bluuebunny/crossref_metadata_2025_split huggingface dataset:
Avian Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and W Degeneration
Authors: Sigeman Hanna , Strandh Maria , Proux-Wéra Estelle , Kutschera Verena E , Ponnikas Suvi , Zhang Hongkai , Lundberg Max , Soler Lucile , Bunikis Ignas , Tarka Maja , Hasselquist Dennis , Nystedt Björn , Westerdahl Helena , Hansson Bengt 
Published: September 2021

Abstract
How the avian sex chromosomes first evolved from autosomes remains elusive as 100 million years (My) of divergence and degeneration obscure their evolutionary history. The Sylvioidea group of songbirds is interesting for understanding avian sex chromosome evolution because a chromosome fusion event ∼24 Ma formed “neo-sex chromosomes” consisting of an added (new) and an ancestral (old) part. Here, we report the complete female genome (ZW) of one Sylvioidea species, the great reed warbler (Acrocephalus arundinaceus). Our long-read assembly shows that the added region has been translocated to both Z and W, and whereas the added-Z has retained its gene order the added-W part has been heavily rearranged. Phylogenetic analyses show that recombination between the homologous added-Z and -W regions continued after the fusion event, and that recombination suppression across this region took several million years to be completed. Moreover, recombination suppression was initiated across multiple positions over the added-Z, which is not consistent with a simple linear progression starting from the fusion point. As expected following recombination suppression, the added-W show signs of degeneration including repeat accumulation and gene loss. Finally, we present evidence for nonrandom maintenance of slowly evolving and dosage-sensitive genes on both ancestral- and added-W, a process causing correlated evolution among orthologous genes across broad taxonomic groups, regardless of sex linkage.
TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response
Authors: Zeng Zexian , Wong Cheryl J , Yang Lin , Ouardaoui Nofal , Li Dian , Zhang Wubing , Gu Shengqing , Zhang Yi , Liu Yang , Wang Xiaoqing , Fu Jingxin , Zhou Liye , Zhang Boning , Kim Sarah , Yates Kathleen B , Brown Myles , Freeman Gordon J , Uppaluri Ravindra , Manguso Robert , Liu X Shirley 
Published: September 2021

Abstract
Syngeneic mouse models are tumors derived from murine cancer cells engrafted on genetically identical mouse strains. They are widely used tools for studying tumor immunity and immunotherapy response in the context of a fully functional murine immune system. Large volumes of syngeneic mouse tumor expression profiles under different immunotherapy treatments have been generated, although a lack of systematic collection and analysis makes data reuse challenging. We present Tumor Immune Syngeneic MOuse (TISMO), a database with an extensive collection of syngeneic mouse model profiles with interactive visualization features. TISMO contains 605 in vitro RNA-seq samples from 49 syngeneic cancer cell lines across 23 cancer types, of which 195 underwent cytokine treatment. TISMO also includes 1518 in vivo RNA-seq samples from 68 syngeneic mouse tumor models across 19 cancer types, of which 832 were from immune checkpoint blockade (ICB) studies. We manually annotated the sample metadata, such as cell line, mouse strain, transplantation site, treatment, and response status, and uniformly processed and quality-controlled the RNA-seq data. Besides data download, TISMO provides interactive web interfaces to investigate whether specific gene expression, pathway enrichment, or immune infiltration level is associated with differential immunotherapy response. TISMO is available at http://tismo.cistrome.org.
Oxidation alters the architecture of the phenylalanyl-tRNA synthetase editing domain to confer hyperaccuracy
Authors: Srinivas Pooja , Steiner Rebecca E , Pavelich Ian J , Guerrero-Ferreira Ricardo , Juneja Puneet , Ibba Michael , Dunham Christine M 
Published: September 2021

