenhancer region, we characterized three-dimensional chromatin structure of this region in CNCCs and mouse embryonic craniofacial tissues using multiple techniques (4C-Seq, HiC). We identified long range interactions that exclude most intervening genes and specifically target the anterior portion of the HOXA gene cluster located 1.2 to 1.8 Mb away. We demonstrate the specificity of the enhancer region for regulation of anterior HOXA genes through CRISPR/Cas9 editing of human embryonic stem cells. Mice homozygous for deletion of the superenhancer confirm the specificity of the enhancer region and demonstrate that the region is essential for viability. At fetal stages homozygotes develop at the same rate as heterozygous and wild type littermates but die at P0-P1 and have high penetrance of orofacial clefts that phenocopy previously described Hoxa2-/- mice. Moreover, we identified a de novo deletion partially overlapping the superenhancer in a human fetus with severe craniofacial abnormalities. This evidence suggests we have identified a critical noncoding locus control region that specifically regulates anterior HOXA genes and whose deletion is likely pathogenic in human patients.
Betting against real earnings management
Authors: Bansal Manish , Ali Asgar 
Published: March 2022

PurposeThe study presents the zero investment strategies based on the pricing impact of real earnings management (REM) on stock returns after taking into account the direction and endogeneity nature of REM.Design/methodology/approachThe authors use standard portfolio methodology and Fama–Macbeth cross-sectional regression to analyze the data for this study. Both upward and downward form of REM has been examined. Accrual earnings management (AEM) has been controlled while examining the association between REM and stock returns.FindingsThe findings demonstrate that the REM anomaly exists in the Indian equity market and is consistent under different market conditions and investment horizons. It is robust after controlling for cross-sectional effects and AEM. Our subsequent analysis suggests that a decile-based zero investment portfolio strategy based on REM loadings generates an annual excess return of 17.90%. The presented annual excess return is highest among quantile and mean-based investment strategies. Further, the authors find that REM sorted proposed investment strategies outperform the AEM sorted investment strategies in all spheres.Practical implicationsThe findings suggest that investors can form an arbitrage profitable investment strategy by taking a long position in the bottom 10% of negative REM stocks, and a short position in the top 10% of positive REM stocks.Originality/valueThis is the first study that examines the pricing impact of REM on stock returns and provides zero investment strategies by betting against REM.
Influence of stator segmentation on iron losses in PMSMs for traction applications
Authors: Garmut Mitja , Petrun Martin 
Published: March 2022

Purpose
This paper presents a comparative study of different stator-segmentation topologies of a permanent magnet synchronous machine (PMSM) used in traction drives and their effect on iron losses. Using stator segmentation allows one to achieve more significant copper fill factors, resulting in increased power densities and efficiencies. The segmentation of the stators creates additional air gaps and changes the soft magnetic material’s material properties due to the cut edge effect. The aim of this paper is to present an in-depth analysis of the influence of stator segmentation on iron losses. The main goal was to compare various segmentation methods under equal excitation conditions in terms of their influence on iron loss.

Design/methodology/approach
A transient finite element method analysis combined with an extended iron-loss model was used to evaluate discussed effects on the stator’s iron losses. The workflow to obtain a homogenized airgap length accounting for cut edge effects was established.

Findings
The paper concludes that the segmentation in most cases slightly decreases the iron losses in the stator because of the overall reduced magnetic flux density B due to the additional air gaps in the magnetic circuit. An increase of the individual components, as well as total power loss, was observed in the Pole Chain segmentation design. In general, segmentation did not change the total iron losses significantly. However, different segmentation methods resulted in the different distortion of the magnetic field and, consequently, in different iron loss compositions. The analysed segmentation methods exhibited different iron loss behaviour with respect to the operation points of the machine. The final finding is that analysed stator segmentations had a negligible influence on the total iron loss. Therefore, applying segmentation is an adequate measure to improve PMSMs as it enables, e.g. increase of the winding fill factor or simplifying the assembly processes, etc.

Originality/value
The influence of stator segmentation on iron losses was analysed. An in-depth evaluation was performed to determine how the discussed changes influence the individual iron loss components. A workflow was developed to achieve a computationally cheap homogenized model.
Finite element analysis and design of beam steering devices with global control
Authors: Alkhateeb Osama , Hossain A.N.M. Shahriyar , Tsukerman Igor , Ida Nathan 
Published: March 2022

Purpose
This paper aims to design metaguide- or metasurface-based compact inexpensive beam-steering devices, which play an important role in modern cellular networks, radar imaging and satellite communication.

Design/methodology/approach
This paper uses finite element analysis to study, design and optimize arrays of resonating elements as beam steering devices. The first set of such devices involves metamaterial-based apertures fed by a waveguide, tunable via the permittivity of the host material. In the second approach, dynamic beam steering is effected by alternating between two or more waveguide feeds.

Findings
Particular examples show how the direction of the main lobe of the radiated beam can be reliably switched by approximately 30° in one of the quadrants by changing a single global control parameter within a very reasonable range.

Research limitations/implications
The findings pave the way for the design and fabrication of inexpensive compact beam steering devices. This study anticipates that the proposed designs can be further improved and fine-tuned using “heavy duty” optimization packages.

Originality/value
In many published designs of similar beam-steering devices, the radiation pattern of an array of resonating elements is controlled by complex circuitry, so that each radiating element is tuned separately. In contrast with these existing approaches, the designs rely just on a simple global control parameter.
Measuring national intellectual capital and its effect on country’s competitiveness
Authors: Vo Duc Hong , Tran Ngoc Phu 
Published: March 2022

Purpose
National intellectual capital is generally considered a strategic advantage for national competitiveness. However, the measurement of intellectual capital across countries for comparison purposes appears to receive little attention. This study aims to use a new index of national intellectual capital (INIC) to examine the relationship between national intellectual capital and national competitiveness.

Design/methodology/approach
This paper uses the INIC, developed by Vo and Tran (2021), to measure, compare and contrast differences in the level of national intellectual capital across 104 countries. INIC comprises the most crucial intellectual capital components: human capital, structural capital and relational capital. Various economic and social indicators are used as the proxies for these components of intellectual capital. Principal component analysis is used to derive INIC.

Findings
The results indicate that during the study period the level of national intellectual capital gradually increased. Europe has attained the highest level of national intellectual capital, whereas Africa has achieved the lowest level. This study’s findings confirm a close relationship between the national intellectual capital level and the national income level. Among the ten biggest countries, the USA achieved the highest national intellectual capital level, and China has significantly improved its cumulative level. Finland achieved the highest level of national intellectual capital in the world. National intellectual capital enhances a country’s competitiveness.

Practical implications
Findings in this study shed light on an international comparison of intellectual capital across countries and understanding how national intellectual capital contributes to and improves national competitiveness. Policymakers can consider and use these findings to support the accumulation of national intellectual capital and boost national competitive advantage, especially low-income countries and emerging markets.

Originality/value
To the best of the authors’ knowledge, this is the first study to estimate a degree of national intellectual capital around the world and examine its impact on national competitiveness based on publicly available data.