bluuebunny/crossref_metadata_2025_split huggingface dataset:
Asymptotic kinematics of globular clusters: The emergence of a Tully–Fisher relation
Authors: Hernandez X , Lara-D I A J 
Published: November 2019

ABSTRACT
Using a recent homogeneous sample of 40 high-quality velocity dispersion profiles for Galactic globular clusters, we study the regime of low gravitational acceleration relevant to the outskirts of these systems. We find that a simple empirical profile having a central Gaussian component and a constant large-radius asymptote, σ∞, accurately describes the variety of observed velocity dispersion profiles. We use published population synthesis models, carefully tailored to each individual cluster, to estimate mass-to-light ratios from which total stellar masses, M, are inferred. We obtain a clear scaling, reminiscent of the galactic Tully–Fisher relation of $\sigma _{\infty }[\, \mathrm{km \, s}^{-1}]= 0.084^{+0.075}_{-0.040} (\mathrm{{\it M}/M}_{\odot })^{0.3 \pm 0.051}$, which is interesting to compare to the deep modified Newtonian dynamics (MOND) limit of $\sigma _{\infty } [\mathrm{km \, s}^{-1}]=0.2(\mathrm{{\it M}/M}_{\odot })^{0.25}$. Under a Newtonian interpretation, our results constitute a further restriction on models where initial conditions are crafted to yield the outer flattening observed today. Within a modified gravity scheme, because the globular clusters studied are not isolated objects in the deep MOND regime, the results obtained point towards a modified gravity where the external field effect of MOND does not appear, or is significantly suppressed.
Variability in extragalactic class I methanol masers: new maser components towards NGC 4945 and NGC 253
Authors: McCarthy T P , Ellingsen S P , Breen S L , Voronkov M A , Chen X , Qiao H-h 
Published: November 2019

ABSTRACT
We have used the Australia Telescope Compact Array (ATCA) to make new observations of the 36.2-GHz (4−1 → 30E) methanol transition towards NGC 4945 and NGC 253. These observations have revealed the presence of new maser components towards these galaxies, and have provided the first clear evidence for variability in extragalactic class I methanol masers. Alongside the new observations of NGC 4945 and NGC 253, we present the results of recent 36.2-GHz methanol maser searches towards 12 galaxies, placing upper limits on the emission from the 36.2-GHz class I transition and the 37.7-GHz (72 → 81E) class II maser line towards these sources. Flux density values for the 7-mm continuum emission towards these sources are also reported where applicable. A re-analysis of the published 36.2-GHz methanol observations of Arp 220 undertaken as part of the search revealed some issues with previous imaging procedures. The re-analysis, combined with non-detections in independent follow-up observations, suggests that there is no 36.2-GHz methanol emission towards Arp 220 stronger than 3.5 mJy in a 10 km s−1 channel (5σ upper limit).
Disentangling magnification in combined shear-clustering analyses
Authors: Thiele Leander , Duncan Christopher A J , Alonso David 
Published: November 2019

ABSTRACT
We investigate the sensitivity to the effects of lensing magnification on large-scale structure analyses combining photometric cosmic shear and galaxy clustering data (i.e. the now commonly called ‘3 × 2-point’ analysis). Using a Fisher matrix bias formalism, we disentangle the contribution to the bias on cosmological parameters caused by ignoring the effects of magnification in a theory fit from individual elements in the data vector, for Stage-III and Stage-IV surveys. We show that the removal of elements of the data vectors that are dominated by magnification does not guarantee a reduction in the cosmological bias due to the magnification signal, but can instead increase the sensitivity to magnification. We find that the most sensitive elements of the data vector come from the shear-clustering cross-correlations, particularly between the highest redshift shear bin and any lower redshift lens sample, and that the parameters ΩM, $S_8=\sigma _8\sqrt{\Omega _\mathrm{ M}/0.3}$, and w0 show the most significant biases for both survey models. Our forecasts predict that current analyses are not significantly biased by magnification, but this bias will become highly significant with the continued increase of statistical power in the near future. We therefore conclude that future surveys should measure and model the magnification as part of their flagship ‘3 × 2-point’ analysis.
LINCS Data Portal 2.0: next generation access point for perturbation-response signatures
Authors: Stathias Vasileios , Turner John , Koleti Amar , Vidovic Dusica , Cooper Daniel , Fazel-Najafabadi Mehdi , Pilarczyk Marcin , Terryn Raymond , Chung Caty , Umeano Afoma , Clarke Daniel J B , Lachmann Alexander , Evangelista John Erol , Ma’ayan Avi , Medvedovic Mario , Schürer Stephan C 
Published: November 2019