Abstract
High fidelity during protein synthesis is accomplished by aminoacyl-tRNA synthetases (aaRSs). These enzymes ligate an amino acid to a cognate tRNA and have proofreading and editing capabilities that ensure high fidelity. Phenylalanyl-tRNA synthetase (PheRS) preferentially ligates a phenylalanine to a tRNAPhe over the chemically similar tyrosine, which differs from phenylalanine by a single hydroxyl group. In bacteria that undergo exposure to oxidative stress such as Salmonella enterica serovar Typhimurium, tyrosine isomer levels increase due to phenylalanine oxidation. Several residues are oxidized in PheRS and contribute to hyperactive editing, including against mischarged Tyr-tRNAPhe, despite these oxidized residues not being directly implicated in PheRS activity. Here, we solve a 3.6 Å cryo-electron microscopy structure of oxidized S. Typhimurium PheRS. We find that oxidation results in widespread structural rearrangements in the β-subunit editing domain and enlargement of its editing domain. Oxidization also enlarges the phenylalanyl-adenylate binding pocket but to a lesser extent. Together, these changes likely explain why oxidation leads to hyperaccurate editing and decreased misincorporation of tyrosine. Taken together, these results help increase our understanding of the survival of S. Typhimurium during human infection.
Low-Level Viremia Is Associated With Cumulative Adherence to Antiretroviral Therapy in Persons With HIV
Authors: Castillo-Mancilla Jose R , Morrow Mary , Coyle Ryan P , Coleman Stacey S , Zheng Jia-Hua , Ellison Lucas , Bushman Lane R , Kiser Jennifer J , Anderson Peter L , MaWhinney Samantha 
Published: September 2021

Abstract
The drivers of low-level viremia (LLV) between 20 and 200 copies/mL remain unclear. In 1042 person-visits from 497 persons with HIV on tenofovir disoproxil fumarate–containing antiretroviral therapy (ART), the association between LLV and cumulative antiretroviral adherence (quantified using tenofovir diphosphate [TFV-DP] in dried blood spots) was assessed. Lower TFV-DP levels were associated with higher odds of LLV. As TFV-DP (fmol/punch) categories decreased from &gt;1650 to 800–1650; 800–1650 to &lt;800; and &gt;1650 to &lt;800, the adjusted odds ratios for LLV vs HIV VL &lt;20 copies/mL were 2.0 (95% CI, 1.2–3.1), 2.4 (95% CI, 1.1–5.0), and 4.6 (95% CI, 2.2–9.9), respectively. This suggests that adherence could impact LLV.
Large-scale supplemental feeding alters lay date and nest survival in Eastern Bluebirds but not in two species of chickadees
Authors: Bailey Robyn L , Bonter David N 
Published: September 2021

Abstract
Wild bird feeding is a popular and growing activity, with approximately half of households participating in nations including the United States, Canada, the United Kingdom, New Zealand, and Australia. Supplemental feeding can increase survival and reproductive success of birds (which is often a goal of supplemental feeding efforts), but it raises concerns about phenological mismatch and possible increased risk of nest predation. Our objectives were to test whether access to supplemental food during the breeding season was correlated with (1) advanced egg-laying phenology, (2) increased clutch size, or (3) improved nest survival of 3 cavity-nesting species (Carolina Chickadee [Poecile carolinensis], Black-capped Chickadee [P. atricapillus], and Eastern Bluebird [Sialia sialis]) at a large spatial scale (the United States and Canada; spanning 22° latitude and 55° longitude). We examined data from 24,528 nest attempts submitted to NestWatch from 2014 to 2019. For Eastern Bluebirds, birds with access to supplemental insects initiated clutches 5.83 ± 0.89 (mean ± SE) days earlier than birds without access to food subsidies, whereas predicted nest survival was 5% greater for birds with access to supplemental insects (probability of nest success = 0.79, 95% CI: 0.77–0.81) than for birds without (0.74, 95% CI: 0.72–0.75). Clutch size of Eastern Bluebirds did not differ between birds with and without access to supplemental insects. For chickadees, supplemental feeding (of seeds, suet, insects, or fruit) was not correlated with phenology, clutch size, or nest survival. Our results suggest that supplemental feeding of insects can be an effective tool for increasing nest survival in Eastern Bluebirds and potentially other food-limited insectivores. However, the efficacy of supplemental feeding for improving reproductive success varies across taxa, likely related to diet. Despite widespread feeding of Black-capped and Carolina Chickadees, supplemental food had no discernable effect on timing of egg-laying, clutch size, or nest survival.
L’évaluation, le diagnostic et la prise en charge du trouble développemental de la coordination
Authors: Ip Angie , Mickelson Elizabeth C R , Zwicker Jill G 
Published: September 2021

