bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole genome analysis for 163 gRNAs in Cas9-edited mice reveals minimal off-target activity
Authors: Peterson Kevin A. , Khalouei Sam , Hanafi Nour , Wood Joshua A. , Lanza Denise G. , Lintott Lauri G. , Willis Brandon J. , Seavitt John R. , Braun Robert E. , Dickinson Mary E. , White Jacqueline K. , Lloyd K. C. Kent , Heaney Jason D. , Murray Stephen A. , Ramani Arun , Nutter Lauryl M. J. 
Published: June 2023

AbstractGenome editing with CRISPR-associated (Cas) proteins holds exceptional promise for “correcting” variants causing genetic disease. To realize this promise, off-target genomic changes cannot occur during the editing process. Here, we use whole genome sequencing to compare the genomes of 50 Cas9-edited founder mice to 28 untreated control mice to assess the occurrence of S. pyogenes Cas9-induced off-target mutagenesis. Computational analysis of whole-genome sequencing data detects 26 unique sequence variants at 23 predicted off-target sites for 18/163 guides used. While computationally detected variants are identified in 30% (15/50) of Cas9 gene-edited founder animals, only 38% (10/26) of the variants in 8/15 founders validate by Sanger sequencing. In vitro assays for Cas9 off-target activity identify only two unpredicted off-target sites present in genome sequencing data. In total, only 4.9% (8/163) of guides tested have detectable off-target activity, a rate of 0.2 Cas9 off-target mutations per founder analyzed. In comparison, we observe ~1,100 unique variants in each mouse regardless of genome exposure to Cas9 indicating off-target variants comprise a small fraction of genetic heterogeneity in Cas9-edited mice. These findings will inform future design and use of Cas9-edited animal models as well as provide context for evaluating off-target potential in genetically diverse patient populations.
Transposons contribute to the acquisition of cell type-specific cis-elements in the brain
Authors: Sekine Kotaro , Onoguchi Masahiro , Hamada Michiaki 
Published: June 2023

AbstractMammalian brains have evolved in stages over a long history to acquire higher functions. Recently, several transposable element (TE) families have been shown to evolve into cis-regulatory elements of brain-specific genes. However, it is not fully understood how TEs are important for gene regulatory networks. Here, we performed a single-cell level analysis using public data of scATAC-seq to discover TE-derived cis-elements that are important for specific cell types. Our results suggest that DNA elements derived from TEs, MER130 and MamRep434, can function as transcription factor-binding sites based on their internal motifs for Neurod2 and Lhx2, respectively, especially in glutamatergic neuronal progenitors. Furthermore, MER130- and MamRep434-derived cis-elements were amplified in the ancestors of Amniota and Eutheria, respectively. These results suggest that the acquisition of cis-elements with TEs occurred in different stages during evolution and may contribute to the acquisition of different functions or morphologies in the brain.
Decadal stability in coral cover could mask hidden changes on reefs in the East Asian Seas
Authors: Chan Y. K. S. , Affendi Y. A. , Ang P. O. , Baria-Rodriguez M. V. , Chen C. A. , Chui A. P. Y. , Giyanto  , Glue M. , Huang H. , Kuo C-Y. , Kim S. W. , Lam V. Y. Y. , Lane D. J. W. , Lian J. S. , Lin S. M. N. N. , Lunn Z. , Nañola C. L. , Nguyen V. L. , Park H. S. , Suharsono  , Sutthacheep M. , Vo S. T. , Vibol O. , Waheed Z. , Yamano H. , Yeemin T. , Yong E. , Kimura T. , Tun K. , Chou L. M. , Huang D. 
Published: June 2023

