bluuebunny/crossref_metadata_2025_split huggingface dataset:
From forest to city: urbanization modulates relative abundance of anti-predator coloration
Authors: Anderson Nigel K , Gutierrez Stephanie O , Bernal Ximena E 
Published: October 2019

AbstractIncreased urbanization has resulted in community changes including alteration of predator communities. Little is known, however, about how such changes affect morphological anti-predator traits. Given the importance of coloration in predator avoidance, this trait in particular is expected to be susceptible to novel selective environments in urban areas. Here, we investigate the coloration pattern of a Neotropical anuran species, the túngara frog (Engystomops pustulosus), along an urbanization gradient. Túngara frogs have two distinct color patterns (unstriped and striped) which we found to occur at different frequencies along an urbanization gradient. Striped individuals increased in frequency with urbanization. To assess the strength of selection imposed by predators on the two color morphs, we deployed clay models of túngara frogs in forest and semi-urban populations. In addition, we examined microhabitat selection by individuals of the different morphs. We found higher predation rates associated with urbanization than forested areas. In particular, frogs from forested habitats had lower number of attacks by avian predators. Contrary to our predictions, however, predation rates were similar for both color morphs independent of urbanization. Also, coloration of the frogs did not affect their microhabitat preference. Overall, túngara frogs are more likely to have a striped coloration pattern in semi-urban areas where predation by birds is higher than in the forest. Our findings suggest that factors other than predation pressure shape the coloration pattern of urban frogs and emphasize the complex nature of effects that anthropogenic changes in habitat and predator communities may have on prey morphology.
Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data
Authors: Wang Li-Gen , Lam Tommy Tsan-Yuk , Xu Shuangbin , Dai Zehan , Zhou Lang , Feng Tingze , Guo Pingfan , Dunn Casey W , Jones Bradley R , Bradley Tyler , Zhu Huachen , Guan Yi , Jiang Yong , Yu Guangchuang 
Published: October 2019

Abstract
Phylogenetic trees and data are often stored in incompatible and inconsistent formats. The outputs of software tools that contain trees with analysis findings are often not compatible with each other, making it hard to integrate the results of different analyses in a comparative study. The treeio package is designed to connect phylogenetic tree input and output. It supports extracting phylogenetic trees as well as the outputs of commonly used analytical software. It can link external data to phylogenies and merge tree data obtained from different sources, enabling analyses of phylogeny-associated data from different disciplines in an evolutionary context. Treeio also supports export of a phylogenetic tree with heterogeneous-associated data to a single tree file, including BEAST compatible NEXUS and jtree formats; these facilitate data sharing as well as file format conversion for downstream analysis. The treeio package is designed to work with the tidytree and ggtree packages. Tree data can be processed using the tidy interface with tidytree and visualized by ggtree. The treeio package is released within the Bioconductor and rOpenSci projects. It is available at https://www.bioconductor.org/packages/treeio/.
ICOSLG-mediated regulatory T cell expansion and IL-10 production promote progression of glioblastoma
Authors: Iwata Ryoichi , Lee Joo Hyoung , Hayashi Mikio , Dianzani Umberto , Ofune Kohei , Maruyama Masato , Oe Souichi , Ito Tomoki , Hashiba Tetsuo , Yoshimura Kunikazu , Nonaka Masahiro , Nakano Yosuke , Norian Lyse , Nakano Ichiro , Asai Akio 
Published: October 2019

Abstract

Background
Targeting immune checkpoint proteins has recently gained substantial attention due to the dramatic success of this strategy in clinical trials for some cancers. Inducible T-cell co-stimulator ligand (ICOSLG) is a member of the B7 family of immune regulatory ligands, expression of which in cancer is implicated in disease progression due to regulation of anti-tumor adaptive immunity. Although aberrant ICOSLG expression has been reported in glioma cells, the underlying mechanisms that promote glioblastoma (GBM) progression remain elusive.

Methods
Here, we investigated a causal role for ICOSLG in GBM progression by analyzing ICOSLG expression in both human glioma tissues and patient-derived GBM sphere cells (GSCs). We further examined its immune modulatory effects and the underlying molecular mechanisms.

Results
Bioinformatics analysis and GBM tissue microarray showed that upregulation of ICOSLG expression was associated with poor prognosis in patients with GBM. ICOSLG expression was upregulated preferentially in mesenchymal GSCs but not in proneural GSCs in a tumor necrosis factor-α-/NF-ĸB-dependent manner. Furthermore, ICOSLG expression by mesenchymal GSCs promoted expansion of T cells that produced interleukin-10. Knockdown of the gene encoding ICOSLG markedly reduced GBM tumor growth in immune competent mice, with a concomitant downregulation of interleukin-10 levels in the tumor microenvironment.

