bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population synthesis of accreting neutron stars emitting gravitational waves
Authors: Gittins Fabian , Andersson Nils 
Published: June 2019

ABSTRACT
The fastest-spinning neutron stars in low-mass X-ray binaries, despite having undergone millions of years of accretion, have been observed to spin well below the Keplerian break-up frequency. We simulate the spin evolution of synthetic populations of accreting neutron stars in order to assess whether gravitational waves can explain this behaviour and provide the distribution of spins that is observed. We model both persistent and transient accretion and consider two gravitational-wave-production mechanisms that could be present in these systems: thermal mountains and unstable rmodes. We consider the case of no gravitational-wave emission and observe that this does not match well with observation. We find evidence for gravitational waves being able to provide the observed spin distribution; the most promising mechanisms being a permanent quadrupole, thermal mountains, and unstable r modes. However, based on the resultant distributions alone, it is difficult to distinguish between the competing mechanisms.
Diverging identities: a model of class formation
Authors: Collier Paul 
Published: June 2019

Abstract
This paper is an application of Identity Economics. Since the literature in this field is recent, the paper begins with an extensive review of the key contributions. The current paper analyses the process and psychological costs of social polarization arising from economic inequalities. It may have some application to the current social divisions evident in the votes for Brexit and Donald Trump, and protest movements such as the gilets jaunes. In a simple model, people rationally maximize their utility from esteem, by selecting a subjective salient identity from two objective identities: nationality and job. The model shows how an increase in wages for the upper half of the population can lead those with high incomes to drop nationality as their salient identity, forming a new ‘elite’ class. This rational switch in the identity of high-income workers has efficiency and redistributive effects, reducing aggregate utility and generating regressive transfers.
Direct Repair of Iatrogenic Vertebral Artery Injury Associated With Anterior Cervical Corpectomy: 2-Dimensional Operative Video
Authors: Almefty Rami O , Albuquerque Felipe C , Spetzler Robert F , Turner Jay D 
Published: June 2019

Abstract
Vertebral artery (VA) injury during anterior cervical spine surgery has potentially devastating neurovascular consequences. Our video highlights the operative nuances of exposing and directly repairing the V2 segment of the VA from an anterior approach. A 67-year-old woman undergoing anterior cervical corpectomy at another hospital began briskly bleeding from a suspected VA injury. Upon emergency transfer of the patient to our facility, angiography confirmed a right VA pseudoaneurysm at the level of the C5 corpectomy. The decision was made to repair the VA directly, thus avoiding vessel sacrifice and stenting. The previous anterior exposure was reopened. The longus colli was mobilized laterally on the right side to expose the C4 and C6 anterior tubercles. A plane was developed in the transverse foramina from C4 to C6, and the foramina were unroofed anteriorly using a high-speed drill and Kerrison rongeurs. The injured segment of the VA was exposed, and the platelet plug over the injured VA was identified. The proximal and distal ends of the injured segment were temporarily clipped, and the platelet plug was removed, revealing a small, ovoid-shaped' full-thickness arterial wall defect. The VA injury was repaired with simple running 10-0 nylon sutures. Indocyanine green angiography confirmed rapid filling of the patent lumen. The corpectomy and anterior fixation were completed. The patient was placed on aspirin therapy postoperatively. The patient remained neurologically intact without neurovascular sequelae at the 1-yr follow-up. The patient consented to surgical treatment (Institutional Review Board review was not necessary). Used with permission from Barrow Neurological Institute.
Endoscope-Assisted, Transmastoid, High Cervical Approach for Resection of a Jugular Foramen Schwannoma: 2-Dimensional Operative Video
Authors: Mooney Michael A , Almefty Kaith K 
Published: June 2019