AbstractCoral reefs in the Central Indo-Pacific region comprise some of the most diverse and yet threatened marine habitats. While reef monitoring has grown throughout the region in recent years, studies of coral reef benthic cover remain limited in spatial and temporal scales. Here, we analysed 24,365 reef surveys performed over 37 years at 1972 sites throughout East Asia by the Global Coral Reef Monitoring Network using Bayesian approaches. Our results show that overall coral cover at surveyed reefs has not declined as suggested in previous studies and compared to reef regions like the Caribbean. Concurrently, macroalgal cover has not increased, with no indications of phase shifts from coral to macroalgal dominance on reefs. Yet, models incorporating socio-economic and environmental variables reveal negative associations of coral cover with coastal urbanisation and sea surface temperature. The diversity of reef assemblages may have mitigated cover declines thus far, but climate change could threaten reef resilience. We recommend prioritisation of regionally coordinated, locally collaborative long-term studies for better contextualisation of monitoring data and analyses, which are essential for achieving reef conservation goals.
Critical scaling of whole-brain resting-state dynamics
Authors: Ponce-Alvarez Adrián , Kringelbach Morten L. , Deco Gustavo 
Published: June 2023

AbstractScale invariance is a characteristic of neural activity. How this property emerges from neural interactions remains a fundamental question. Here, we studied the relation between scale-invariant brain dynamics and structural connectivity by analyzing human resting-state (rs-) fMRI signals, together with diffusion MRI (dMRI) connectivity and its approximation as an exponentially decaying function of the distance between brain regions. We analyzed the rs-fMRI dynamics using functional connectivity and a recently proposed phenomenological renormalization group (PRG) method that tracks the change of collective activity after successive coarse-graining at different scales. We found that brain dynamics display power-law correlations and power-law scaling as a function of PRG coarse-graining based on functional or structural connectivity. Moreover, we modeled the brain activity using a network of spins interacting through large-scale connectivity and presenting a phase transition between ordered and disordered phases. Within this simple model, we found that the observed scaling features were likely to emerge from critical dynamics and connections exponentially decaying with distance. In conclusion, our study tests the PRG method using large-scale brain activity and theoretical models and suggests that scaling of rs-fMRI activity relates to criticality.
Integrative genomic analyses of promoter G-quadruplexes reveal their selective constraint and association with gene activation
Authors: Li Guangyue , Su Gongbo , Wang Yunxuan , Wang Wenmeng , Shi Jinming , Li Dangdang , Sui Guangchao 
Published: June 2023

AbstractG-quadruplexes (G4s) regulate DNA replication and gene transcription, and are enriched in promoters without fully appreciated functional relevance. Here we show high selection pressure on putative G4 (pG4) forming sequences in promoters through investigating genetic and genomic data. Analyses of 76,156 whole-genome sequences reveal that G-tracts and connecting loops in promoter pG4s display lower or higher allele frequencies, respectively, than pG4-flanking regions, and central guanines (Gs) in G-tracts show higher selection pressure than other Gs. Additionally, pG4-promoters produce over 72.4% of transcripts, and promoter G4-containing genes are expressed at relatively high levels. Most genes repressed by TMPyP4, a G4-ligand, regulate epigenetic processes, and promoter G4s are enriched with gene activation histone marks, chromatin remodeler and transcription factor binding sites. Consistently, cis-expression quantitative trait loci (cis-eQTLs) are enriched in promoter pG4s and their G-tracts. Overall, our study demonstrates selective constraint of promoter G4s and reinforces their stimulative role in gene expression.
Mixed-linker strategy for suppressing structural flexibility of metal-organic framework membranes for gas separation
Authors: Chang Chung-Kai , Ko Ting-Rong , Lin Tsai-Yu , Lin Yen-Chun , Yu Hyun Jung , Lee Jong Suk , Li Yi-Pei , Wu Heng-Liang , Kang Dun-Yen 
Published: June 2023