Résumé
Le trouble développemental de la coordination est une affection neurodéveloppementale qui touche de 5 % à 6 % des enfants d’âge scolaire. Il peut avoir des effets considérables sur le début du développement et le fonctionnement tout au long de la vie. Les données probantes appuient des interventions prometteuses, mais ce trouble continue d’être sous-estimé et sous-diagnostiqué. Les pédiatres jouent un rôle important dans son diagnostic et sa prise en charge. Le présent point de pratique et les tableaux qui l’accompagnent visent à aider les pédiatres à diagnostiquer et prendre en charge les cas de trouble développemental de la coordination non compliqué.
Phytoplankton photosynthesis: an unexplored source of biogenic methane emission from oxic environments
Authors: Bizic Mina 
Published: September 2021

Abstract
Recent studies show that all evaluated Cyanobacteria, diatoms and haptophytes, major constituents of freshwater and marine phytoplankton, emit methane during photosynthesis. This is independent of external methylated precursors, whose demethylation by prokaryotic phytoplankton (and other microorganisms) has been already shown to be a potent methane source. Methane is the second most significant anthropogenically influenced greenhouse gas with a global warming potential 85 times higher than carbon-dioxide, over a period of 20 years. Atmospheric methane has been steadily increasing, yet its natural sources are not well constrained, with the largest uncertainties occurring in aquatic ecosystems. Already for several decades, increasing evidence has been pointing out that methane produced under oxic conditions through non-traditional pathways (i.e. not archaeal methanogenesis) significantly contributes to the methane flux from marine and freshwater environments. This paper highlights the potential significance of phytoplankton as methane producers, particularly through the ubiquitous process of photosynthesis. Currently, available data serve as a proof of principle for the process and its potential rates, yet further extensive research is required to successfully provide emission estimates at a global scale. Therefore, studies investigating the taxonomic breadth of the process and the correlation of the methane emission rate with environmental factors should be conducted.
Diverse phosphate and auxin transport loci distinguish phosphate tolerant from sensitive Arabidopsis accessions
Authors: Yi Changyu , Wang Xinchao , Chen Qian , Callahan Damien L , Fournier-Level Alexandre , Whelan James , Jost Ricarda 
Published: September 2021

Abstract
Phosphorus (P) is an essential element for plant growth often limiting agroecosystems. To identify genetic determinants of performance under variable phosphate (Pi) supply, we conducted genome-wide association studies on five highly predictive Pi starvation response traits in 200 Arabidopsis (Arabidopsis thaliana) accessions. Pi concentration in Pi-limited organs had the strongest, and primary root length had the weakest genetic component. Of 70 trait-associated candidate genes, 17 responded to Pi withdrawal. The PHOSPHATE TRANSPORTER1 gene cluster on chromosome 5 comprises PHT1;1, PHT1;2, and PHT1;3 with known impact on P status. A second locus featured uncharacterized endomembrane-associated auxin efflux carrier encoding PIN-LIKES7 (PILS7) which was more strongly suppressed in Pi-limited roots of Pi-starvation sensitive accessions. In the Col-0 background, Pi uptake and organ growth were impaired in both Pi-limited pht1;1 and two pils7 T-DNA insertion mutants, while Pi -limited pht1;2 had higher biomass and pht1;3 was indistinguishable from wild-type. Copy number variation at the PHT1 locus with loss of the PHT1;3 gene and smaller scale deletions in PHT1;1 and PHT1;2 predicted to alter both protein structure and function suggest diversification of PHT1 is a key driver for adaptation to P limitation. Haplogroup analysis revealed a phosphorylation site in the protein encoded by the PILS7 allele from stress-sensitive accessions as well as additional auxin-responsive elements in the promoter of the “stress tolerant” allele. The former allele’s inability to complement the pils7-1 mutant in the Col-0 background implies the presence of a kinase signaling loop controlling PILS7 activity in accessions from P-rich environments, while survival in P-poor environments requires fine-tuning of stress-responsive root auxin signaling.
Liquidity Constraints in the U.S. Housing Market
Authors: Boar Corina , Gorea Denis , Midrigan Virgiliu 
Published: September 2021

Abstract
We study the severity of liquidity constraints in the U.S. housing market using a life-cycle model with uninsurable idiosyncratic risks in which houses are illiquid, but agents can extract home equity by refinancing their mortgages. The model implies that four-fifths of homeowners are liquidity constrained and willing to pay an average of 13 cents to extract an additional dollar of liquidity from their home. Most homeowners value liquidity for precautionary reasons, anticipating the possibility of income declines and the need to make mortgage payments. The model reproduces well the observed response of consumption to tax rebates and mortgage relief programs and predicts large welfare gains from policies aimed at providing temporary liquidity relief to homeowners.
The Equilibrium Consequences of Indexing
Authors: Bond Philip , García Diego 
Published: September 2021

