bluuebunny/crossref_metadata_2025_split huggingface dataset:
GREPore-Seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-Range PCR and Nanopore Sequencing
Authors: Quan Zi-Jun , Li Si-Ang , Yang Zhi-Xue , Zhao Juan-Juan , Li Guo-Hua , Zhang Feng , Wen Wei , Cheng Tao , Zhang Xiao-Bing 
Published: June 2022

Abstract
To achieve the enormous potential of gene-editing technology in clinical therapies, one needs to evaluate both the on-target efficiency and unintended editing consequences comprehensively. However, there is a lack of a pipelined, large-scale, and economical workflow for detecting genome editing outcomes, in particular insertion or deletion of a large fragment. Here, we describe an approach for efficient and accurate detection of multiple genetic changes after CRISPR/Cas9 editing by pooled nanopore sequencing of barcoded long-range PCR products. Recognizing the high error rates of Oxford nanopore sequencing, we developed a novel pipeline to capture the barcoded sequences by grepping reads of nanopore amplicon sequencing (GREPore-seq). GREPore-seq can assess nonhomologous end-joining (NHEJ)-mediated double-stranded oligodeoxynucleotide (dsODN) insertions with comparable accuracy to Illumina next-generation sequencing (NGS). GREPore-seq also reveals a full spectrum of homology-directed repair (HDR)-mediated large gene knock-in, correlating well with the fluorescence-activated cell sorting (FACS) analysis results. Of note, we discovered low-level fragmented and full-length plasmid backbone insertion at the CRISPR cutting site. Therefore, we have established a practical workflow to evaluate various genetic changes, including quantifying insertions of short dsODNs, knock-ins of long pieces, plasmid insertions, and large fragment deletions after CRISPR/Cas9-mediated editing. GREPore-seq is freely available at GitHub (https://github.com/lisiang/GREPore-seq) and the National Genomics Data Center (NGDC) BioCode (https://ngdc.cncb.ac.cn/biocode/tools/BT007293).
Biostratigraphy and paleoecology of the trilobite faunas from the Mount Clark and Mount Cap formations (early and middle Cambrian), eastern Mackenzie Mountains, northwestern Canada
Authors: Handkamer Neal M. , Pratt Brian R. , MacNaughton Robert B. 
Published: June 2022

AbstractLower and middle Cambrian strata of the eastern Mackenzie Mountains, Northwest Territories, Canada, were deposited in a semi-enclosed basin along the eastern flank of the Mackenzie Arch. The Mount Clark Formation is predominantly composed of nearshore sandstone and is overlain by deeper water siltstone, mudstone, and carbonates of the Mount Cap Formation. The contact between these formations is interpreted as a flooding surface. Trilobite biostratigraphy indicates the presence of the traditional upper Olenellus through Glossopleura zones (Cambrian Series 2, Stage 4–Miaolingian, Wuliuan) and suggests the flooding surface is diachronous, spanning the Dyeran-Delamaran boundary. Above the Olenellus Zone, the Amecephalus arrojosensis-Eokochaspis nodosa Zone, the new Aitkenaspis keelensis Zone, the new Albertelloides mischi Zone, and the Glossopleura walcotti Zone are recognized. Whereas the older zones are comparable to those in other areas of Laurentia, the trilobite faunas in the Albertelloides mischi and Glossopleura walcotti zones show a greater abundance of zacanthoidids and dolichometopids. They also have a lower diversity of ptychoparioids and oryctocephalids, and lack agnostoids, eodiscoids, dorypygids, and ogygopsidids. This suggests that zacanthoidids and dolichometopids were able to tolerate conditions that were unfavorable to the other groups, probably related to semi-restricted conditions in the basin. Four endemic species exhibit characteristics that are considered paedomorphic. This developmental process took place in three separate lineages, suggesting that heterochrony was also environmentally provoked.New taxonomic names are authored by Handkamer and Pratt. New genera are Eobathyuriscus, Sahtuia, Mexicaspidella Aitkenaspis, Dodoella, and Mackenzieaspis. New species are Bolbolenellus dodoensis, Eobathyuriscus mackenziensis, E. macqueeni, Glossopleura youngi, Sahtuia carcajouensis, Aitkenaspis keelensis, Albertelloides eliasi, Dodoella kobayashii, Mackenzieaspis parallelispinosa, and M. divergens.UUID: http://zoobank.org/a10a2470-853c-4ce8-bf62-7de1d2c99fab.
Differences in growth patterns and catch-up growth of small for gestational age preterm infants fed on fortified mother’s own milk v. preterm formula
Authors: Hofi Lilach , Flidel-Rimon Orna , Hershkovich–Shporen Calanit , Zaharoni Hilla , Birk Ruth 
Published: June 2022

