bluuebunny/crossref_metadata_2025_split huggingface dataset:
A reference genome for the nectar-robbing Black-throated Flowerpiercer (Diglossa brunneiventris)
Authors: Hiller Anna E , Brumfield Robb T , Faircloth Brant C 
Published: August 2021

Abstract
Black-throated Flowerpiercers (Diglossa brunneiventris) are one species representing a phenotypically specialized group of tanagers (Thraupidae) that have hooked bills which allow them to feed by stealing nectar from the base of flowers. Members of the genus are widely distributed in montane regions from Mexico to northern Argentina, and previous studies of Diglossa have focused on their systematics, phylogenetics, and interesting natural history. Despite numerous studies of species within the genus, no genome assembly exists to represent these nectivorous tanagers. We described the assembly of a genome sequence representing a museum-vouchered, wild, female D. brunneiventris collected in Peru. By combining Pacific Biosciences Sequel long-read technology with 10× linked-read and reference-based scaffolding, we produced a 1.08 Gbp pseudochromosomal assembly including 600 scaffolds with a scaffold N50 of 67.3 Mbp, a scaffold L50 of 6, and a BUSCO completeness score of 95%. This new assembly improves representation of the diverse species that comprise the tanagers, improves on scaffold lengths and contiguity when compared to existing genomic resources for tanagers, and provides another avenue of research into the genetic basis of adaptations common to a nectivorous lifestyle among vertebrates.
Admixture mapping reveals loci for carcass mass in red deer x sika hybrids in Kintyre, Scotland
Authors: McFarlane S Eryn , Pemberton Josephine M 
Published: August 2021

Abstract
We deployed admixture mapping on a sample of 386 deer from a hybrid swarm between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon) sampled in Kintyre, Scotland to search for quantitative trait loci (QTLs) underpinning phenotypic differences between the species. These two species are highly diverged genetically [Fst between pure species, based on 50K single nucleotide polymorphism (SNPs) = 0.532] and phenotypically: pure red have on average twice the carcass mass of pure sika in our sample (38.7 kg vs 19.1 kg). After controlling for sex, age, and population genetic structure, we found 10 autosomal genomic locations with QTL for carcass mass. Effect sizes ranged from 0.191 to 1.839 kg and as expected, in all cases the allele derived from sika conferred lower carcass mass. The sika population was fixed for all small carcass mass alleles, whereas the red deer population was typically polymorphic. GO term analysis of genes lying in the QTL regions are associated with oxygen transport. Although body mass is a likely target of selection, none of the SNPs marking QTL are introgressing faster or slower than expected in either direction.
One year of sound recorded by a mermaid float in the Pacific: hydroacoustic earthquake signals and infrasonic ambient noise
Authors: Pipatprathanporn Sirawich , Simons Frederik J 
Published: August 2021

SUMMARY
A fleet of autonomously drifting profiling floats equipped with hydrophones, known by their acronym mermaid, monitors worldwide seismic activity from inside the oceans. The instruments are programmed to detect and transmit acoustic pressure conversions from teleseismic P wave arrivals for use in mantle tomography. Reporting seismograms in near-real time, within hours or days after they were recorded, the instruments are not usually recovered, but if and when they are, their memory buffers can be read out. We present a unique 1-yr-long data set of sound recorded at frequencies between 0.1 and 20 Hz in the South Pacific around French Polynesia by a mermaid float that was, in fact, recovered. Using time-domain, frequency-domain and time-frequency-domain techniques to comb through the time-series, we identified signals from 213 global earthquakes known to published catalogues, with magnitudes 4.6–8.0, and at epicentral distances between 24° and 168°. The observed signals contain seismoacoustic conversions of compressional and shear waves travelling through crust, mantle and core, including P, S, Pdif, Sdif, PKIKP, SKIKS, surface waves and hydroacoustic T phases. Only 10 earthquake records had been automatically reported by the instrument—the others were deemed low-priority by the onboard processing algorithm. After removing all seismic signals from the record, and also those from other transient, dominantly non-seismic, sources, we are left with the infrasonic ambient noise field recorded at 1500 m depth. We relate the temporally varying noise spectral density to a time-resolved ocean-wave model, WAVEWATCH III. The noise record is extremely well explained, both in spectral shape and in temporal variability, by the interaction of oceanic surface gravity waves. These produce secondary microseisms at acoustic frequencies between 0.1 and 1 Hz according to the well-known frequency-doubling mechanism.
GTXplorer: A portal to navigate and visualize the evolutionary information encoded in fold A glycosyltransferases
Authors: Taujale Rahil , Soleymani Saber , Priyadarshi Amitabh , Venkat Aarya , Yeung Wayland , Kochut Krzysztof J , Kannan Natarajan 
Published: August 2021

