bluuebunny/crossref_metadata_2025_split huggingface dataset:
Are we sacrificing the future of coral reefs on the altar of the “climate change” narrative?
Authors: Abelson Avigdor 
Published: November 2019

Abstract
Following a series of mass-bleaching events that have seriously degraded coral reefs, notably the Great Barrier Reef of Australia, a common narrative is now dominating the discourse, according to which “the only sure way to save the world’s coral reefs is climate change mitigation”. However, climate change is not a sole stressor. Most coral reefs around the world are threatened by a myriad of local stressors, including overfishing, destructive fishing, untreated sewage, agriculture effluents (nutrients and pesticides), and siltation due to deforestation. Reefs will not survive the severe effects of this plethora of stressors while waiting until we mitigate climate change. In order to safeguard reefs, we need to adopt a new narrative—“there are diverse ways in which we can improve the chances of saving coral reefs”—by acting now to: (i) improve their local protection and marine protected area networks, (ii) alleviate their critical local stressors, (iii) restore degraded and damaged reefs, and (iv) promote reef resilience and adaptation (e.g. adaptation networks, assisted evolution) to the changing conditions, notably climate change effects. It is time for us to move on from the impractical goals of the climate change narrative (“interventions beyond our field of expertise”) to building up resilience and adaptation of social-ecological systems of coral reefs.
Large Deviation Estimates and Hölder Regularity of the Lyapunov Exponents for Quasi-periodic Schrödinger Cocycles
Authors: Han Rui , Zhang Shiwen 
Published: November 2019

AbstractWe consider one-dimensional quasi-periodic Schrödinger operators with analytic potentials. In the positive Lyapunov exponent regime, we prove large deviation estimates, which lead to refined Hölder continuity of the Lyapunov exponents and the integrated density of states, in both small Lyapunov exponent and large coupling regimes. Our results cover all the Diophantine frequencies and some Liouville frequencies.
Association of HLA Genotype With T-Cell Activation in Human Immunodeficiency Virus (HIV) and HIV/Hepatitis C Virus–Coinfected Women
Authors: Kovacs Andrea A Z , Kono Naoko , Wang Chia-Hao , Wang Daidong , Frederick Toni , Operskalski Eva , Tien Phyllis C , French Audrey L , Minkoff Howard , Kassaye Seble , T. Golub Elizabeth , Aouizerat Bradley E , Kuniholm Mark H , Millstein Joshua 
Published: November 2019

Abstract

Background
Global immune activation and HLA alleles are each associated with the pathogenesis of human immunodeficiency virus (HIV) and hepatitis C virus .

Methods
We evaluated the relationship between 44 HLA class I and 28 class II alleles and percentages of activated CD8 (CD8+CD38+DR+) and CD4 (CD4+CD38+DR+) T cells in 586 women who were naive to highly active antiretroviral therapy. We used linear generalized estimating equation regression models, adjusting for race/ethnicity, age, HIV load, and hepatitis C virus infection and controlling for multiplicity using a false discovery rate threshold of 0.10.

Results
Ten HLA alleles were associated with CD8 and/or CD4 T-cell activation. Lower percentages of activated CD8 and/or CD4 T cells were associated with protective alleles B*57:03 (CD8 T cells, −6.6% [P = .002]; CD4 T cells, −2.7% [P = .007]), C*18:01 (CD8 T cells, −6.6%; P &lt; .0008) and DRB1*13:01 (CD4 T cells, −2.7%; P &lt; .0004), and higher percentages were found with B*18:01 (CD8 T cells, 6.2%; P &lt; .0003), a detrimental allele. Other alleles/allele groups associated with activation included C*12:03, group DQA1*01:00, DQB1*03:01, DQB1*03:02, DQB1*06:02, and DQB1*06:03.