Conclusions
Inhibition of the ICOSLG-ICOS axis in GBM may provide a promising immunotherapeutic approach for suppressing a subset of GBM with an elevated mesenchymal signature.
Characteristics of Upper Limb Impairment Related to Degenerative Cervical Myelopathy: Development of a Sensitive Hand Assessment (Graded Redefined Assessment of Strength, Sensibility, and Prehension Version Myelopathy)
Authors: Kalsi-Ryan Sukhvinder , Riehm Lauren E , Tetreault Lindsay , Martin Allan R , Teoderascu Florentina , Massicotte Eric , Curt Armin , Verrier Mary C , Velstra Inge-Marie , Fehlings Michael G 
Published: October 2019

Abstract

BACKGROUND
Degenerative cervical myelopathy (DCM) involves spinal cord compression, which causes neurological decline. Neurological impairment in DCM is variable and can involve complex upper limb dysfunction including loss of manual dexterity, hyperreflexia, focal weakness, and sensory impairment. The modified Japanese Orthopaedic Association (mJOA) score relies on the patients’ subjective perceptions, whereas existing objective measures such as strength and sensory testing do not capture subtle changes in dexterity and function.

OBJECTIVE
1) To characterize arm and hand function in DCM; and 2) To develop and validate Graded Redefined Assessment of Strength, Sensibility, and Prehension Version-Myelopathy (GRASSP-M), a clinical assessment that quantifies upper limb impairment.

METHODS
A total of 148 DCM patients (categorized into mild, moderate, and severe based on mJOA grade) and 21 healthy subjects were enrolled. A complete neurological exam, the mJOA, the QuickDASH, grip dynamometry, and the GRASSP-M were administered.

RESULTS
Strength, sensation, and manual dexterity significantly declined with increasing DCM severity (P ≤ .05). Impairment in hand dexterity showed better discrimination between mild, moderate, and severe DCM categories than strength or sensation. The GRASSP-M was found to be both a reliable (intraclass correlation coefficient >0.75 for intra- and inter-rater reliability) and valid (with both concurrent and construct validity) tool.

CONCLUSION
These results demonstrate that patients’ subjective reporting of functional status, especially in the mild DCM category, may underrepresent the extent of functional impairment. The GRASSP-M is an objective tool designed to characterize patients’ functional impairment related to the upper limb, which proves useful to diagnose and quantify mild dysfunction, monitor patients for deterioration, and help determine when patients should be treated surgically.
Skyrmion–electron interaction in the separated spin-up and spin-down quantum hydrodynamics approach
Authors: Trukhanova Mariya Iv 
Published: October 2019

Abstract
The Berry gauge field associated with adiabatic quantum evolution represents a very interesting area of research, especially for the description of non-relativistic fermions coupled to a skyrmion texture. We construct a quantum hydrodynamics model that describes the electron–skyrmion interactions, with separate descriptions of spin-up and spin-down electrons as two different fluids. The quantum effects, represented by the quantum Bohm potential, are taken into account. We investigate the electron gas moving in a smooth magnetic texture, where the magnetic moments adjust to the local magnetization direction of the skyrmion, and derive the equations of motion and evolution of spin density for two fluids of electrons in the emergent gauge fields. Applying the separated spin evolution quantum hydrodynamics to the 2D electron gas, traveling on the background of the Berry gauge field in plane samples, located in an external magnetic field, we predict a wave of a new kind in the electron gas. This novel wave appears as an influence of emergent fields and quantum effects.
Paradoxical association between blood modular interferon signatures and quality of life in patients with systemic lupus erythematosus
Authors: Seguier Julie , Jouve Elisabeth , Bobot Mickaël , Whalen Elisabeth , Dussol Bertrand , Gentile Stéphanie , Burtey Stéphane , Halfon Philippe , Retornaz Frédérique , Chaussabel Damien , Chiche Laurent , Jourde-Chiche Noémie 
Published: October 2019

Abstract

Objectives
Blood transcriptomic IFN signature is a hallmark of SLE. The impaired health-related quality of life (HRQOL) observed in SLE is poorly related to disease activity. The aim of this study was to test how IFN signatures were associated with HRQOL in SLE patients.

Methods
Among consecutive patients, blood transcriptomic profiles were analysed with a modular framework comprising 3 IFN modules: M1.2, M3.4 and M5.12. Disease activity was evaluated by the SLEDAI score, and HRQOL was assessed with the SF-36 questionnaire, which includes eight domains: physical function, role physical, bodily pain, general health, vitality, social functioning, role emotional, and mental health (MH) and physical component summary and mental component summary scores.