Abstract
Glycosyltransferases (GTs) play a central role in sustaining all forms of life through the biosynthesis of complex carbohydrates. Despite significant strides made in recent years to establish computational resources, databases and tools to understand the nature and role of carbohydrates and related glycoenzymes, a data analytics framework that connects the sequence-structure–function relationships to the evolution of GTs is currently lacking. This hinders the characterization of understudied GTs and the synthetic design of GTs for medical and biotechnology applications. Here, we present GTXplorer as an integrated platform that presents evolutionary information of GTs adopting a GT-A fold in an intuitive format enabling in silico investigation through comparative sequence analysis to derive informed hypotheses about their function. The tree view mode provides an overview of the evolutionary relationships of GT-A families and allows users to select phylogenetically relevant families for comparisons. The selected families can then be compared in the alignment view at the residue level using annotated weblogo stacks of the GT-A core specific to the selected clade, family, or subfamily. All data are easily accessible and can be downloaded for further analysis. GTXplorer can be accessed at https://vulcan.cs.uga.edu/gtxplorer/ or from GitHub at https://github.com/esbgkannan/GTxplorer to deploy locally. By packaging multiple data streams into an accessible, user-friendly format, GTXplorer presents the first evolutionary data analytics platform for comparative glycomics.
Evaluation of eye tracking for a decision support application
Authors: Visweswaran Shyam , King Andrew J , Tajgardoon Mohammadamin , Calzoni Luca , Clermont Gilles , Hochheiser Harry , Cooper Gregory F 
Published: August 2021

Abstract
Eye tracking is used widely to investigate attention and cognitive processes while performing tasks in electronic medical record (EMR) systems. We explored a novel application of eye tracking to collect training data for a machine learning-based clinical decision support tool that predicts which patient data are likely to be relevant for a clinical task. Specifically, we investigated in a laboratory setting the accuracy of eye tracking compared to manual annotation for inferring which patient data in the EMR are judged to be relevant by physicians. We evaluated several methods for processing gaze points that were recorded using a low-cost eye-tracking device. Our results show that eye tracking achieves accuracy and precision of 69% and 53%, respectively compared to manual annotation and are promising for machine learning. The methods for processing gaze points and scripts that we developed offer a first step in developing novel uses for eye tracking for clinical decision support.
Effective use of biosensors for high-throughput library screening for metabolite production
Authors: Kaczmarek Jennifer A , Prather Kristala L J 
Published: August 2021

Abstract
The development of fast and affordable microbial production from recombinant pathways is a challenging endeavor, with targeted improvements difficult to predict due to the complex nature of living systems. To address the limitations in biosynthetic pathways, much work has been done to generate large libraries of various genetic parts (promoters, RBSs, enzymes, etc.) to discover library members that bring about significantly improved levels of metabolite production. To evaluate these large libraries, high throughput approaches are necessary, such as those that rely on biosensors. There are various modes of operation to apply biosensors to library screens that are available at different scales of throughput. The effectiveness of each biosensor-based method is dependent on the pathway or strain to which it is applied, and all approaches have strengths and weaknesses to be carefully considered for any high throughput library screen. In this review, we discuss the various approaches used in biosensor screening for improved metabolite production, focusing on transcription factor-based biosensors.
Mechanistic investigation of synergistic interaction of tocopherol succinate with a quinoline-based inhibitor of mammalian target of rapamycin
Authors: Behera Chittaranjan , Kour Jaspreet , Banjare Nagma , Verma Praveen K , Chashoo Gousia , Sawant Sanghapal D , Gupta Prem N 
Published: August 2021

Abstract

Objectives
Cancer monotherapy is associated with various limitations; therefore, combination chemotherapy is widely explored for optimum drug efficacy. In this study, 4-(N-Phenyl-N′-substituted benzenesulfonyl)-6-(4-hydroxyphenyl) quinoline-based mammalian target of rapamycin (mTOR) inhibitor (IIIM-4Q) was investigated in combination with tocopherol succinate (TOS), and the mechanism of cytotoxicity was elucidated.

