bluuebunny/crossref_metadata_2025_split huggingface dataset:
Post-transplant outcomes of standard and extended criteria donation after circulatory death donor lungs categorized by donation after brain death lung criteria
Authors: Tanaka Shin , Campo-Cañaveral de la Cruz Jose Luis , Barturen Mariana Gil , Carrasco Silvana Crowley , Román Alejandra Romero , León María Trujillo Sánchez de , Mejía Lucas Hoyos , Gómez Jose Manuel Naranjo , Peláez Mar Córdoba , Calle Álvaro Sánchez , Redondo Marina Pérez , Fadul Christian García , Ugarte Andrés Varela de , de-Antonio David Gómez- 
Published: February 2021

Abstract

OBJECTIVES
Most transplant centres use donation after brain death (DBD) criteria to assess the quality of controlled donation after circulatory death (cDCD) lungs. However, research on the relationship between DBD extended criteria and cDCD lung transplantation outcomes is limited. We investigated the outcomes of using DBD extended criteria donor organs in cDCD lung transplantation, compared to the standard criteria cDCD lung transplantation.

METHODS
A retrospective chart review of consecutive cDCD lung referrals to Hospital Universitario Puerta de Hierro-Majadahonda from June 2013 to December 2019 was undertaken. Donors were divided into standard and extended criteria groups. Early outcomes after lung transplant were compared between these groups using the Kaplan–Meier method and log-rank test.

RESULTS
Thirty out of 91 cDCD donor lung offers were accepted for transplantation, of which 11 were from standard criteria donors and 19 were extended criteria donors. The baseline characteristics of the 2 recipient groups were similar. There were no differences in the rates of grade 3 primary graft dysfunction at 72 h after lung transplantation (21% vs 18%), duration of mechanical ventilation (48 h vs 36 h), total intensive care unit stay (10 days vs 7 days) and 1-year survival (89% vs 90%).

CONCLUSIONS
Carefully selecting cDCD lungs from outside the standard acceptability criteria may expand the existing donor pool with no detrimental effects on lung transplantation outcomes.
Fluorescent toys ‘n’ tools lighting the way in fungal research
Authors: Van Genechten Wouter , Van Dijck Patrick , Demuyser Liesbeth 
Published: February 2021

ABSTRACTAlthough largely overlooked compared to bacterial infections, fungal infections pose a significant threat to the health of humans and other organisms. Many pathogenic fungi, especially Candida species, are extremely versatile and flexible in adapting to various host niches and stressful situations. This leads to high pathogenicity and increasing resistance to existing drugs. Due to the high level of conservation between fungi and mammalian cells, it is hard to find fungus-specific drug targets for novel therapy development. In this respect, it is vital to understand how these fungi function on a molecular, cellular as well as organismal level. Fluorescence imaging allows for detailed analysis of molecular mechanisms, cellular structures and interactions on different levels. In this manuscript, we provide researchers with an elaborate and contemporary overview of fluorescence techniques that can be used to study fungal pathogens. We focus on the available fluorescent labelling techniques and guide our readers through the different relevant applications of fluorescent imaging, from subcellular events to multispecies interactions and diagnostics. As well as cautioning researchers for potential challenges and obstacles, we offer hands-on tips and tricks for efficient experimentation and share our expert-view on future developments and possible improvements.
First annotated draft genomes of nonmarine ostracods (Ostracoda, Crustacea) with different reproductive modes
Authors: Tran Van Patrick , Anselmetti Yoann , Bast Jens , Dumas Zoé , Galtier Nicolas , Jaron Kamil S , Martens Koen , Parker Darren J , Robinson-Rechavi Marc , Schwander Tanja , Simion Paul , Schön Isa 
Published: February 2021