Abstract
Jugular foramen schwannomas (JFSs) are relatively rare, benign lesions that account for 10% to 30% of all tumors in the region of the jugular foramen. Given their slow-growing nature, JFSs can become quite large before causing symptoms of lower cranial nerve (LCN) dysfunction, making microsurgical resection a challenge. Successful resection of any JFS is dependent on the identification and preservation of the adjacent, uninvolved LCNs to alleviate nerve compression and preserve function. We report a transmastoid, high cervical approach to a dumbbell-shaped, extracranial JFS that was causing symptomatic LCN compression. The patient presented with dysphagia and was found to have left vocal cord paralysis on video laryngoscopy and intermittent aspiration on a swallowing evaluation. The transmastoid, high cervical exposure allowed for early identification of the tumor as well as the adjacent LCNs. Neurophysiological monitoring included somatosensory evoked potentials; brainstem auditory evoked responses; and cranial nerve VII, X, XI, and XII electromyographic monitoring. Endoscopic assistance allowed for improved LCN visualization from the high cervical exposure and gross-total resection of the tumor. The patient's dysphagia improved both subjectively and objectively following the resection. The patient gave written informed consent for surgery and publication of the case report. Institutional review board approval was not required for this case report. Used with permission from Barrow Neurological Institute.
Editing for Expansion: Railroad Photography, Native Peoples, and the American West, 1860–1880
Authors: Link Alessandra 
Published: June 2019

Abstract
In the nineteenth century, both railroad expansion and photography influenced relations between the United States and Native peoples in powerful ways. Scholars have often dealt with these two technological developments separately, but photographs and railroads have a shared history. Throughout the mid-to-late nineteenth century railroad companies engaged with photographs and photographers to promote travel on their lines. This article evaluates the production and circulation of transcontinental railroad photographs, and it concludes that the so-called golden age of landscape photography was built on the suppression of peopled scenes in the West. Images of Indians and trains that reached broad audiences placed Indigenous peoples in opposition to the modern forces cast in steel and running on steam. Picturing an unpeopled West and anti-modern Indians brightened business prospects for those investing in the promise of U.S. expansion beyond the 100th meridian.
Expanding the CRISPR Toolbox with ErCas12a in Zebrafish and Human Cells
Authors: Wierson Wesley A. , Simone Brandon W. , WareJoncas Zachary , Mann Carla , Welker Jordan M. , Kar Bibekananda , Gendron William A. C. , Barry Michael A. , Clark Karl J. , Dobbs Drena L. , McGrail Maura A. , Ekker Stephen C. , Essner Jeffrey J. 
Published: June 2019

AbstractClustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR associated (Cas) effector proteins enable the targeting of DNA double-strand breaks (DSBs) to defined loci based on a variable length RNA guide specific to each effector. The guide RNAs are generally similar in size and form, consisting of a ~20 nucleotide sequence complementary to the DNA target and an RNA secondary structure recognized by the effector. However, the effector proteins vary in Protospacer Adjacent Motif (PAM) requirements, nuclease activities, and DNA binding kinetics. Recently, ErCas12a, a new member of the Cas12a family, was identified in Eubacterium rectale. Here, we report the first characterization of ErCas12a activity in zebrafish and human cells. Using a fluorescent reporter system, we show that CRISPR/ErCas12a elicits strand annealing mediated DNA repair more efficiently than CRISPR/Cas9. Further, using our previously reported gene targeting method that utilizes short homology, GeneWeld, we demonstrate the use of CRISPR/ErCas12a to integrate reporter alleles into the genomes of both zebrafish and human cells. Together, this work provides methods for deploying an additional CRISPR/Cas system, thus increasing the flexibility researchers have in applying genome engineering technologies.
Intergenerational transmission of education and ADHD: Effects of parental genotypes
Authors: de Zeeuw Eveline L. , Hottenga Jouke-Jan , Ouwens Klaasjan G. , Dolan Conor V. , Ehli Erik A. , Davies Gareth E. , Boomsma Dorret I. , van Bergen Elsje 
Published: June 2019