AbstractSmall for gestational age (SGA) is typically defined as birth weight < 10th percentile for age. Limited data are available regarding the growth of SGA preterm infants in relation to feeding type. We aimed to study SGA preterm infants fed fortified mother’s own milk (MOM) or preterm formula (PF) on growth patterns and catch-up growth at discharge and 2-year corrected age (CA). Our retrospective cohort study included data from medical records and follow-up questionnaires about SGA preterm infants born at < 37 weeks fed on MOM (n 40) and PF (n 40). Weight, length/height and head circumference (HC) were collected at birth, discharge and at 2-year CA, and Δ z-scores were calculated. The MOM group had significantly larger negative change in weight and length z-scores between birth and discharge, and smaller positive change in HC z-score (–0·47 (sd 0·41) v. −0·25 (sd 0·36), P = 0·01; −0·63 (sd 0·75) v. −0·27 (sd 0·75), P = 0·03; 0·13 (sd 0·67) v. 0·41 (sd 0·55), P = 0·04, respectively). Almost half of the MOM-fed infants experienced poor length growth by discharge compared with 22 % of PF-fed infants (P = 0·03). By 2-year CA, both groups had similar positive change in weight and HC z-scores, but MOM-fed infants had a slower increase in height z-score (0·64 (sd 1·30) v. 1·33 (sd 1·33), P = 0·02), and only 40 % had achieved catch-up height compared with 68 % of the PF group (P = 0·02). Our study indicates that fortified MOM-fed SGA preterm infants may need extra nutritional support in the first 2 years of life to achieve height growth potential.
Tectonometamorphic evolution of the Trivandrum and Southern Madurai blocks in the Southern Granulite Terrane, south India: correlation with south-central Madagascar
Authors: Praharaj P , Rekha S 
Published: June 2022

AbstractDetailed structural investigations across the Achankovil terrane boundary shear zone (AKSZ) system show distinct differences in the geometry of superposed fold structures between the Trivandrum (TB) and Southern Madurai (SMB) blocks separated by the AKSZ. The metamorphic temperatures and pressures estimated from the SMB and TB have a similar range, that is, 600–880°C and 5–8 kbar. The similar clockwiseP-Tpaths retrieved by phase equilibrium modelling from both the blocks represent the last deformation and metamorphism shared between them during their accretion along the AKSZ. The distinct evolutionary history of the SMB and TB prior to their amalgamation is supported by the contrasting structural, metamorphic and chronological patterns, particularly the lack of prominent middle Neoproterozoic ages and the presence of Palaeoproterozoic ages in the TB, and vice versa in the SMB. The prominent 600–500 Ma monazite ages in the TB, SMB and AKSZ attest to their timing of accretion along the AKSZ. The study corroborates the S-directed subduction model proposed for terrane accretion along the AKSZ, and provides further insight into the subduction–accretion–collision tectonics associated with the late Neoproterozoic – Cambrian evolutionary history of this region.The tectonothermal histories and geochronology of the SMB and TB are compared to the once adjoined crustal domains of Madagascar within Gondwanaland. It is suggested that the TB is equivalent to the Androyan and Anosyan domains of southern Madagascar, the SMB is equivalent to the Antananarivo and Itremo–Ikalamavony blocks of the central Madagascar, and the sinistral AKSZ is contiguous with the Ranotsara Shear Zone in southern Madagascar.
Foodborne trematodes: old foes, new kids on the block and research perspectives for control and understanding host–parasite interactions
Authors: Robinson Mark W. , Sotillo Javier 
Published: June 2022

AbstractFoodborne trematodes (FBTs) have a worldwide distribution (with particular prevalence in south-east Asia) and are believed to infect almost 75 million people, with millions more living at risk of infection. Although mortality due to trematodiasis is low, these infections cause considerable morbidity and some species are associated with the development of cancer in hyperendemic regions. Despite this, FBTs are often side-lined in terms of research funding and have been dubbed neglected tropical diseases by the World Health Organisation. Thus, the aim of this special issue was to provide an update of our understanding of FBT infections, to shine a light on current work in the field and to highlight some research priorities for the future. With contributions from leading researchers, many from endemic regions, we review the major FBT species. In doing so we revisit some old foes, uncover emerging infections and discover how outbreaks are being dealt with as a result of new approaches to parasite control. We also report advances in our understanding of the interactions of FBTs with their mammalian hosts and uncover new interplay between trematodes and host microbiome components. We hope that this article collection will stimulate discussion and further research on the FBTs and help raise them from their neglected status.
Tree recruitment after native frugivore extinction? A field experiment to test the impact of fruit flesh persistence in a tropical oceanic island
Authors: Albert Sébastien , Flores Olivier , Stahl Mikael , Guilhabert Florian , Strasberg Dominique 
Published: June 2022