Abstract
The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program with the goal of generating a large-scale and comprehensive catalogue of perturbation-response signatures by utilizing a diverse collection of perturbations across many model systems and assay types. The LINCS Data Portal (LDP) has been the primary access point for the compendium of LINCS data and has been widely utilized. Here, we report the first major update of LDP (http://lincsportal.ccs.miami.edu/signatures) with substantial changes in the data architecture and APIs, a completely redesigned user interface, and enhanced curated metadata annotations to support more advanced, intuitive and deeper querying, exploration and analysis capabilities. The cornerstone of this update has been the decision to reprocess all high-level LINCS datasets and make them accessible at the data point level enabling users to directly access and download any subset of signatures across the entire library independent from the originating source, project or assay. Access to the individual signatures also enables the newly implemented signature search functionality, which utilizes the iLINCS platform to identify conditions that mimic or reverse gene set queries. A newly designed query interface enables global metadata search with autosuggest across all annotations associated with perturbations, model systems, and signatures.
RiboVIEW: a computational framework for visualization, quality control and statistical analysis of ribosome profiling data
Authors: Legrand Carine , Tuorto Francesca 
Published: November 2019

Abstract
Recently, newly developed ribosome profiling methods based on high-throughput sequencing of ribosome-protected mRNA footprints allow to study genome-wide translational changes in detail. However, computational analysis of the sequencing data still represents a bottleneck for many laboratories. Further, specific pipelines for quality control and statistical analysis of ribosome profiling data, providing high levels of both accuracy and confidence, are currently lacking. In this study, we describe automated bioinformatic and statistical diagnoses to perform robust quality control of ribosome profiling data (RiboQC), to efficiently visualize ribosome positions and to estimate ribosome speed (RiboMine) in an unbiased way. We present an R pipeline to setup and undertake the analyses that offers the user an HTML page to scan own data regarding the following aspects: periodicity, ligation and digestion of footprints; reproducibility and batch effects of replicates; drug-related artifacts; unbiased codon enrichment including variability between mRNAs, for A, P and E sites; mining of some causal or confounding factors. We expect our pipeline to allow an optimal use of the wealth of information provided by ribosome profiling experiments.
A heterodimer of evolved designer-recombinases precisely excises a human genomic DNA locus
Authors: Lansing Felix , Paszkowski-Rogacz Maciej , Schmitt Lukas Theo , Schneider Paul Martin , Rojo Romanos Teresa , Sonntag Jan , Buchholz Frank 
Published: November 2019

AbstractSite-specific recombinases (SSRs) such as the Cre/loxP system are useful genome engineering tools that can be repurposed by altering their DNA-binding specificity. However, SSRs that delete a natural sequence from the human genome have not been reported thus far. Here, we describe the generation of an SSR system that precisely excises a 1.4 kb fragment from the human genome. Through a streamlined process of substrate-linked directed evolution we generated two separate recombinases that, when expressed together, act as a heterodimer to delete a human genomic sequence from chromosome 7. Our data indicates that designer-recombinases can be generated in a manageable timeframe for precision genome editing. A large-scale bioinformatics analysis suggests that around 13% of all human protein-coding genes could be targetable by dual designer-recombinase induced genomic deletion (dDRiGD). We propose that heterospecific designer-recombinases, which work independently of the host DNA repair machinery, represent an efficient and safe alternative to nuclease-based genome editing technologies.
Cognitive impairment after cytotoxic chemotherapy
Authors: Huehnchen Petra , van Kampen Antonia , Boehmerle Wolfgang , Endres Matthias 
Published: November 2019

Abstract

Background
Neurotoxicity is a frequent side effect of cytotoxic chemotherapy and affects a large number of patients. Despite the high medical need, few research efforts have addressed the impact of cytotoxic agents on cognition (ie, postchemotherapy cognitive impairment; PCCI). One unsolved question is whether individual cytotoxic drugs have differential effects on cognition. We thus examine the current state of research regarding PCCI. Neurological symptoms after targeted therapies and immunotherapies are not part of this review.

Methods
A literature search was conducted in the PubMed database, and 1215 articles were reviewed for predefined inclusion and exclusion criteria. Thirty articles were included in the systematic review.

Results
Twenty-five of the included studies report significant cognitive impairment. Of these, 21 studies investigated patients with breast cancer. Patients mainly received combinations of 5-fluorouracil, epirubicin, cyclophosphamide, doxorubicin, and taxanes (FEC/FEC-T). Five studies found no significant cognitive impairment in chemotherapy patients. Of these, 2 studies investigated patients with colon cancer receiving 5-fluorouracil and oxaliplatin (FOLFOX). Independent risk factors for PCCI were patient age, mood alterations, cognitive reserve, and the presence of apolipoprotein E e4 alleles.