AbstractStructural flexibility is a critical issue that limits the application of metal-organic framework (MOF) membranes for gas separation. Herein we propose a mixed-linker approach to suppress the structural flexibility of the CAU-10-based (CAU = Christian-Albrechts-University) membranes. Specifically, pure CAU-10-PDC membranes display high separation performance but at the same time are highly unstable for the separation of CO2/CH4. A partial substitution (30 mol.%) of the linker PDC with BDC significantly improves its stability. Such an approach also allows for decreasing the aperture size of MOFs. The optimized CAU-10-PDC-H (70/30) membrane possesses a high separation performance for CO2/CH4 (separation factor of 74.2 and CO2 permeability of 1,111.1 Barrer under 2 bar of feed pressure at 35°C). A combination of in situ characterization with X-ray diffraction (XRD) and diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy, as well as periodic density functional theory (DFT) calculations, unveils the origin of the mixed-linker approach to enhancing the structural stability of the mixed-linker CAU-10-based membranes during the gas permeation tests.
Structure of a 10-23 deoxyribozyme exhibiting a homodimer conformation
Authors: Cramer Evan R. , Starcovic Sarah A. , Avey Rebekah M. , Kaya Ali I. , Robart Aaron R. 
Published: June 2023

AbstractDeoxyribozymes (DNAzymes) are in vitro evolved DNA sequences capable of catalyzing chemical reactions. The RNA-cleaving 10-23 DNAzyme was the first DNAzyme to be evolved and possesses clinical and biotechnical applications as a biosensor and a knockdown agent. DNAzymes do not require the recruitment of other components to cleave RNA and can turnover, thus they have a distinct advantage over other knockdown methods (siRNA, CRISPR, morpholinos). Despite this, a lack of structural and mechanistic information has hindered the optimization and application of the 10-23 DNAzyme. Here, we report a 2.7 Å crystal structure of the RNA-cleaving 10-23 DNAzyme in a homodimer conformation. Although proper coordination of the DNAzyme to substrate is observed along with intriguing patterns of bound magnesium ions, the dimer conformation likely does not capture the true catalytic form of the 10-23 DNAzyme.
Accounting for 16S rRNA copy number prediction uncertainty and its implications in bacterial diversity analyses
Authors: Gao Yingnan , Wu Martin 
Published: June 2023

Abstract
16S rRNA gene copy number (16S GCN) varies among bacterial species and this variation introduces potential biases to microbial diversity analyses using 16S rRNA read counts. To correct the biases, methods have been developed to predict 16S GCN. A recent study suggests that the prediction uncertainty can be so great that copy number correction is not justified in practice. Here we develop RasperGade16S, a novel method and software to better model and capture the inherent uncertainty in 16S GCN prediction. RasperGade16S implements a maximum likelihood framework of pulsed evolution model and explicitly accounts for intraspecific GCN variation and heterogeneous GCN evolution rates among species. Using cross-validation, we show that our method provides robust confidence estimates for the GCN predictions and outperforms other methods in both precision and recall. We have predicted GCN for 592605 OTUs in the SILVA database and tested 113842 bacterial communities that represent an exhaustive and diverse list of engineered and natural environments. We found that the prediction uncertainty is small enough for 99% of the communities that 16S GCN correction should improve their compositional and functional profiles estimated using 16S rRNA reads. On the other hand, we found that GCN variation has limited impacts on beta-diversity analyses such as PCoA, NMDS, PERMANOVA and random-forest test.
A shape‐based clustering algorithm and its application to load data
Authors: Li Naiwen , Wu Xian , Dong Jianjun , Zhang Dan 
Published: June 2023

AbstractThe popularity of smart metres has brought a huge amount of demand‐side data, which provides important information for the demand response of the power sector, to guide practitioners to understand the customers' electricity usage behaviours and patterns. Clustering analysis of customers' daily load data is an important tool for mining users' consumption habits and achieve non‐fixed market segmentation. Since the load data is time series, it is inappropriate to perform clustering directly without extracting targeted features. Therefore, according to the shape features of the daily load curve, a shape‐based clustering algorithm called BDKM is proposed. The algorithm first uses the B‐splines regression to fit the time series data to extract morphological features, and then the objects are segmented based on the dynamic time warping distance by clustering. Finally, the real world daily customers' load data is used to prove the effectiveness of the proposed algorithm based on B‐splines regression.
Robust tube‐based distributed MPC for PWA systems
Authors: Ma Aoyun , Li Dewei , Xi Yugeng 
Published: June 2023