Methods
The cytotoxic potential of IIIM-4Q and TOS was evaluated in five cell lines. Further, to understand the mechanism of cytotoxicity of IIIM-4Q, TOS and their combination, various studies including morphological analysis using scanning electron microscopy and 6-diamidino-2-phenylindole (DAPI) staining, estimation of reactive oxygen species (ROS) level, measurement of mitochondrial membrane potential (MMP), in-vitro cell migration assay, Western blotting and staining with acridine orange (AO) for autophagy detection were performed.

Key findings
Investigated combination was synergistic in nature and exhibited greater oxidative stress and mitochondrial dysfunction in pancreatic cancer cells. The migration potential of MIA PaCa-2 cells was significantly mitigated under the influence of this combination, and morphological changes such as chromatin condensation and nuclear blebbing were observed. Also, poly (adenosine diphosphate-ribose) polymerase cleavage and caspase-3 activation were observed in IIIM-4Q and TOS combination-treated cells.

Conclusions
The investigated combination synergistically inhibited proliferation of MIA PaCa-2 cells through simultaneous induction of autophagy followed by apoptosis, and this combination demonstrated potential for further translational studies.
Inferring properties of neutron stars born in short gamma-ray bursts with a plerion-like X-ray plateau
Authors: Strang L C , Melatos A , Sarin N , Lasky P D 
Published: August 2021

ABSTRACT
Time-resolved spectra of six short gamma-ray bursts (sGRBs), measured by the Swift telescope, are used to estimate the parameters of a plerion-like model of the X-ray afterglow. The unshrouded, optically thin component of the afterglow is modelled as emanating from an expanding bubble of relativistic, shock-accelerated electrons fuelled by a central object. The electrons are injected with a power-law distribution and cool mainly by synchrotron losses. We compute posteriors for model parameters describing the central engine (e.g. spin frequency at birth, magnetic field strength) and shock acceleration (e.g. power-law index, minimum injection energy). It is found that the central engine is compatible with a millisecond magnetar, and the shock physics is compatible with what occurs in Galactic supernova remnants, assuming standard magnetic field models for the magnetar wind. Separately, we allow the magnetic field to vary arbitrarily and infer that it is roughly constant and lower in magnitude than the wind-borne extension of the inferred magnetar field. This may be due to the expansion history of the bubble, or the magnetization of the circumstellar environment of the sGRB progenitor.
A dynamical analysis of the Taurid Complex: evidence for past orbital convergences
Authors: Egal A , Wiegert P , Brown P G , Spurný P , Borovička J , Valsecchi G B 
Published: August 2021

ABSTRACT
The goal of this work is to determine if the dynamics of individual Taurid Complex (TC) objects are consistent with the formation of the complex via fragmentation of a larger body, or if the current orbital affinities between the TC members result from other dynamical processes. To this end, the orbital similarity through the time of comet 2P/Encke, 51 near-Earth asteroids (NEAs), and 16 Taurid fireballs was explored. Clones of each body were numerically simulated backwards in time, and epochs when significant fractions of the clones of any two bodies approached each other with both a low Minimum Orbit Intersection Distance and small relative velocity were identified. Only 12 pairs of bodies in our sample show such an association in the past 20 000 yr, primarily circa 3200 BCE. These include 2P/Encke and NEAs 2004 TG10, 2005 TF50, 2005 UR, 2015 TX24, and several Southern Taurid fireballs. We find this orbital convergence to be compatible with the fragmentation of a large parent body 5000–6000 yr ago, resulting in the separation of 2P/Encke and several NEAs associated with the TC, as well as some larger meteoroids now recorded in the Taurid stream. However, the influence of purely dynamical processes may offer an alternative explanation for this orbital rapprochement without requiring a common origin between these objects. In order to discriminate between these two hypotheses, future spectral surveys of the TC asteroids are required.
SpecHap: a diploid phasing algorithm based on spectral graph theory
Authors: YU Yonghan , Chen Lingxi , Miao Xinyao , Li Shuai Cheng 
Published: August 2021