AbstractOstracods are one of the oldest crustacean groups with an excellent fossil record and high importance for phylogenetic analyses but genome resources for this class are still lacking. We have successfully assembled and annotated the first reference genomes for three species of nonmarine ostracods; two with obligate sexual reproduction (Cyprideis torosa and Notodromas monacha) and the putative ancient asexual Darwinula stevensoni. This kind of genomic research has so far been impeded by the small size of most ostracods and the absence of genetic resources such as linkage maps or BAC libraries that were available for other crustaceans. For genome assembly, we used an Illumina-based sequencing technology, resulting in assemblies of similar sizes for the three species (335–382 Mb) and with scaffold numbers and their N50 (19–56 kb) in the same orders of magnitude. Gene annotations were guided by transcriptome data from each species. The three assemblies are relatively complete with BUSCO scores of 92–96. The number of predicted genes (13,771–17,776) is in the same range as Branchiopoda genomes but lower than in most malacostracan genomes. These three reference genomes from nonmarine ostracods provide the urgently needed basis to further develop ostracods as models for evolutionary and ecological research.
Uniparental Genome Elimination in Australian Carp Gudgeons
Authors: Majtánová Zuzana , Dedukh Dmitrij , Choleva Lukáš , Adams Mark , Ráb Petr , Unmack Peter J , Ezaz Tariq 
Published: February 2021

AbstractMetazoans usually reproduce sexually, blending the unique identity of parental genomes for the next generation through functional crossing-over and recombination in meiosis. However, some metazoan lineages have evolved reproductive systems where offspring are either full (clonal) or partial (hemiclonal) genetic replicas. In the latter group, the process of uniparental genome elimination selectively eliminates either the maternal or paternal genome from germ cells, and only one parental genome is selected for transmission. Although fairly common in plants, hybridogenesis (i.e., clonal haploidization via chromosome elimination) remains a poorly understood process in animals. Here, we explore the proximal cytogenomic mechanisms of somatic and germ cell chromosomes in sexual and hybrid genotypes of Australian carp gudgeons (Hypseleotris) by tracing the fate of each set during mitosis (in somatic tissues) and meiosis (in gonads). Our comparative study of diploid hybrid and sexual individuals revealed visually functional gonads in male and female hybrid genotypes and generally high karyotype variability, although the number of chromosome arms remains constant. Our results delivered direct evidence for classic hybridogenesis as a reproductive mode in carp gudgeons. Two parental sets with integral structure in the hybrid soma (the F1 constitution) contrasted with uniparental chromosomal inheritance detected in gonads. The inheritance mode happens through premeiotic genome duplication of the parental genome to be transmitted, whereas the second parental genome is likely gradually eliminated already in juvenile individuals. The role of metacentric chromosomes in hybrid evolution is also discussed.
Rapid evolution at the Drosophila telomere: transposable element dynamics at an intrinsically unstable locus
Authors: McGurk Michael P , Dion-Côté Anne-Marie , Barbash Daniel A 
Published: February 2021

AbstractDrosophila telomeres have been maintained by three families of active transposable elements (TEs), HeT-A, TAHRE, and TART, collectively referred to as HTTs, for tens of millions of years, which contrasts with an unusually high degree of HTT interspecific variation. While the impacts of conflict and domestication are often invoked to explain HTT variation, the telomeres are unstable structures such that neutral mutational processes and evolutionary tradeoffs may also drive HTT evolution. We leveraged population genomic data to analyze nearly 10,000 HTT insertions in 85  Drosophila melanogaster genomes and compared their variation to other more typical TE families. We observe that occasional large-scale copy number expansions of both HTTs and other TE families occur, highlighting that the HTTs are, like their feral cousins, typically repressed but primed to take over given the opportunity. However, large expansions of HTTs are not caused by the runaway activity of any particular HTT subfamilies or even associated with telomere-specific TE activity, as might be expected if HTTs are in strong genetic conflict with their hosts. Rather than conflict, we instead suggest that distinctive aspects of HTT copy number variation and sequence diversity largely reflect telomere instability, with HTT insertions being lost at much higher rates than other TEs elsewhere in the genome. We extend previous observations that telomere deletions occur at a high rate, and surprisingly discover that more than one-third do not appear to have been healed with an HTT insertion. We also report that some HTT families may be preferentially activated by the erosion of whole telomeres, implying the existence of HTT-specific host control mechanisms. We further suggest that the persistent telomere localization of HTTs may reflect a highly successful evolutionary strategy that trades away a stable insertion site in order to have reduced impact on the host genome. We propose that HTT evolution is driven by multiple processes, with niche specialization and telomere instability being previously underappreciated and likely predominant.
Evading resistance to gene drives
Authors: Gomulkiewicz Richard , Thies Micki L , Bull James J 
Published: February 2021