Conclusions
There is evidence that certain chemotherapy regimens cause PCCI more frequently than others as evidenced by 21 out of 23 studies in breast cancer patients (mainly FEC-T), whereas 2 out of 3 studies with colon cancer patients (FOLFOX) did not observe significant changes. Further studies are needed defining patient cohorts by treatment protocol in addition to cancer type to elucidate the effects of individual cytotoxic drugs on cognitive functions.
Wearable Egocentric Camera as a Monitoring Tool of Free-Living Cigarette Smoking: A Feasibility Study
Authors: Imtiaz Masudul H , Hossain Delwar , Senyurek Volkan Y , Belsare Prajakta , Tiffany Stephen , Sazonov Edward 
Published: November 2019

Abstract

Introduction
Wearable sensors may be used for the assessment of behavioral manifestations of cigarette smoking under natural conditions. This paper introduces a new camera-based sensor system to monitor smoking behavior. The goals of this study were (1) identification of the best position of sensor placement on the body and (2) feasibility evaluation of the sensor as a free-living smoking-monitoring tool.

Methods
A sensor system was developed with a 5MP camera that captured images every second for continuously up to 26 hours. Five on-body locations were tested for the selection of sensor placement. A feasibility study was then performed on 10 smokers to monitor full-day smoking under free-living conditions. Captured images were manually annotated to obtain behavioral metrics of smoking including smoking frequency, smoking environment, and puffs per cigarette. The smoking environment and puff counts captured by the camera were compared with self-reported smoking.

Results
A camera located on the eyeglass temple produced the maximum number of images of smoking and the minimal number of blurry or overexposed images (53.9%, 4.19%, and 0.93% of total captured, respectively). During free-living conditions, 286,245 images were captured with a mean (±standard deviation) duration of sensor wear of 647(±74) minutes/participant. Image annotation identified consumption of 5(±2.3) cigarettes/participant, 3.1(±1.1) cigarettes/participant indoors, 1.9(±0.9) cigarettes/participant outdoors, and 9.02(±2.5) puffs/cigarette. Statistical tests found significant differences between manual annotations and self-reported smoking environment or puff counts.

Conclusions
A wearable camera-based sensor may facilitate objective monitoring of cigarette smoking, categorization of smoking environments, and identification of behavioral metrics of smoking in free-living conditions.

Implications
The proposed camera-based sensor system can be employed to examine cigarette smoking under free-living conditions. Smokers may accept this unobtrusive sensor for extended wear, as the sensor would not restrict the natural pattern of smoking or daily activities, nor would it require any active participation from a person except wearing it. Critical metrics of smoking behavior, such as the smoking environment and puff counts obtained from this sensor, may generate important information for smoking interventions.
Parental Unemployment and the Transition into Tertiary Education: Can Institutions Moderate the Adverse Effects?
Authors: Lindemann Kristina , Gangl Markus 
Published: November 2019

Abstract
We examine how parental unemployment affects children’s transition to postsecondary education in different institutional contexts. Drawing on theoretical perspectives in intergenerational mobility research and sociology of higher education, we estimate the extent to which these intergenerational effects depend on social and education policies. We use data from five longitudinal surveys to analyze the effects of parental unemployment on entry to postsecondary education in 21 countries. The results of multilevel regression analysis show that in contexts that provide better insurance against unemployment, in terms of generous earnings replacement, the adverse effect of parental unemployment is alleviated. Moreover, entry gaps between youth from unemployed and employed households are smaller in tertiary education systems with more opportunity-equalizing education policies that provide more financial support to students and reduce the role of private expenditure. Some evidence also indicates that policies are more relevant for children of less-educated unemployed parents.
Impossibility Results on Stability of Phylogenetic Consensus Methods
Authors: Delucchi Emanuele , Hoessly Linard , Paolini Giovanni 
Published: November 2019

Abstract
We answer two questions raised by Bryant, Francis, and Steel in their work on consensus methods in phylogenetics. Consensus methods apply to every practical instance where it is desired to aggregate a set of given phylogenetic trees (say, gene evolution trees) into a resulting, “consensus” tree (say, a species tree). Various stability criteria have been explored in this context, seeking to model desirable consistency properties of consensus methods as the experimental data are updated (e.g., more taxa, or more trees, are mapped). However, such stability conditions can be incompatible with some basic regularity properties that are widely accepted to be essential in any meaningful consensus method. Here, we prove that such an incompatibility does arise in the case of extension stability on binary trees and in the case of associative stability. Our methods combine general theoretical considerations with the use of computer programs tailored to the given stability requirements. [Associative stability; consensus; extension stability; phylogeny.]
Reticulate Evolution Helps Explain Apparent Homoplasy in Floral Biology and Pollination in Baobabs (Adansonia; Bombacoideae; Malvaceae)
Authors: Karimi Nisa , Grover Corrinne E , Gallagher Joseph P , Wendel Jonathan F , Ané Cécile , Baum David A 
Published: November 2019