Conclusion
These findings suggest that a person’s HLA type may play a role in modulating T-cell activation independent of viral load and sheds light on the relationship between HLA, T-cell activation, immune control, and HIV pathogenesis.
Human Immunodeficiency Virus Exposure but Not Early Cytomegalovirus Infection Is Associated With Increased Hospitalization and Decreased Memory T-Cell Responses to Tetanus Vaccine
Authors: Smith Christiana , Moraka Natasha O , Ibrahim Maryanne , Moyo Sikhulile , Mayondi Gloria , Kammerer Betsy , Leidner Jean , Gaseitsiwe Simani , Li Shaobing , Shapiro Roger , Lockman Shahin , Weinberg Adriana 
Published: November 2019

AbstractBackgroundHuman immunodeficiency virus (HIV)-exposed, uninfected (HEU) infants experience high rates of infectious morbidity. We hypothesized that early cytomegalovirus (CMV) infection was associated with increased hospitalization rates and decreased vaccine responses in HEU compared with HIV-unexposed (HUU) infants.MethodsAmong infants enrolled in the Tshipidi study in Botswana, we determined CMV infection status by 6 months of age and compared hospitalization rates and responses to tetanus and Bacille Calmette-Guérin vaccines among HEU and HUU vaccinees.ResultsFifteen of 226 (6.6%) HEU infants and 17 (19.3%) of 88 HUU infants were CMV-infected by 6 months. The HEU infants were approximately 3 times as likely to be hospitalized compared with HUU infants (P = .02). The HEU peripheral blood cells produced less interleukin (IL)-2 (P = .004), but similar amounts of interferon-γ, after stimulation with tetanus toxoid. Antitetanus immunoglobulin G titers were similar between groups. Cellular responses to purified protein derivative stimulation did not differ between groups. Maternal receipt of 3-drug antiretroviral therapy compared with zidovudine was associated with increased IL-2 expression after tetanus toxoid stimulation. The infants’ CMV infection status was not associated with clinical or vaccine response outcomes.ConclusionsWe observed that increased rates of hospitalization and decreased memory T-cell responses to tetanus vaccine were associated with HIV exposure and incomplete treatment of maternal HIV infection, but not early CMV infection.
Identification of AbaR4 Acinetobacter baumannii resistance island in clinical isolates of blaOXA-23-positive Proteus mirabilis
Authors: Octavia Sophie , Xu Weizhen , Ng Oon Tek , Marimuthu Kalisvar , Venkatachalam Indumathi , Cheng Bernadette , Lin Raymond T P , Teo Jeanette W P 
Published: November 2019

Abstract

Objectives
bla OXA-23 is a class D carbapenemase-encoding gene typical of the Acinetobacter genus. However, its occurrence in the Enterobacteriaceae is uncommon. Here we provide the genome characterization of blaOXA-23-positive Proteus mirabilis.

Methods
In Singapore, a national surveillance of carbapenem non-susceptible clinical Enterobacteriaceae has enabled the collection of OXA-23 bearing isolates. Three clinical P. mirabilis were whole-genome sequenced using Oxford Nanopore MinION and Illumina platforms. The sequence accuracy of MinION long-read contigs was enhanced by polishing with Illumina-derived short-read data.

Results
In two P. mirabilis genomes, blaOXA-23 was detected as two copies, present on the chromosome and on a 60018 bp plasmid. blaOXA-23 was associated with the classic Acinetobacter composite transposon Tn2006, bounded by two copies of ISAba1 bracketing the carbapenemase gene. The Tn2006 itself was embedded within an Acinetobacter baumannii AbaR4 resistance island. In the chromosome, the AbaR4 was found integrated into the comM gene, which is also the preferred ‘hotspot’ in A. baumannii. In the plasmid, AbaR4 integrated into a putative colicin gene.