AbstractThe loss of large frugivores leads to seed dispersal loss and regeneration failure of numerous large-seeded trees near mother trees. Although Janzen–Connell effects are considered as the primary underlying cause, other factors remain understudied. Here, we used a field experiment to test the impact of flesh persistence on the recruitment of two large-seeded Sapotaceae species that lost their dispersers. In the rainforest of Mare Longue (Réunion), we sowed 3840 seeds in a four-factor design: seed treatment (seed cleaning; flesh persistence), canopy closure (understory; gap), year of sowing (01/2018; 11/2019) and species (Labourdonnaisia calophylloides, Mimusops balata). We also used camera traps to evaluate the impact of extant vertebrates. Seed treatment was by far the most influential factor: flesh persistence led to seedling recruitment divided by 3,2 on average, mainly due to failure of germination or seedling emergence. There were also significant variations in recruitment between species, years and canopy closure levels, notably due to the behaviour of the invasive fauna, especially giant snails that could unexpectedly restore recruitment by feeding on fruit flesh. Together, our results demonstrate strongly depleted recruitment due to flesh persistence and the importance of field experiments to understand the processes at work in complex ecosystems with novel plant–animal interactions.
A value-at-risk approach to futures hedge
Authors: Chiu Wan-Yi 
Published: June 2022

AbstractThis paper examines the value-at-risk (VaR) implications of mean-variance hedging. We derive an equivalence between the VaR-based hedge and the mean-variance hedging. This method transfers the investor's subjective risk-aversion coefficient into the estimated VaR measure. As a result, we characterize the collapse probability bounds under which the VaR-based hedge could be insignificantly different from the minimum-variance hedge in the presence of estimation risk. The results indicate that the squared information ratio of futures returns is the primary factor determining the difference between the minimum-variance and VaR-based hedges.
Influencing the choice of pension distribution at retirement
Authors: Clark Robert L. , Mitchell Olivia S. 
Published: June 2022

AbstractOne of the most important financial decisions that pension participants make concerns how they access their pension assets when they terminate employment with their plan sponsor. Their choices depend both on own preferences and the options offered by their retirement plan. This paper examines both past and future pension withdrawal choices for those with defined benefit (DB) and defined contribution (DC) pensions, separately. Our data are drawn from a set of pension distribution questions we fielded in the Understanding American Study. Results show significant differences in distribution choices based on the type of retirement plan, with individuals covered by DB plans significantly more likely to select annuities compared to similar employees covered by DC plans. We also find differences in how higher annual income affects annuity choices based on coverage by DB plans. Individuals with lower levels of financial literacy and lower annual income have less knowledge of basic pension characteristics.
Volume, Effusion Rate, and Lava Transport During the 2021 Fagradalsfjall Eruption: Results From Near Real‐Time Photogrammetric Monitoring
Authors: Pedersen Gro B. M. , Belart Joaquin M. C. , Óskarsson Birgir Vilhelm , Gudmundsson Magnús Tumi , Gies Nils , Högnadóttir Thórdís , Hjartardóttir Ásta Rut , Pinel Virginie , Berthier Etienne , Dürig Tobias , Reynolds Hannah Iona , Hamilton Christopher W. , Valsson Guðmundur , Einarsson Páll , Ben‐Yehosua Daniel , Gunnarsson Andri , Oddsson Björn 
Published: June 2022