AbstractIt is challenging to study whether children resemble their parents due to nature, nurture, or a mixture of both. Here we used a novel design that employs the fact that parents transmit 50% of their alleles to their offspring. The combined effect of these transmitted and non-transmitted alleles on a trait are summarized in a polygenic score (PGS). The non-transmitted PGS can only affect offspring through the environment, via genetically influenced behaviours in the parents, called genetic nurturing. For genotyped mother-father-offspring trios (1,120-2,518 per analysis) we calculated transmitted and non-transmitted PGSs for adult educational attainment (EA) and childhood ADHD and tested if these predicted outcomes in offspring. In adults, both transmitted (R2= 7.6%) and non-transmitted (R2= 1.7%) EA PGSs predicted offspring EA, evidencing genetic nurturing. In children around age 12, academic achievement was predicted only by transmitted EA PGSs (R2= 5.7%), but we did not find genetic nurturing (R2∼ 0.1%). The ADHD PGSs did not significantly predict academic achievement (R2∼ 0.6%). ADHD symptoms in children were predicted by transmitted EA PGSs and ADHD PGSs (R2= 1-2%). Based on these results, we conclude that previously reported associations between parent characteristics and offspring outcomes seem to be mainly a marker of genetic effects shared by parents and children.
Single Cell Profiling Reveals Sex, Lineage and Regional Diversity in the Mouse Kidney
Authors: Ransick Andrew , Lindström Nils O. , Liu Jing , Qin Zhu , Guo Jin-Jin , Alvarado Gregory F. , Kim Albert D. , Black Hannah G. , Kim Junhyong , McMahon Andrew P. 
Published: June 2019

SummaryChronic kidney disease affects 10% of the population with notable differences in ethnic and sex-related susceptibility to kidney injury and disease. Kidney dysfunction leads to significant morbidity and mortality, and chronic disease in other organ systems. A mouse organ-centered understanding underlies rapid progress in human disease modeling, and cellular approaches to repair damaged systems. To enhance an understanding of the mammalian kidney, we combined anatomy-guided single cell RNA sequencing of the adult male and female mouse kidney with in situ expression studies and cell lineage tracing. These studies reveal cell diversity and marked sex differences, distinct organization and cell composition of nephrons dependent on the time of nephron specification, and lineage convergence, in which contiguous functionally-related cell types are specified from nephron and collecting system progenitor populations. A searchable database integrating findings to highlight gene-cell relationships in a normal anatomical framework will facilitate study of the mammalian kidney.
Novelty gates memory formation through ventro-dorsal hippocampal interaction
Authors: Fredes Felipe , Silva Maria Alejandra , Koppensteiner Peter , Kobayashi Kenta , Joesch Maximilian , Shigemoto Ryuichi 
Published: June 2019

SummaryNovelty facilitates formation of memories. The detection of novelty and storage of contextual memories are both mediated by the hippocampus, yet the mechanisms that link these two functions remain to be defined. Dentate granule cells (GCs) of the dorsal hippocampus fire upon novelty exposure forming engrams of contextual memory. However, their key excitatory inputs from the entorhinal cortex are not responsive to novelty and are insufficient to make dorsal GCs fire reliably. Here we uncover a powerful glutamatergic pathway to dorsal GCs from ventral hippocampal mossy cells (MCs) that relays novelty, and is necessary and sufficient for driving dorsal GCs activation. Furthermore, manipulation of ventral MCs activity bidirectionally regulates novelty-induced contextual memory acquisition. Our results show that ventral MCs activity controls memory formation through an intra-hippocampal interaction mechanism gated by novelty.
Pyrazinamide triggers degradation of its target aspartate decarboxylase
Authors: Gopal Pooja , Sarathy Jickky , Yee Michelle , Ragunathan Priya , Shin Joon , Bhushan Shashi , Zhu Junhao , Akopian Tatos , Kandror Olga , Lim Teck Kwang , Gengenbacher Martin , Lin Qingsong , Rubin Eric J. , Grüber Gerhard , Dick Thomas 
Published: June 2019

AbstractThe introduction of pyrazinamide (PZA) in the tuberculosis drug regimen shortened treatment from 12 to 6 months 1. PZA is a prodrug that is activated by a Mycobacterium tuberculosis (Mtb) amidase to release its bioactive component pyrazinoic acid (POA) 2. Aspartate decarboxylase PanD, a proenzyme activated by autocatalytic cleavage (Supplementary Fig. 1A, 3) and required for Coenzyme A (CoA) biosynthesis, emerged as a target of POA 4-7. In vitro and in vivo screening to isolate spontaneous POA-resistant Mtb mutants identified missense mutations in either panD or the unfoldase clpC1, encoding a component of the caseinolytic protease ClpC1-ClpP 4,6-9. Overexpression and binding studies of PanD or ClpC1 pointed to PanD as the direct target of POA whereas clpC1 mutations appeared to indirectly cause resistance 4,5,7,9,10. Indeed, supplementing growth media with CoA precursors downstream of the PanD catalyzed step conferred POA resistance 4,7,11. Metabolomic analyses and biophysical studies using recombinant proteins confirmed targeting of PanD by POA 5. However, the exact molecular mechanism of PanD inhibition by POA remained unknown. While most drugs act by inhibiting protein function upon target binding, we show here that POA is not a bona fide enzyme inhibitor. Rather, POA binding to PanD triggers degradation of the protein by ClpC1-ClpP. Thus, the old tuberculosis drug PZA promotes degradation of its target. While novel for an antibacterial, drug-induced target degradation has recently emerged as a strategy in drug discovery across disease indications. Our findings provide the basis for the rational discovery of next generation PZA.
DNA damage response clamp loader Rad24(Rad17) and Mec1(ATR) kinase have distinct functions in regulating meiotic crossovers
Authors: Shinohara Miki , Bishop Douglas K. , Shinohara Akira 
Published: June 2019