Conclusions
Our description of an A. baumannii AbaR4 encoding blaOXA-23 in P. mirabilis is to our knowledge the first description of an Acinetobacter resistance island in Proteus and suggests that P. mirabilis may be a reservoir for this class D carbapenemase gene.
Detailing postoperative pain and opioid utilization after periacetabular osteotomy with automated mobile messaging
Authors: Hajewski Christina , Anthony Chris A , Rojas Edward O , Westermann Robert , Willey Michael 
Published: November 2019

Abstract
In the setting of periacetabular osteotomy (PAO), this investigation sought to (i) describe patient-reported pain scores and opioid utilization in the first 6 weeks following surgery and (ii) evaluate the effectiveness of postoperative communication using a robotic mobile messaging platform. Subjects indicated for PAO were enrolled from a young adult hip clinic. For the first 2 weeks after surgery, subjects received daily mobile messages inquiring about pain level on a 0–10 scale and the number of opioid pain medication tablets they consumed in the previous 24 h. Messaging frequency decreased to 3 per week in Weeks 3–6. Pain scores, opioid utilization and response rates with our mobile messaging platform were quantified for the 6-week postoperative period. Twenty-nine subjects underwent PAO. Twenty-one had concurrent hip arthroscopy. Average daily pain scores decreased over the first four postoperative days. Average pain scores reported were 5.9 ± 1.9, 4.1 ± 3.3 and 3.0 ± 3.5 on Day 1, Day 14 and Week 6, respectively. Reported opioid tablet utilization was 5.0 ± 3.2, 2.2 ± 2.0 and 0.0 ± 0.0 on Days 1 and 14 and at 6 weeks. Response rate for participants completing the 6-week messaging protocol was 84.1%. Patient-reported pain scores decreased over the first two postoperative weeks following PAO before plateauing in weeks 3–6. Opioid pain medication utilization increased in the first postoperative week before gradually declining to no tabs consumed at 6 weeks after PAO. Automated mobile messaging is an effective method of perioperative communication for the collection of pain scores and opioid utilization in patients undergoing PAO.
Factors Associated With Use of High-Cost Agents for the Treatment of Metastatic Non–Small Cell Lung Cancer
Authors: Bradley Cathy J , Eguchi Megan , Perraillon Marcelo C 
Published: November 2019

AbstractBackgroundAntineoplastic agents approved in recent decades are a marked advancement in cancer treatment, but they come at considerable cost. These drugs may widen survival disparities between patients who receive these agents and those who do not. We examine factors associated with the use of high-cost antineoplastic agents for the treatment of metastatic non–small cell lung cancer.MethodsWe conducted a retrospective observational study using 2007–2015 Surveillance, Epidemiology, and End-Results–Medicare data supplemented with the Area Health Resource File. Patients were aged 66 years and older, were enrolled in fee-for-service Medicare Part D, were diagnosed with a first primary diagnosis of metastatic non–small cell lung cancer, and had received an antineoplastic agent. “High-cost agents” were defined as agents costing $5000 or more per month. Independent variables include race/ethnicity, urban or rural residency, census tract poverty, and treatment facility type (eg, National Cancer Institute designation).ResultsPatients who lived in areas of high poverty were 4 percentage points less likely to receive high-cost agents (two-sided P &lt; .001). Patients who were not treated at a National Cancer Institute–designated center were 10 percentage points less likely to receive these agents (two-sided P &lt; .001). A 27 percentage-point increase in the likelihood of receiving a high-cost agent was observed in 2015, as compared to 2007, highlighting the rapid change in practice patterns (two-sided P &lt; .001).ConclusionPotential policy and care delivery solutions involve outreach and support to community physicians who treat patients in remote areas. We estimate that widespread use of these agents conservatively cost approximately $3 billion per year for the treatment of metastatic non–small cell lung cancer alone.
Abdominal cocoon: an unexpected cause of ascites in a healthy patient
Authors: Kappauf Catharine , Rahaman Jamal , Popowich Daniel 
Published: November 2019

Abstract
Abdominal cocoon is the idiopathic fibrotic encasement of abdominal organs. It classically presents as small bowel obstruction in young women. In this case report, we present a rare example of a patient presenting solely with massive ascites of presumed gynecologic origin, who upon surgical exploration was found to have abdominal cocoon. We discuss the patient’s unique disease presentation, unrevealing work-up and the treatment strategy pursued, and provide a review of the literature.
Theatrical Marginalia: Pierre Baillot and the Prototype of the Modern Performer
Authors: Morabito Fabio 
Published: November 2019