Results
A total of 57 SLE patients were evaluated, among whom 27 (47%) were clinically quiescent, 30 (53%) were flaring, and 19 (33%) had active lupus nephritis. All SF-36 domains were altered in SLE patients compared with the general French population (P &lt; 0.0001). In multivariate analysis, taking into account flares, age, ethnicity, smoking and renal severity, social functioning was independently associated with the IFN score (P = 0.027). Analyses restrained to quiescent patients (n = 27) yielded greater associations between social functioning and the three IFN modules, and between MH and M3.4. Considering all quiescent visits (n = 51), the IFN score was independently correlated with social functioning (P = 0.022) and MH (P = 0.038).

Conclusion
This unexpected paradoxical association between IFN signature and some specific HRQOL domains argues against a pivotal role of IFNs in the persistently altered HRQOL of SLE patients.
Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture
Authors: McGowen Michael R , Tsagkogeorga Georgia , Álvarez-Carretero Sandra , dos Reis Mario , Struebig Monika , Deaville Robert , Jepson Paul D , Jarman Simon , Polanowski Andrea , Morin Phillip A , Rossiter Stephen J 
Published: October 2019

AbstractThe evolution of cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, although the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for $\sim $3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from $&gt;$38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic data set for cetaceans, spanning 6,527,596 aligned base pairs (bp) and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among oceanic dolphins, especially the problematic subfamily Delphinidae. We carried out Bayesian estimation of species divergence times using MCMCTree and compared our complete data set to a subset of clocklike genes. Analyses using the complete data set consistently showed less variance in divergence times than the reduced data set. In addition, integration of new fossils (e.g., Mystacodon selenensis) indicates that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene. [Cetaceans; phylogenomics; Delphinidae; Ziphiidae; dolphins; whales.]
SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing
Authors: Araújo Pedro M M , Martins Joana S , Osório Nuno S 
Published: October 2019

AbstractHuman immunodeficiency virus 1 (HIV-1) genome sequencing is routinely done for drug resistance monitoring in hospitals worldwide. Subtyping these extensive datasets of HIV-1 sequences is a critical first step in molecular epidemiology and evolution studies. The clinical relevance of HIV-1 subtypes is increasingly recognized. Several studies suggest subtype-related differences in disease progression, transmission route efficiency, immune evasion, and even therapeutic outcomes. HIV-1 subtyping is mainly done using web-servers. These tools have limitations in scalability and potential noncompliance with data protection legislation. Thus, the aim of this work was to develop an efficient method for large-scale local HIV-1 subtyping. We designed SNAPPy: a snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing. It contains several tasks of phylogenetic inference and BLAST queries, which can be executed sequentially or in parallel, taking advantage of multiple-core processing units. Although it was built for subtyping, SNAPPy is also useful to perform extensive HIV-1 alignments. This tool facilitates large-scale sequence-based HIV-1 research by providing a local, resource efficient and scalable alternative for HIV-1 subtyping. It is capable of analyzing full-length genomes or partial HIV-1 genomic regions (GAG, POL, and ENV) and recognizes more than ninety circulating recombinant forms. SNAPPy is freely available at: https://github.com/PMMAraujo/snappy/releases.
The Incidence and Magnitude of Cerebral Desaturation in Traumatic Brain Injury: An Observational Cohort Study
Authors: Davie Sophie , Mutch W. Alan C. , Monterola Marita , Fidler Kelsi , Funk Duane J. 
Published: October 2019

Background:
Cerebral ischemia in patients with traumatic brain injury (TBI) may propagate secondary neurological injury. Episodes of cerebral ischemia can be revealed through the use of cerebral oximetry monitoring. The objective of this study was to determine the incidence and severity of regional cerebral oxygen (rSO2) desaturation (rSO2<65%) in patients with severe TBI. Secondary outcomes included changes in other monitoring parameters associated with cerebral desaturation.

Materials and Methods:
In this single-center prospective observational cohort study, cerebral oximetry data were collected continuously for up to 72 hours in 18 adult patients with a diagnosis of severe nonpenetrating TBI who were being mechanically ventilated and undergoing intracranial pressure (ICP) monitoring an in intensive care unit in Canada. Mean arterial pressure (MAP), ICP, and cerebral perfusion pressure were collected at 5-minute intervals during the study period.