Abstract
We develop a benchmark model to study the equilibrium consequences of indexing in a standard rational expectations setting. Individuals incur costs to participate in financial markets, and these costs are lower for individuals who restrict themselves to indexing. A decline in indexing costs directly increases the prevalence of indexing, thereby reducing the price efficiency of the index and augmenting relative price efficiency. In equilibrium, these changes in price efficiency in turn further increase indexing, and raise the welfare of uninformed traders. For well-informed traders, the share of trading gains stemming from market timing increases relative to stock selection trades.
When does a beneficiary benefit?
Authors: Alexander Stephen 
Published: September 2021

Abstract
It is a well-recognised principle that trustees, acting as fiduciaries, must exercise their discretionary powers for the benefit of the beneficiaries of the trust. A wrongful exercise of those powers will be a breach and may be set aside by a court. In most cases, the question of whether the exercise of the discretion is of “benefit” to the beneficiary is obvious. However, there are occasions where it is not so, particularly where the “benefit” to the beneficiary is not direct or is not fiscal in nature. In these cases, trustees must tread carefully. The Royal Court's recent decision in In the matter of the May Trust [2021] JRC137 provides important clarification on what constitutes a “benefit” and is essential guidance for trustees in this often misunderstood area.
Online misinformation and vaccine hesitancy
Authors: Garett Renee , Young Sean D 
Published: September 2021

Lay Summary
Vaccine hesitancy, the rejection or delay to get vaccinated even if there is an effective vaccine available, may be instrumental in the resurgence of vaccine-preventable disease. Studies have shown that the rise in nonmedical exemptions for vaccination increases rates of childhood vaccine-preventable disease. One factor that influences vaccine hesitancy is online misinformation. False or misleading information online regarding vaccines can be found in independent news outlets, websites, and social media. The spread of vaccine misinformation is especially important during the COVID-19 pandemic as false information can decrease pro-vaccine opinions. The recent announcement of an effective COVID-19 vaccine became a hot topic online, with many adults hesitant to take the vaccine. Public health experts, medical professionals, and pro-vaccine individuals can help curb the spread of misinformation by correcting false statements online. Social media companies can also aid in stopping misinformation by implementing and enforcing policy that limits misinformation on their platforms.
Exploring the Role of Fungal Endophytes in the Sudden Death Syndrome of the Invasive Shrub Chrysanthemoides monilifera subsp. rotundata in Australia
Authors: Morin Louise , Bissett Andrew B. , van Klinken Rieks D. 
Published: September 2021

Pathogens that attack invasive plants can positively affect the integrity and functioning of ecosystems. Stem-tip dieback and extensive wilting followed by sudden death have been observed in Chrysanthemoides monilifera subsp. rotundata (bitou bush), one of Australia’s worst invasive shrubs. Metabarcoding and culturing methods were used to investigate whether fungi are implicated in this syndrome. Metabarcoding results revealed significantly different endophytic fungal communities within healthy and diseased bitou bush, and colocated native plants. There was no difference in fungal communities between soil sampled in the root zone of healthy and diseased bitou bush at the same site. Two Diaporthe sp. operational taxonomic units (OTUs), dominant at sites with extensive wilting explained 30% of the similarity between diseased bitou bush across all sites. Two other OTUs, Austropleospora osteospermi and Coprinellus sp., explained 20 and 40% of the similarity between diseased plants, respectively, and were only dominant at sites with dead or stunted, partially defoliated but not wilted bitou bush. A Penicillium sp. OTU explained 90% of the similarity between healthy bitou bush plants. Various Diaporthe spp. dominated isolations from diseased bitou bush. Manipulative experiments confirmed Diaporthe spp. pathogenicity on bitou bush excised and in situ stems. In another experiment, Diaporthe masirevicii infected flowers and, from there, colonized stems endophytically; however, wilting and sudden death of bitou bush did not occur within the experimental timeframe. Our study provides circumstantial evidence that bitou bush sudden death syndrome is the result of a shift in the composition of its endophytic fungal community from mutualist to pathogenic species. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Carbon Footprint of General, Regional, and Combined Anesthesia for Total Knee Replacements
Authors: McGain Forbes , Sheridan Nicole , Wickramarachchi Kasun , Yates Simon , Chan Brandon , McAlister Scott 
Published: September 2021

Background
Health care itself contributes to climate change. Anesthesia is a “carbon hotspot,” yet few data exist to compare anesthetic choices. The authors examined the carbon dioxide equivalent emissions associated with general anesthesia, spinal anesthesia, and combined (general and spinal anesthesia) during a total knee replacement.