Abstract
In Western art music, the idea of the professional performer as a versatile interpreter of someone else’s music consolidated around the turn of the nineteenth century. The institutionalization of instrumental training in dedicated schools (such as the Paris Conservatoire, established in 1795) favoured an increasing specialization of composers and performers in their respective tasks. Scholars have often traced the development of these modern professional identities to fundamental innovations in the fabric and conceptions of musical notation. The newly detailed scores by Haydn, Mozart, and Beethoven specify articulation, phrasing, and even fingerings, suggesting a growing authority of the composer over the performer’s moves, and the score itself as an increasingly important focus of the musical event (scripting both what performers should do and what listeners, ideally, should discern). Rather than focusing on how music was notated by composers, this article proposes to explore the perspective of the performers handling it: how they understood their role in bringing the score to life, and the realms of commentary they inspired in Parisian debates about the progress of the art and the mechanization of performance in the early nineteenth century. At the core of the Paris Conservatoire’s universal pedagogical project, the violinist Pierre Baillot (1771–1842) devised a prototype professional figure for the future of instrumental performance across genres: not a puppet-musician controlled via invisible strings, but an architect of musical impersonations, able to stimulate images or stories in the listeners’ minds and leave them theatrically spellbound.
Susceptibility of uncommon Candida species to systemic antifungals by the EUCAST methodology
Authors: Díaz-García Judith , Alcalá Luis , Martín-Rabadán Pablo , Mesquida Aina , Sánchez-Carrillo Carlos , Reigadas Elena , Muñoz Patricia , Escribano Pilar , Guinea Jesús 
Published: November 2019

Abstract
The incidence of infections by uncommon Candida species has increased in recent years, however, in vitro susceptibility data are scarce. Here we assess the susceptibility of C. krusei, C. dubliniensis, C. lusitaniae, and C. guilliermondii complex isolates (n = 120) to antifungal agents by the EUCAST methodology. C. dubliniensis proved to be the most susceptible species, similar to that of C. albicans (P &lt; .05), whereas C. guilliermondii was the least susceptible. Two C. krusei isolates were echinocandin-resistant and harbored a point mutation (L701M) in the FKS1. Some isolates were either fluconazole-resistant (C. lusitaniae, n = 2) or fluconazole non-wild type (C. guilliermondii, n = 3).
Rotation measure synthesis applied to synthetic SKA images of galaxy clusters
Authors: Loi F , Murgia M , Govoni F , Vacca V , Bonafede A , Ferrari C , Prandoni I , Feretti L , Giovannini G , Li H 
Published: November 2019

ABSTRACT
Future observations with next-generation radio telescopes will help us to understand the presence and evolution of magnetic fields in galaxy clusters through determination of the so-called rotation measure (RM). In this work, we applied the RM synthesis technique to synthetic first phase Square Kilometre Array mid frequency element (i.e. the SKA1-MID) radio images of a pair of merging galaxy clusters, measured between 950 and 1750 MHz with a resolution of 10 arcsec and thermal noise of 0.1μJy beam−1. The results of our RM synthesis analysis are compared with the simulation input parameters. We study two cases: one with radio haloes at the cluster centres and another without. We found that the information obtained with RM synthesis is in general agreement with the input information; however, some discrepancies are present. We characterize them in this work, with the final goal of determining the potential impact of SKA1-MID on the study of cluster magnetic fields.
Phylogenomics Identifies an Ancestral Burst of Gene Duplications Predating the Diversification of Aphidomorpha
Authors: Julca Irene , Marcet-Houben Marina , Cruz Fernando , Vargas-Chavez Carlos , Johnston John Spencer , Gómez-Garrido Jèssica , Frias Leonor , Corvelo André , Loska Damian , Cámara Francisco , Gut Marta , Alioto Tyler , Latorre Amparo , Gabaldón Toni 
Published: November 2019

AbstractAphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106–227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings.
Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools
Authors: Gonzalez-Galarza Faviel F , McCabe Antony , Santos Eduardo J Melo dos , Jones James , Takeshita Louise , Ortega-Rivera Nestor D , Cid-Pavon Glenda M Del , Ramsbottom Kerry , Ghattaoraya Gurpreet , Alfirevic Ana , Middleton Derek , Jones Andrew R 
Published: November 2019

Abstract
The Allele Frequency Net Database (AFND, www.allelefrequencies.net) provides the scientific community with a freely available repository for the storage of frequency data (alleles, genes, haplotypes and genotypes) related to human leukocyte antigens (HLA), killer-cell immunoglobulin-like receptors (KIR), major histocompatibility complex Class I chain related genes (MIC) and a number of cytokine gene polymorphisms in worldwide populations. In the last five years, AFND has become more popular in terms of clinical and scientific usage, with a recent increase in genotyping data as a necessary component of Short Population Report article submissions to another scientific journal. In addition, we have developed a user-friendly desktop application for HLA and KIR genotype/population data submissions. We have also focused on classification of existing and new data into ‘gold–silver–bronze’ criteria, allowing users to filter and query depending on their needs. Moreover, we have also continued to expand other features, for example focussed on HLA associations with adverse drug reactions. At present, AFND contains >1600 populations from >10 million healthy individuals, making AFND a valuable resource for the analysis of some of the most polymorphic regions in the human genome.
Sensitive CometChip assay for screening potentially carcinogenic DNA adducts by trapping DNA repair intermediates
Authors: Ngo Le P , Owiti Norah A , Swartz Carol , Winters John , Su Yang , Ge Jing , Xiong Aoli , Han Jongyoon , Recio Leslie , Samson Leona D , Engelward Bevin P 
Published: November 2019

AbstractGenotoxicity testing is critical for predicting adverse effects of pharmaceutical, industrial, and environmental chemicals. The alkaline comet assay is an established method for detecting DNA strand breaks, however, the assay does not detect potentially carcinogenic bulky adducts that can arise when metabolic enzymes convert pro-carcinogens into a highly DNA reactive products. To overcome this, we use DNA synthesis inhibitors (hydroxyurea and 1-β-d-arabinofuranosyl cytosine) to trap single strand breaks that are formed during nucleotide excision repair, which primarily removes bulky lesions. In this way, comet-undetectable bulky lesions are converted into comet-detectable single strand breaks. Moreover, we use HepaRG™ cells to recapitulate in vivo metabolic capacity, and leverage the CometChip platform (a higher throughput more sensitive comet assay) to create the ‘HepaCometChip’, enabling the detection of bulky genotoxic lesions that are missed by current genotoxicity screens. The HepaCometChip thus provides a broadly effective approach for detection of bulky DNA adducts.
In vitro and in vivo properties of therapeutic oligonucleotides containing non-chiral 3′ and 5′ thiophosphate linkages
Authors: Duschmalé Jörg , Hansen Henrik Frydenlund , Duschmalé Martina , Koller Erich , Albaek Nanna , Møller Marianne Ravn , Jensen Klaus , Koch Troels , Wengel Jesper , Bleicher Konrad 
Published: November 2019

Abstract
The introduction of non-bridging phosphorothioate (PS) linkages in oligonucleotides has been instrumental for the development of RNA therapeutics and antisense oligonucleotides. This modification offers significantly increased metabolic stability as well as improved pharmacokinetic properties. However, due to the chiral nature of the phosphorothioate, every PS group doubles the amount of possible stereoisomers. Thus PS oligonucleotides are generally obtained as an inseparable mixture of a multitude of diastereoisomeric compounds. Herein, we describe the introduction of non-chiral 3′ thiophosphate linkages into antisense oligonucleotides and report their in vitro as well as in vivo activity. The obtained results are carefully investigated for the individual parameters contributing to antisense activity of 3′ and 5′ thiophosphate modified oligonucleotides (target binding, RNase H recruitment, nuclease stability). We conclude that nuclease stability is the major challenge for this approach. These results highlight the importance of selecting meaningful in vitro experiments particularly when examining hitherto unexplored chemical modifications.