AbstractA robust tube‐based distributed model predictive control method is proposed for spatially interconnected systems with constraints and disturbances. The system contains multiple discrete‐time piecewise affine subsystems, which are coupled to each other through states. The predictive states of each subsystem are dependent on its states, inputs, and neighbouring states, and shrinking constraints are constructed to deal with the disturbances and the model mismatches. The differences between the predicted states at the current time instant and the optimal states at the previous time instant are constrained, which improves the accuracy of the predicted model and enhances the control performance. The conditions which ensure the recursive feasibility of optimization problems and the asymptotic stability of closed‐loop system are obtained. The effectiveness of the proposed method is verified by the simulation results.
All‐SiC 99.4%‐efficient three‐phase T‐type inverter with DC‐side common‐mode filter
Authors: Anderson Jon Azurza , Marciano Daniele , Huber Jonas , Deboy Gerald , Busatto Giovanni , Kolar Johann W. 
Published: June 2023

AbstractThis letter presents a hardware demonstrator of an all‐SiC three‐level T‐type (3LTT) inverter with the common‐mode (CM) EMI filter stages placed on the DC input instead of the AC output side, targeting, for example, high‐efficiency PV applications. The extensive experimental characterization shows that state‐of‐the‐art SiC transistors and a DC‐side CM filter enable an unprecedented peak/full‐load efficiency of 99.4% (calorimetric measurement) at 12.5 kW and a power density of 2.4 kW/dm3 (39 W/in3). The demonstrator fulfills CISPR 11 Class A EMI regulations as well as upcoming EMI standards for the frequency range of 9–150 kHz. Compared to other high‐efficiency converters, which often employ bridge legs with more output voltage levels, the described 3LTT concept thus offers a very favorable trade‐off between complexity and performance.
A progressive segmentation with weight contrast label enhancement for weakly supervised video salient object detection
Authors: Lu Zelin , Liang Haoran , Xu Binwei , Liang Ronghua 
Published: June 2023

AbstractScribble labels have gained increasing attention in the field of weakly supervised video salient object detection (VSOD). Based on scribble labels, latest methods can spread labeled pixels to unlabeled regions using local coherence loss, but predicted objects often lose detail and boundary information. In this work, a novel method based on back‐foreground weight contrast is proposed that adds label enhancement points to facilitate the model to learn the edge, detail and location of salient object. Additionally, a new VSOD framework based on global structural localization is introduced. Enhanced scribble labels are used to assist the model for global localization, and then the located regions are finely segmented by the trained model. Extensive experiments demonstrate that the method achieves the state‐of‐the‐art performance on common VSOD datasets, with an improvement of 3.75%, 4.68%, and 0.88% in S‐measure, F‐measure, and MAE, respectively.
Automatic refinement of ephemeris‐derived range‐Doppler model through the least‐squares matching of Sentinel‐1 Single‐Look Complex images and DEM in mountainous areas
Authors: Saeedi Amale Hamidreza , Safdarinezhad Alireza 
Published: June 2023

AbstractRange‐Doppler model is a transformation that relates ground and Single‐Look Complex SAR image spaces by knowing the instantaneous position and velocity of the sensor in its trajectory. Its instantaneous position and velocities are determined with the help of vectorial functions, which their precisions directly influence the accuracy of the range‐Doppler model. Ephemeris data is one of the sources used for the estimation of temporal functions. Some reasons can cause uncertainty in the temporal function directly derived from the satellite navigation data. Ground control points are other alternatives for calibration of the range‐Doppler model whose visual measurements are difficult in the mountainous areas of Sentinel‐1 Single‐Look Complex images due to their resolutions and distortions. The temporal functions of the range‐Doppler model are refined through numerous control points extracted from the automatic matching between Single‐Look Complex images and Digital Elevation Model. For this purpose, the radiometric and geometric similarities of the Single‐Look Complex images and Digital Elevation Model in mountainous areas are first increased based on the initial range‐Doppler model, and then their geometric discrepancies are compensated with the least‐squares image matching method. The results indicated that the proposed method in mountainous areas could automatically compensate for up to 30 pixels errors and reach sub‐pixel accuracies.
Recognizing technique variation in rock engravings: ArchCUT3-D for micromorphological analysis
Authors: Dubinsky Lena , David Marcelo , Grosman Leore 
Published: June 2023