AbstractGene drives offer the possibility of altering and even suppressing wild populations of countless plant and animal species, and CRISPR technology now provides the technical feasibility of engineering them. However, population-suppression gene drives are prone to select resistance, should it arise. Here, we develop mathematical and computational models to identify conditions under which suppression drives will evade resistance, even if resistance is present initially. Previous models assumed resistance is allelic to the drive. We relax this assumption and show that linkage between the resistance and drive loci is critical to the evolution of resistance and that evolution of resistance requires (negative) linkage disequilibrium between the two loci. When the two loci are unlinked or only partially so, a suppression drive that causes limited inviability can evolve to fixation while causing only a minor increase in resistance frequency. Once fixed, the drive allele no longer selects resistance. Our analyses suggest that among gene drives that cause moderate suppression, toxin-antidote systems are less apt to select for resistance than homing drives. Single drives of moderate effect might cause only moderate population suppression, but multiple drives (perhaps delivered sequentially) would allow arbitrary levels of suppression. The most favorable case for evolution of resistance appears to be with suppression homing drives in which resistance is dominant and fully suppresses transmission distortion; partial suppression by resistance heterozygotes or recessive resistance are less prone to resistance evolution. Given that it is now possible to engineer CRISPR-based gene drives capable of circumventing allelic resistance, this design may allow for the engineering of suppression gene drives that are effectively resistance-proof.
The heat is on: Gulf of Alaska Pacific cod and climate-ready fisheries
Authors: Peterson Williams Megan J , Robbins Gisclair Becca , Cerny-Chipman Elizabeth , LeVine Michael , Peterson Theresa 
Published: February 2021

Abstract
Rapidly changing ocean conditions pose substantial challenges for coastal communities, fishermen, and managers. From 2014 to 2016, the Gulf of Alaska (GOA) experienced a marine heatwave and corollary decline in Pacific cod (Gadus macrocephalus). Here, we explore the 2020 closure of the directed Pacific cod federal fishery in the GOA as a case study of the needs and opportunities for managing fisheries in the context of environmental change. We build on climate-ready fishery research and conversations with experienced commercial fishermen, including Alutiiq fishers, and fishery managers to: (i) discuss ecosystem-based management in Alaska, (ii) explore early warning signs and management challenges preceding the decline of Pacific cod, (iii) recommend tools to enhance adaptive capacity in fishery management. We conclude that a strong foundation of science-based management that incorporates ecosystem information and multiple ways of knowing, increased monitoring and evaluation of indicators, and new tools for managers to respond and adapt will be essential to sustainable fishery management. New mechanisms highlighted in this essay include: a GOA Fishery Ecosystem Plan, climate risk and vulnerability analyses, habitat protections, and the development of original metrics, such as food web production or function targets to inform stock assessments and fishery management.
Exotic Nonleaves with Infinitely Many Ends
Authors: Meniño Cotón Carlos , Schweitzer Paul A 
Published: February 2021

Abstract
We show that any simply connected topological closed $4$-manifold punctured along any compact, totally disconnected tame subset $\Lambda $ admits a continuum of smoothings, which are not diffeomorphic to any leaf of a $C^{1,0}$ codimension one foliation on a compact manifold. This includes the remarkable case of $S^4$ punctured along a tame Cantor set. This is the lowest reasonable regularity for this realization problem. These results come from a new criterion for nonleaves in $C^{1,0}$ regularity. We also include a new criterion for nonleaves in the $C^2$-category. Some of our smooth nonleaves are “exotic”, that is, homeomorphic but not diffeomorphic to leaves of codimension one foliations on a compact manifold, being the 1st examples in this class.
Theorizing Liberal Orders in Crisis Then and Now: Returning to Carr and Horkheimer
Authors: Molloy Seán 
Published: February 2021