AbstractThe basaltic effusive eruption at Mt. Fagradalsfjall lasted from 19 March to 18 September 2021, ending a 781‐year repose period on Reykjanes Peninsula, Iceland. By late September 2021, 33 near real‐time photogrammetric surveys were completed using satellite and airborne images, usually processed within 3–6 hr. The results provide unprecedented temporal data sets of lava volume, thickness, and effusion rate. This enabled rapid assessment of eruption evolution and hazards to populated areas, important infrastructure, and tourist centers. The lava flow field has a mean lava thickness exceeding 30 m, covers 4.8 km2 and has a bulk volume of 150 ± 3 × 106 m3. The March–September mean bulk effusion rate is 9.5 ± 0.2 m3/s, ranging between 1 and 8 m3/s in March–April and increasing to 9–13 m3/s in May–September. This is uncommon for recent Icelandic eruptions, where the highest discharge usually occurs in the opening phase.
Increasing Inhomogeneity of the Global Oceans
Authors: Ren Qiuping , Kwon Young‐Oh , Yang Jiayan , Huang Rui Xin , Li Yuanlong , Wang Fan 
Published: June 2022

AbstractThe ocean is inhomogeneous in hydrographic properties with diverse water masses. Yet, how this inhomogeneity has evolved in a rapidly changing climate has not been investigated. Using multiple observational and reanalysis datasets, we show that the spatial standard deviation (SSD) of the global ocean has increased by 1.4 ± 0.1% in temperature and 1.5 ± 0.1% in salinity since 1960. A newly defined thermohaline inhomogeneity index, a holistic measure of both temperature and salinity changes, has increased by 2.4 ± 0.1%. Climate model simulations suggest that the observed ocean inhomogeneity increase is dominated by anthropogenic forcing and projected to accelerate by 200%–300% during 2015–2100. Geographically, the rapid upper‐ocean warming at mid‐to‐low latitudes dominates the temperature inhomogeneity increase, while the increasing salinity inhomogeneity is mainly due to the amplified salinity contrast between the subtropical and subpolar latitudes.
Extension of Aseismic Slip Propagation Theory to Slow Earthquake Migration
Authors: Ariyoshi Keisuke 
Published: June 2022

AbstractNatural faults host various types of migrating slow earthquake phenomena, with migration speeds much lower than seismic wave speeds and different moment‐duration scaling from regular earthquakes. To advance the obtained quantitative understanding of the migration process and long duration of slow earthquakes, I study a chain reaction model in a population of brittle asperities based on a rate‐ and state‐dependent friction on a 3‐D subduction plate boundary. Simulation results show that the migration speed is quantitatively related to frictional properties by an analytical relation derived here. By assuming that local pore water in front of the migration drives rapid tremor reversal and is so local as to hold a constant stress drop, the application of the analytical solution to observational results suggests that (a) the temporal changes of observed migration speeds for the rapid tremor reversal could be explained by about 70% reduction of the effective normal stress; (b) effective normal stress for the deeper extension of seismogenic segment in the western part of Shikoku is about 1.5 times greater than that in the central part. Applying rupture time delay between slow earthquake asperities for the duration longer than regular earthquake, I also conclude that (c) the characteristic slip distance of rate‐and‐state friction for low‐frequency earthquakes is roughly between 30 µm and 30 mm; (d) the stress and strength drops of very low‐frequency earthquakes is much smaller than 1 MPa.
India (Tethyan Himalaya Series) in Central Myanmar: Implications for the Evolution of the Eastern Himalayan Syntaxis and the Sagaing Transform‐Fault System
Authors: Min Myo , Ratschbacher Lothar , Franz Leander , Hacker Bradley R. , Enkelmann Eva , Toreno Eko Yoan , Härtel Birk , Schurr Bernd , Tichomirowa Marion , Pfänder Jörg A. 
Published: June 2022

AbstractIn the Katha Range of central Myanmar, lithologic tracers and pressure‐temperature‐deformation‐time data identify Cambro‐Ordovician, Indian‐affinity Tethyan Himalaya Series, located ∼700 km from their easternmost outcrop in S‐Tibet, and ∼450 km from Himalayan rocks in the Eastern Himalayan Syntaxis. Metamorphism began at ∼65 Ma, peaked at ∼45 Ma (∼510°C, 0.93 GPa), and exhumation/cooling (∼25°C/Myr) occurred until ∼30 Ma in a subduction‐early collision tectonic setting. When the Burma microplate—part of the intra‐Tethyan Incertus arc—accreted to SE‐Asia, its eastern boundary, the southern continuation of the Indus‐Yarlung suture (IYS), was reactivated as the Sagaing fault (SF), which propagated northward into Indian rocks. In the Katha rocks, this strike‐slip stage is marked by ∼4°C/Myr exhumation/cooling. Restoring the SF system defines a continental collision‐oceanic subduction transition junction, where the IYS bifurcates into the SF at the eastern edge of the Burma microplate and the Jurassic ophiolite‐Jadeite belts that include the Incertus‐arc suture.
Human RIPK3 C-lobe phosphorylation is essential for necroptotic signaling
Authors: Meng Yanxiang , Horne Christopher R. , Samson Andre L. , Dagley Laura F. , Young Samuel N. , Sandow Jarrod J. , Czabotar Peter E. , Murphy James M. 
Published: June 2022