AbstractAncient rock engravings evoke the interest of archeologists and art historians as an important remnant of human cultures. Traditionally, engraved images are studied based on iconography, iconology, and stylistic characteristics, with little emphasis on execution technology. In contrast, the research method presented in this study strives to characterize the techniques adopted for making rock engravings in ancient times, with technological variations considered as indicators of the engraver’s production process. 3-D scans of two ancient engravings and contemporary graffiti were obtained from Site 25 in Timna Park, Southern Israel. The models were analyzed with ArchCUT3-D, a software specifically developed to precisely evaluate the 3-D micromorphological characteristics of the incisions making up the engraving. The software analyzes the surface micromorphology by extracting 3-D slices of the incisions using an accurate and repeatable method. Our results indicate that different incisions were executed by remarkably distinct techniques of stroking the rock surface with a sharp tool. The identification of discriminant characteristics enabled us to demonstrate the particularities of the engraving operations, such as ergonomic conditions and the level of consistency of the engraving gesture. ArchCUT3-D thus provides a computational method for incision technique recognition through micromorphology specifications, and the reconstruction of engraving gestures and individual production procedures.
Poverty and Private Law: Beyond Distributive Justice
Authors: Dagan Hanoch , Dorfman Avihay 
Published: June 2023

Abstract
Poverty has so far been overwhelmingly understood as a state of distributive injustice. As a result, the debate in private law theory about the role of private law in alleviating poverty has essentially collapsed into the question of whether private law could, and should, promote distributive justice. We challenge the terms of this debate and, in particular, poverty’s reduction to its distributive dimension. We argue that poverty is a social condition with direct implications for the transactional freedom and equal standing of the person affected by it. In particular, poverty can impair one person’s ability to interact with another on terms reflecting reciprocal respect for their self-determination and substantive equality. Our account identifies institutional limitations on the operationalization of poverty accommodation in private law on the one hand, while elaborating promising ways for incorporating poverty into a broad range of private law interactions on the other.
The diverse diaspora of CAM: a pole-to-pole sketch
Authors: Holtum Joseph A M 
Published: June 2023

Abstract

Background
Crassulacean acid metabolism (CAM) photosynthesis is a successful adaptation that has evolved often in angiosperms, gymnosperms, ferns and lycophytes. Present in ~5 % of vascular plants, the CAM diaspora includes all continents apart from Antarctica. Species with CAM inhabit most landscapes colonized by vascular plants, from the Arctic Circle to Tierra del Fuego, from below sea level to 4800 m a.s.l., from rainforests to deserts. They have colonized terrestrial, epiphytic, lithophytic, palustrine and aquatic systems, developing perennial, annual or geophyte strategies that can be structurally arborescent, shrub, forb, cladode, epiphyte, vine or leafless with photosynthetic roots. CAM can enhance survival by conserving water, trapping carbon, reducing carbon loss and/or via photoprotection.

Scope
This review assesses the phylogenetic diversity and historical biogeography of selected lineages with CAM, i.e. ferns, gymnosperms and eumagnoliids, Orchidaceae, Bromeliaceae, Crassulaceae, Euphorbiaceae, Aizoaceae, Portulacineae (Montiaceae, Basellaceae, Halophytaceae, Didiereaceae, Talinaceae, Portulacaceae, Anacampserotaceae and Cactaceae) and aquatics.

Conclusions
Most extant CAM lineages diversified after the Oligocene/Miocene, as the planet dried and CO2 concentrations dropped. Radiations exploited changing ecological landscapes, including Andean emergence, Panamanian Isthmus closure, Sundaland emergence and submergence, changing climates and desertification. Evidence remains sparse for or against theories that CAM biochemistry tends to evolve before pronounced changes in anatomy and that CAM tends to be a culminating xerophytic trait. In perennial taxa, any form of CAM can occur depending upon the lineage and the habitat, although facultative CAM appears uncommon in epiphytes. CAM annuals lack strong CAM. In CAM annuals, C3 + CAM predominates, and inducible or facultative CAM is common.