AbstractThis article pursues an original line of inquiry by placing E.H. Carr in direct relation with his contemporary, Max Horkheimer. Although Carr is often cited as a progenitor by realists and critical theorists, these invocations of ancestry rarely go beyond passing references to Carr in presentist terms—i.e., how he relates to their present-day projects. By means of an extensive engagement with Horkheimer and Carr, the article reveals a shared commitment to ideology critique directed at bourgeois civilization. The article demonstrates that Carr's epistemology, critique of the harmony of interests, complex treatment of utopianism, and theorization of social transformation all have their counterparts in Horkheimer. The recovery of Carr's depth and sophistication as a theorist by means of a comparison of his positions with those of Horkheimer shows that at the time of its composition The Twenty Years’ Crisis was a cutting-edge exercise in critique by a theorist working on an ambitious canvas of civilizational scale. The article concludes with a section that demonstrates the continued relevance of Carr and Horkheimer by reference to contemporary debates about the crises currently affecting the liberal international order.
Forum: Nonuse of Nuclear Weapons in World Politics: Toward the Third Generation of “Nuclear Taboo” Research
Authors: Smetana Michal , Wunderlich Carmen 
Published: February 2021

Abstract
That nuclear weapons have not been used in war since 1945 is one of the most intriguing research puzzles in the field of international relations. It has sparked a fruitful scholarly debate: Can the persistence of the nonuse of nuclear weapons be understood with reference to a normative “taboo” subject to a constructivist logic of appropriateness, or does it rather constitute a prudent tradition based on a logic of consequences as rationalist scholars would have it? Recently, a study by Daryl Press, Scott Sagan, and Benjamin Valentino provided further impetus for this debate and opened up a “second generation” of “taboo” research. Unlike the first generation, the second wave examined attitudes toward nuclear use among the general public rather than elite decision-makers and used large-N experimental surveys rather than in-depth interviews and archival research. In particular, these studies raised several methodological questions on how to capture the “atomic aversion”: Is it meaningful to examine public attitudes in order to grasp the validity of the nuclear “taboo” (as opposed to elite perspectives) and can we infer a weakening of the normative aversion toward nuclear use from public surveys? Bringing together the pioneers of the original debate as well as more recent contributors, this special forum seeks to take stock of the progress that has been made by discussing the theoretical, conceptual, and methodological underpinnings of the research on the nonuse of nuclear weapons. Specifically, the contributions critically reflect upon the second wave of nuclear taboo scholarship with the overall aim to build bridges between different theoretical approaches and to identify avenues for further research in this area. Ultimately, this forum seeks to present the relevance of re-envisioning nuclear taboo research to a broader audience.
Deep sequencing analysis of M184V/I mutation at the switch and at the time of virological failure of boosted protease inhibitor plus lamivudine or boosted protease inhibitor maintenance strategy (substudy of the ANRS-MOBIDIP trial)
Authors: Delaugerre Constance , Nere Marie-Laure , Eymard-Duvernay Sabrina , Armero Alix , Ciaffi Laura , Koulla-Shiro Sinata , Sawadogo Adrien , Ngom Gueye Ndaye Fatou , Ndour Cheik Tidiane , Mpoudi Ngolle Mireille , Amara Ali , Chaix Marie-Laure , Reynes Jacques ,   the ANRS 12286/MOBIDIP study group
Published: February 2021