AbstractNecroptosis is a caspase-independent, pro-inflammatory mode of programmed cell death which relies on the activation of the terminal effector, MLKL, by the upstream protein kinase RIPK3. To mediate necroptosis, RIPK3 must stably interact with, and phosphorylate the pseudokinase domain of MLKL, although the precise molecular cues that provoke RIPK3 necroptotic signaling are incompletely understood. The recent finding that RIPK3 S227 phosphorylation and the occurrence of a stable RIPK3:MLKL complex in human cells prior to exposure to a necroptosis stimulus raises the possibility that additional, as-yet-unidentified phosphorylation events activate RIPK3 upon initiation of necroptosis signaling. Here, we sought to identify phosphorylation sites of RIPK3 and dissect their regulatory functions. Phosphoproteomics identified 21 phosphorylation sites in HT29 cells overexpressing human RIPK3. By comparing cells expressing wild-type and kinase-inactive D142N RIPK3, autophosphorylation sites and substrates of other cellular kinases were distinguished. Of these 21 phosphosites, mutational analyses identified only pT224 and pS227 as crucial, synergistic sites for stable interaction with MLKL to promote necroptosis, while the recently reported activation loop phosphorylation at S164/T165 negatively regulate the kinase activity of RIPK3. Despite being able to phosphorylate MLKL to a similar or higher extent than wild-type RIPK3, mutation of T224, S227, or the RHIM in RIPK3 attenuated necroptosis. This finding highlights the stable recruitment of human MLKL by RIPK3 to the necrosome as an essential checkpoint in necroptosis signaling, which is independent from and precedes the phosphorylation of MLKL.
Asparagine synthetase regulates lung-cancer metastasis by stabilizing the β-catenin complex and modulating mitochondrial response
Authors: Cai Dong-Jing , Zhang Zi-Yu , Bu Yue , Li Li , Deng Yue-Zhen , Sun Lun-Quan , Hu Cheng-Ping , Li Min 
Published: June 2022

AbstractThe availability of asparagine is the limitation of cell growth and metastasis. Asparagine synthetase (ASNS) was an essential enzyme for endogenous asparagine products. In our study, ASNS-induced asparagine products were essential to maintain tumor growth and colony formations in vitro. But mutated ASNS which defected endogenous asparagine products still upregulated cell invasiveness, which indicated that ASNS promoted invasiveness by alternative pathways. Mechanically, ASNS modulated Wnt signal transduction by promoting GSK3β phosphorylation on ser9 and stabilizing the β-catenin complex, as result, ASNS could promote more β-catenin translocation into nucleus independent of endogenous asparagine. At the same time, ASNS modulated mitochondrial response to Wnt stimuli with increased mitochondrial potential and membrane fusion. In summary, ASNS promoted metastasis depending on Wnt pathway and mitochondrial functions even without endogenous asparagine products.
Ecological networks of dissolved organic matter and microorganisms under global change
Authors: Hu Ang , Choi Mira , Tanentzap Andrew J. , Liu Jinfu , Jang Kyoung-Soon , Lennon Jay T. , Liu Yongqin , Soininen Janne , Lu Xiancai , Zhang Yunlin , Shen Ji , Wang Jianjun 
Published: June 2022

AbstractMicrobes regulate the composition and turnover of organic matter. Here we developed a framework called Energy-Diversity-Trait integrative Analysis to quantify how dissolved organic matter and microbes interact along global change drivers of temperature and nutrient enrichment. Negative and positive interactions suggest decomposition and production processes of organic matter, respectively. We applied this framework to manipulative field experiments on mountainsides in subarctic and subtropical climates. In both climates, negative interactions of bipartite networks were more specialized than positive interactions, showing fewer interactions between chemical molecules and bacterial taxa. Nutrient enrichment promoted specialization of positive interactions, but decreased specialization of negative interactions, indicating that organic matter was more vulnerable to decomposition by a greater range of bacteria, particularly at warmer temperatures in the subtropical climate. These two global change drivers influenced specialization of negative interactions most strongly via molecular traits, while molecular traits and bacterial diversity similarly affected specialization of positive interactions.