AbstractBaobabs (Adansonia) are a cohesive group of tropical trees with a disjunct distribution in Australia, Madagascar, and continental Africa, and diverse flowers associated with two pollination modes. We used custom-targeted sequence capture in conjunction with new and existing phylogenetic comparative methods to explore the evolution of floral traits and pollination systems while allowing for reticulate evolution. Our analyses suggest that relationships in Adansonia are confounded by reticulation, with network inference methods supporting at least one reticulation event. The best supported hypothesis involves introgression between Adansonia rubrostipa and core Longitubae, both of which are hawkmoth pollinated with yellow/red flowers, but there is also some support for introgression between the African lineage and Malagasy Brevitubae, which are both mammal-pollinated with white flowers. New comparative methods for phylogenetic networks were developed that allow maximum-likelihood inference of ancestral states and were applied to study the apparent homoplasy in floral biology and pollination mode seen in Adansonia. This analysis supports a role for introgressive hybridization in morphological evolution even in a clade with highly divergent and geographically widespread species. Our new comparative methods for discrete traits on species networks are implemented in the software PhyloNetworks. [Comparative methods; Hyb-Seq; introgression; network inference; population trees; reticulate evolution; species tree inference; targeted sequence capture.]
Orogeny, sympatry and emergence of a new genus of Alpine subterranean Trechini (Coleoptera: Carabidae)
Authors: Delić Teo , Kapla Andrej , Colla Andrea 
Published: November 2019

AbstractDespite two centuries of research in European subterranean habitats, which resulted in descriptions of numerous obligate subterranean beetle species, the role of ecological differentiation in speciation of subterranean beetles remains understudied. Discovery of a new genus and a species of Alpine subterranean Trechini beetles, Petraphaenops unguiculatus gen. & sp. nov., enables us to question the reasons for its morphological and ecological divergence. Multilocus, time-calibrated phylogeny and extensive morphological analyses were used to place the evolution of the species in a temporal and palaeogeographical framework. Set within the phylogeny of Alpine Trechini, the new genus is shown to have split from its sister-genus, Aphaenopidius, by the end of the Pliocene. The timeline of the split between these closely related genera corresponds to the onset of major orogenetic events in the southern Calcareous Alps. The orogeny dynamics, coupled with simultaneous diversification of subterranean habitats, presumably initiated ecological speciation and morphological diversification of this highly troglomorphic subterranean trechine genus.
Common Types of Gender-Based Microaggressions in Medicine
Authors: Periyakoil Vyjeyanthi S. , Chaudron Linda , Hill Emorcia V. , Pellegrini Vincent , Neri Eric , Kraemer Helena C. 
Published: November 2019

Purpose
Microaggressions are subtle verbal or nonverbal everyday behaviors that arise from unconscious bias, covert prejudice, or hostility. They may contribute to the persistent disparities faced by women in medicine. In this study, the authors sought to identify common microaggressions experienced by women faculty in medicine and to determine if specific demographic characteristics affect the reported frequencies of these microaggressions.

Method
The authors used chain referral sampling to collect real-life anecdotes about microaggressions from women faculty across the nation. Thirty-four unique experiences from those reported were identified and scripted then reenacted using professional actors to create 34 videos of the real-life microaggressions and 34 corresponding fictional “control” versions of the same situations. The videos, presented in a random order, were evaluated by faculty from 4 academic medical centers from 2016 to 2018.

Results
A total of 124 faculty (79 women, 45 men) participated. Women reported higher frequencies of microaggressions than men in 33 of the 34 videos depicting microaggressions (P value range: < .001 to .042, area under the curve range: 0.60–0.69). No such differences were seen with the control videos. Women identified 21 microaggressions as occurring frequently. No significant differences were found with respect to participants’ age, race/ethnicity, academic rank, or years in medicine. Post hoc analyses showed that the microaggressions fell into 6 themes: encountering sexism, encountering pregnancy- and child care–related bias, having abilities underestimated, encountering sexually inappropriate comments, being relegated to mundane tasks, and feeling excluded/marginalized.

Conclusions
Privilege is often invisible to those who have it, whereas bias and discrimination are readily apparent to those who experience it. Knowledge of common microaggressions will allow for targeted individual, interpersonal, and institutional solutions to mitigate disparities in medicine.