AbstractBackgroundThe ANRS12286/MOBIDIP trial showed that boosted protease inhibitor (bPI) plus lamivudine dual therapy was superior to bPI monotherapy as maintenance treatment in subjects with a history of M184V mutation.ObjectivesWe aimed to deep analyse the detection of M184V/I variants at time of switch and at the time of virological failure (VF).MethodsUltra-deep sequencing (UDS) was performed on proviral HIV-DNA at inclusion among 265 patients enrolled in the ANRS 12026/MOBIDIP trial, and on plasma from 31 patients experiencing VF. The proportion of M184V/I variants was described and the association between the M184V/I mutation at 1% of threshold and VF was explored with logistic regression models.ResultsM184V and I mutations were detected in HIV-DNA for 173/252 (69%) and 31/252 (12%) of participants, respectively. Longer duration of first-line treatment, higher plasma viral load at first-line treatment failure and higher baseline HIV-DNA load were associated with the archived M184V. M184I mutation was always associated with a STOP codon, suggesting defective virus. The 48 week estimated probability of remaining free from VF was comparable with or without the M184V/I mutation for dual therapy. At failure, M184V and major PI mutations were detected in 1/17 and 5/15 patients in the bPI arm and in 2/2 and 0/3 in the bPI+lamivudine arm, respectively.ConclusionsUsing UDS evidenced that archiving of M184V in HIV-DNA is heterogeneous despite past historical M184V in 96% of cases. The antiviral efficacy of lamivudine-based dual therapy regimens is mainly due to the residual lamivudine activity.
Uniformed Services and the Field Hospital Experience During Coronovirus Disease 2019 (SARS-CoV-2) Pandemic: Open to Closure in 30 Days With 1,100 Patients: The Javits New York Medical Station
Authors: Brady Kevin , Milzman Dave , Walton Edward , Sommer Darren , Neustadtl Alan , Napoli Anthony 
Published: February 2021

ABSTRACT

Introduction
The surge of SARS-CoV-2-virus infected (COVID-19) patients presenting to New York City (NYC) hospitals quickly overwhelmed and outnumbered the available acute care and intensive care resources in NYC in early March 2020. Upon the arrival of military medical assets to the Javits Convention Center in NYC, the planned mission to care for non-SARS-CoV-2 patients was immediately changed to manage patients with (SARS-CoV-2)COVID-19 and their comorbid conditions.
Healthcare professionals from every branch of the uniformed services, augmented by state and local resources, staffed the Javits New York Medical Station (JNYMS) from April 2020.

Methods
The data review reported aggregated summary statistics and participant observations collected by N.Y. State and U.S. military officials.

Results
During the 28 days of patient intake at the JNYMS, 1,095 SARS-CoV-2-positive patients were transferred from NYC hospitals to the JNYMS. At its peak, the JNYMS accepted 119 patients in a single day, had a maximum census of 453, and had a peak intensive care unit census of 35. The median length of stay was 4.6 days (interquartile range: 3.1-6.9 days). A total of 103 patients were transferred back to local hospitals, and there were 6 deaths, with an overall mortality rate of 0.6% (95% CI, 0.3-1.2).

Discussion and Conclusions
This is the first report of the care provided at the JNYMS. Within 2 weeks, this multi-agency effort was able to mobilize to care for over 1,000 SARS-CoV-2 patients with varying degrees of illness in a 1-month period. This was the largest field hospital mobilization in the U.S. medical history in response to a non-wartime pandemic. Its success with huge patient throughput including disposition and low mortality relieved critical overcrowding and supply deficiencies throughout NYC hospitals. The downstream impact likely saved additional hundreds of lives and reduced stress on the system during this healthcare crisis.
Intraoperative Transesophageal Echocardiography in Management of Acute Type I Aortic Dissection With Malperfusion: A Case Report
Authors: Beyrau Kaitlin E , Finne Huckelberry A , Wilson Sara M , Gibson Steven L , Koelling Erin E , Hudson Arlene J 
Published: February 2021

ABSTRACT
Acute type I aortic dissection is a life-threatening emergency with potentially devastating complications, including end-organ malperfusion. Early detection of malperfusion with intraoperative imaging allows for efficient transition to appropriate interventions. We present a case of a 65-year-old male with acute type I aortic dissection who underwent emergent surgical repair of the aortic root and hemiarch followed by acutely worsening distal malperfusion. The use of intraoperative transesophageal echocardiography played a critical role in visualizing diversion of flow to the false lumen, prompting urgent vascular surgery consultation and life-saving thoracic endovascular aortic repair.