AbstractCrossover (CO) recombination is essential for chromosome segregation during meiosis I. The number and distribution of COs are tightly regulated during meiosis. CO control includes CO assurance and CO interference, which guarantee at least one CO per a bivalent and evenly-spaced CO distribution, respectively. Previous studies showed the role of DNA damage response (DDR) clamp and its loader in efficient formation of meiotic COs by promoting the recruitment of a pro-CO protein Zip3 and interhomolog recombination, and also by suppressing ectopic recombination. In this study, by classical tetrad analysis ofSaccharomyces cerevisiae, we showed that a mutant defective in theRAD24 gene(RAD17in other organisms), which encodes the DDR clamp loader, displayed reduced CO frequencies on two shorter chromosomes (IIIandV) but not on a long chromosome (chromosomeVII). The residual COs in therad24mutant do not show interference. In contrast to therad24mutant, mutants defective in the ATR kinase homolog Mec1/Esr1, including amec1null and amec1kinase-dead mutant, show little or no defect in CO frequency. On the other hand,mec1COs show defects in interference, similar to therad24mutant. Moreover, CO formation and its control are implemented in a chromosome-specific manner, which may reflect a role for chromosome size in regulation.
How heterogeneous thymic output and homeostatic proliferation shape naive T cell receptor clone abundance distributions
Authors: Dessalles Renaud , D’Orsogna Maria R. , Chou Tom 
Published: June 2019

AbstractThe set of T cells that express the same T cell receptor (TCR) sequence represent a T cell clone. The number of different naive T cell clones in an organism reflects the number of different T cell receptors (TCRs) arising from recombination of the V(D)J gene segments during T cell development in the thymus. TCR diversity and more specifically, the clone abundance distribution is an important factor in immune function. Specific recombination patterns occur more frequently than others while subsequent interactions between TCRs and self-antigens are known to trigger proliferation and sustain naive T cell survival. These processes are TCR-dependent, leading to clone-dependent thymic export and naive T cell proliferation rates. Using a mean-field approximation to the solution of a regulated birth-death-immigration model, we systematically quantify how TCR-dependent heterogeneities in immigration and proliferation rates affect the shape of clone abundance distributions (the number of different clones that are represented by a specific number of cells). By comparing predicted clone abundances derived from our heterogeneous birth-death-immigration model with experimentally sampled clone abundances, we quantify the heterogeneity necessary to generate the observed abundances. Our findings indicate that heterogeneity in proliferation rates is more likely the mechanism underlying the observed clone abundance distributions than heterogeneity in immigration rates.Author SummaryThe abundance distribution of different T cell receptors (TCRs) expressed on naive T cells depends on their rates of thymic output, homeostatic proliferation, and death. However, measured TCR count distributions do not match, even qualitatively, those predicted from a multiclone birth death-immigration process when constant birth, death, and immigration rates are used (a neutral model). We show how non-neutrality in the birth-death-immigration process, where naive T cells with different TCRs are produced and proliferate with a distribution of rates shape the predicted sampled clone abundance distributions (the clone counts). Using physiological parameters, we find that heterogeneity in proliferation rates, and not in thymic output rates, is the main determinant in generating the observed clone counts. These findings are consistent with proliferation-driven maintenance of the T cell population in humans.
The late blooming amphipods: global change promoted post-Jurassic ecological radiation despite Palaeozoic origin
Authors: Copilaş-Ciocianu Denis , Borko Špela , Fišer Cene 
Published: June 2019