Methods
A prospective life cycle assessment of 10 patients in each of three groups undergoing knee replacements was conducted in Melbourne, Australia. The authors collected input data for anesthetic items, gases, and drugs, and electricity for patient warming and anesthetic machine. Sevoflurane or propofol was used for general anesthesia. Life cycle assessment software was used to convert inputs to their carbon footprint (in kilogram carbon dioxide equivalent emissions), with modeled international comparisons.

Results
Twenty-nine patients were studied. The carbon dioxide equivalent emissions for general anesthesia were an average 14.9 (95% CI, 9.7 to 22.5) kg carbon dioxide equivalent emissions; spinal anesthesia, 16.9 (95% CI, 13.2 to 20.5) kg carbon dioxide equivalent; and for combined anesthesia, 18.5 (95% CI, 12.5 to 27.3) kg carbon dioxide equivalent. Major sources of carbon dioxide equivalent emissions across all approaches were as follows: electricity for the patient air warmer (average at least 2.5 kg carbon dioxide equivalent [20% total]), single-use items, 3.6 (general anesthesia), 3.4 (spinal), and 4.3 (combined) kg carbon dioxide equivalent emissions, respectively (approximately 25% total). For the general anesthesia and combined groups, sevoflurane contributed an average 4.7 kg carbon dioxide equivalent (35% total) and 3.1 kg carbon dioxide equivalent (19%), respectively. For spinal and combined, washing and sterilizing reusable items contributed 4.5 kg carbon dioxide equivalent (29% total) and 4.1 kg carbon dioxide equivalent (24%) emissions, respectively. Oxygen use was important to the spinal anesthetic carbon footprint (2.8 kg carbon dioxide equivalent, 18%). Modeling showed that intercountry carbon dioxide equivalent emission variability was less than intragroup variability (minimum/maximum).

Conclusions
All anesthetic approaches had similar carbon footprints (desflurane and nitrous oxide were not used for general anesthesia). Rather than spinal being a default low carbon approach, several choices determine the final carbon footprint: using low-flow anesthesia/total intravenous anesthesia, reducing single-use plastics, reducing oxygen flows, and collaborating with engineers to augment energy efficiency/renewable electricity.

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Use of a Motorized Intramedullary Bone Transport Nail for Trauma: Tips, Tricks, Corticotomy Techniques, and Rate and Rhythm
Authors: Quinnan Stephen Matthew 
Published: September 2021

Summary:
The introduction of internal magnetic nails (IMNs) for bone lengthening and bone transport has given us exciting new tools with which to treat segmental bone loss. Distraction osteogenesis has a long record of success in recreating even large segments of bone, but the availability of IMNs now offers the possibility of performing distraction osteogenesis without the drawbacks of external fixation. However, there are aspects of treatment with IMNs that are critical to understand to achieve success and minimize complications. These include assessment of feasibility in relation to available bone stock and segment configuration, the condition of the soft tissue envelope, and the presence of contamination or infection. They also include execution aspects such as bone end preparation, nail placement, need for and positioning of adjuvant fixation, corticotomy techniques, rate and rhythm of distraction, staged screw exchange, docking site preparation, and nail extraction. We discuss these issues in detail and introduce some novel techniques not previously described including the comminuted wedge osteotomy, testing of the nail with initial compression, and retention plug application for nail extraction to assist in optimizing success in certain clinical situations.
Segmental Bone Defects and the History of Bone Transport
Authors: Dahl Mark Thomas , Morrison Stewart 
Published: September 2021

Summary:
This article describes the etiology of segmental bone defects and reviews the options of care, past and present. A brief description of distraction osteogenesis and how the Ilizarov method was used to treat bone defects with circular external fixation leading to the latest method of transport with motorized internal lengthening nails is presented.