Results:
Twelve of 18 (67%) patients experienced an episode of cerebral desaturation. The median (interquartile range) nadir rSO2 was 57% (51% to 62%). The duration of desaturation was 265 (57 to 1277) minutes or 8.1% (2.6% to 26.0%) of recording time. In all patients, a linear regression analysis of the area under threshold of 65% for rSO2 was moderately correlated with the area above an ICP threshold of 20 mm Hg (R
2=0.52; P<0.01). Similarly, there was a modest correlation between rSO2 and MAP (R
2=0.41; P<0.01). These relationships also held true for those patients who experienced cerebral desaturation. Patients having episodes of ICP >20 mm Hg were 6 times more likely to have a cerebral desaturation (relative risk: 6.0; 95% confidence interval: 1.3-34.7).

Conclusions:
Cerebral desaturations occur frequently in patients with severe TBI, and their duration can be protracted. Episodes of desaturation were moderately correlated with increased ICP and decreased MAP.
Recording Obligatory Cortical Auditory Evoked Potentials in Infants: Quantitative Information on Feasibility and Parent Acceptability
Authors: Munro Kevin J. , Purdy Suzanne C. , Uus Kai , Visram Anisa , Ward Rachel , Bruce Iain A. , Marsden Antonia , Stone Michael A. , Van Dun Bram 
Published: October 2019

Objectives:
With the advent of newborn hearing screening and early intervention, there is a growing interest in using supra-threshold obligatory cortical auditory evoked potentials (CAEPs) to complement established pediatric clinical test procedures. The aim of this study was to assess the feasibility, and parent acceptability, of recording infant CAEPs.

Design:
Typically developing infants (n = 104) who had passed newborn hearing screening and whose parents expressed no hearing concerns were recruited. Testing was not possible in 6 infants, leaving 98, age range 5 to 39 weeks (mean age = 21.9, SD = 9.4). Three short duration speech-like stimuli (/m/, /g/, /t/) were presented at 65 dB SPL via a loudspeaker at 0° azimuth. Three criteria were used to assess clinical feasibility: (i) median test duration <30 min, (ii) >90% completion rate in a single test session, and (iii) >90% response detection for each stimulus. We also recorded response amplitude, latency, and CAEP signal to noise ratio. Response amplitudes and residual noise levels were compared for Fpz (n = 56) and Cz (n = 42) noninverting electrode locations. Parental acceptability was based on an 8-item questionnaire (7-point scale, 1 being best). In addition, we explored the patient experience in semistructured telephone interviews with seven families.

Results:
The median time taken to complete 2 runs for 3 stimuli, including preparation, was 27 min (range 17 to 59 min). Of the 104 infants, 98 (94%) were in an appropriate behavioral state for testing. A further 7 became restless during testing and their results were classified as “inconclusive.” In the remaining 91 infants, CAEPs were detected in every case with normal bilateral tympanograms. Detection of CAEPs in response to /m/, /g/, and /t/ in these individuals was 86%, 100%, and 92%, respectively. Residual noise levels and CAEP amplitudes were higher for Cz electrode recordings. Mean scores on the acceptability questionnaire ranged from 1.1 to 2.6. Analysis of interviews indicated that parents found CAEP testing to be a positive experience and recognized the benefit of having an assessment procedure that uses conversational level speech stimuli.

Conclusions:
Test duration, completion rates, and response detection rates met (or were close to) our feasibility targets, and parent acceptability was high. CAEPs have the potential to supplement existing practice in 3- to 9-month olds.
Does Surgical Approach Influence the Risk of Postoperative Infection After Surgical Treatment of Tibial Pilon Fractures?
Authors: Esposito John G. , van der Vliet Quirine M. J. , Heng Marilyn , Potter Jeffrey , Cronin Patrick K. , Harris Mitchel B. , Weaver Michael J. 
Published: October 2019

Objectives:
To determine whether a particular surgical approach or combination of approaches is a risk factor for infection.

Design:
Retrospective review.

Setting:
Two Level-1 trauma centers.

Patients/Participants:
Five hundred ninety pilon fractures in 581 patients (66% male) with a median age of 45 years were identified.

Intervention:
Open reduction internal fixation of pilon fractures.

Main Outcome Measures:
Postoperative deep surgical site infection and risk factors for postoperative deep infection.

Results:
The most common primary surgical approach was medial (54%), followed by anterolateral (25%), anteromedial (11%), posterolateral (8%), and posteromedial (2%). A dual approach to the distal tibia was used in 18% of the cases. The overall deep infection rate was 19%. There was no association between primary surgical approach and development of infection (P = 0.19–0.78). Independent risk factors for infection were smoking (hazard ratio, 2.1; P < 0.001) and need for soft tissue coverage (hazard ratio, 6.9; P < 0.001).

Conclusions:
Surgical approach does not appear to be a significant risk factor for postoperative infection after open reduction internal fixation of distal tibial pilon fractures. When treating tibial plafond fractures, surgeons should select the approach they feel best addresses the specific fracture pattern.

Level of Evidence:
Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.