AbstractThe ecological radiation of amphipods is striking among crustaceans. Despite high diversity, global distribution and key roles in all aquatic environments, little is known about their ecological transitions, evolutionary timescale and phylogenetic relationships. It has been proposed that the amphipod ecological diversification began in the Late Palaeozoic. By contrast, due to their affinity for cold/oxygenated water and absence of pre-Cenozoic fossils, we hypothesized that the ecological divergence of amphipods arose throughout the cool Late Mesozoic/Cenozoic. We tested our hypothesis by inferring a large-scale, time-calibrated, multilocus phylogeny, and reconstructed evolutionary patterns for major ecological traits. Although our results reveal a Late Palaeozoic amphipod origin, diversification and ecological divergence ensued only in the Late Mesozoic, overcoming a protracted stasis in marine littoral habitats. Multiple independent post-Jurassic radiations took place in deep-sea, freshwater, terrestrial, pelagic and symbiotic environments, usually postdating deep-sea faunal extinctions, and corresponding with significant climatic cooling, tectonic reconfiguration, continental flooding, and increased oceanic oxygenation. We conclude that the profound Late Mesozoic global changes triggered a tipping point in amphipod evolution by unlocking ecological opportunities that promoted radiation into many new niches. Our study also provides a solid, time-calibrated, evolutionary framework to accelerate research on this overlooked, yet globally important taxon.
ShinyLearner: A containerized benchmarking tool for machine-learning classification of tabular data
Authors: Piccolo Stephen R. , Lee Terry J. , Suh Erica , Hill Kimball 
Published: June 2019

AbstractClassification algorithms assign observations to groups based on patterns in data. The machine-learning community have developed myriad classification algorithms, which are employed in diverse life-science research domains. When applying such algorithms, researchers face the challenge of deciding which algorithm(s) to apply in a given research domain. Algorithm choice can affect classification accuracy dramatically, so it is crucial that researchers optimize these choices based on empirical evidence rather than hearsay or anecdotal experience. In benchmark studies, multiple algorithms are applied to multiple datasets, and the researcher examines overall trends. In addition, the researcher may evaluate multiple hyperparameter combinations for each algorithm and use feature selection to reduce data dimensionality. Although software implementations of classification algorithms are widely available, robust benchmark comparisons are difficult to perform when researchers wish to compare algorithms that span multiple software packages.Programming interfaces, data formats, and evaluation procedures differ across software packages; and dependency conflicts may arise during installation. To address these challenges, we created ShinyLearner, an open-source project for integrating machine-learning packages into software containers. ShinyLearner provides a uniform interface for performing classification, irrespective of the library that implements each algorithm, thus facilitating benchmark comparisons. In addition, ShinyLearner enables researchers to optimize hyperparameters and select features via nested cross validation; it tracks all nested operations and generates output files that make these steps transparent. ShinyLearner includes a Web interface to help users more easily construct the commands necessary to perform benchmark comparisons. ShinyLearner is freely available at https://github.com/srp33/ShinyLearner.
Identification of antibodies targeting the H3N2 hemagglutinin receptor binding site following vaccination of humans
Authors: Zost Seth J. , Lee Juhye , Gumina Megan E. , Parkhouse Kaela , Henry Carole , Wilson Patrick C. , Bloom Jesse D. , Hensley Scott E. 
Published: June 2019

SUMMARYAntibodies targeting the receptor binding site (RBS) of the influenza virus hemagglutinin (HA) protein are usually not broadly-reactive because their footprints are typically large and extend to nearby variable HA residues. Here, we identified several human H3N2 HA RBS-targeting monoclonal antibodies (mAbs) that were sensitive to substitutions in conventional antigenic sites and were not broadly-reactive. However, we also identified one H3N2 HA RBS-targeting mAb that was exceptionally broadly reactive despite being sensitive to substitutions in residues outside of the RBS. We determined that similar antibodies are present at measurable levels in the sera of some individuals but that they are inefficiently elicited by conventional vaccines. Our data indicate that some HA RBS-targeting antibodies can be surprisingly effective against variable viral strains even if they are somewhat sensitive to substitutions in HA residues adjacent to the RBS.