Abstract
Haplotype phasing plays an important role in understanding the genetic data of diploid eukaryotic organisms. Different sequencing technologies (such as next-generation sequencing or third-generation sequencing) produce various genetic data that require haplotype assembly. Although multiple diploid haplotype phasing algorithms exist, only a few will work equally well across all sequencing technologies. In this work, we propose SpecHap, a novel haplotype assembly tool that leverages spectral graph theory. On both in silico and whole-genome sequencing datasets, SpecHap consumed less memory and required less CPU time, yet achieved comparable accuracy with state-of-art methods across all the test instances, which comprises sequencing data from next-generation sequencing, linked-reads, high-throughput chromosome conformation capture, PacBio single-molecule real-time, and Oxford Nanopore long-reads. Furthermore, SpecHap successfully phased an individual Ambystoma mexicanum, a species with gigantic diploid genomes, within 6 CPU hours and 945MB peak memory usage, while other tools failed to yield results either due to memory overflow (40GB) or time limit exceeded (5 days). Our results demonstrated that SpecHap is scalable, efficient, and accurate for diploid phasing across many sequencing platforms.
Data-Driven Residency Training: A Scoping Review of Educational Interventions for Neurosurgery Residency Programs
Authors: Kelly Patrick D , Yengo-Kahn Aaron M , Roth Steven G , Zuckerman Scott L , Chitale Rohan V , Wellons John C , Chambless Lola B 
Published: August 2021

Abstract

BACKGROUND
Neurosurgery residency programs are tasked with imparting large volumes of both clinical knowledge and technical skill to trainees in limited time. Many investigators have described local practices, which may offer evidence-based interventions in neurosurgical residency education, but this literature has not been systematically reviewed.

OBJECTIVE
To perform a scoping review of educational practices in neurosurgery, which are supported by quantitative, peer-reviewed research.

METHODS
A scoping review of the literature was performed. PubMed, Embase, and Web of Science databases were queried for articles describing educational interventions for neurosurgery residents, which included a quantitative assessment of the effect on resident performance.

RESULTS
From an initial set of 1785 unique articles, 29 studies were ultimately screened and included. Studies were into the following 6 topics: (1) didactics and curricula (n = 13), (2) nontechnical skills (n = 6), (3) wellness and burnout (n = 4), (4) assessment and feedback (n = 2), (5) mentorship and career development (n = 2), and (6) research (n = 2). Individual study results were described.

CONCLUSION
Several educational interventions in neurosurgical training are supported by quantitative evidence. Methodological shortcomings are prevalent among studies of education, particularly in the selection of meaningful outcome measures. A summary of evidence-based considerations is provided for current and future program directors.
Embodied design using augmented reality: the case of the gradient
Authors: Bos Rogier , Doorman Michiel , Drijvers Paul , Shvarts Anna 
Published: August 2021

Abstract
We study the augmented reality sandbox (ARSB) as an embodied learning environment to foster meaning making in the context of bivariable calculus. We present the case of Tiago, a first-year bachelor chemistry student, performing a series of tasks based on embodied design, including perception-based, action-based and incorporation-based tasks. Tiago’s work demonstrates the affordances of the ARSB, e.g. to trace a height line and to manipulate plastic planes either with or without feedback from projected height lines. Tiago’s reasoning about mathematical concepts, e.g. the parameters in a plane equation and the gradient vector, is supported by perceptual structures that he discovers during these embodied tasks. We distinguished two ways in which ARSB affordances were used in the learning sequence. In perception-based and action-based tasks, the affordances of the ARSB were immediately available and intensively involved in the interaction. In incorporation tasks, on the contrary, a critical affordance was deliberately removed and the student was able to reproduce its functionality without technology.
Effect of titanium dioxide nanoparticles on DNA methylation of human peripheral blood mononuclear cells
Authors: Malakootian Mohammad , Nasiri Alireza , Osornio-Vargas Alvaro R , Faraji Maryam 
Published: August 2021

Abstract
The aim of the current study was to investigate the effect of well-characterized TiO2 nanoparticles on DNA methylation of peripheral blood mononuclear cells (PBMCs) in vitro. Maximum non-toxic concentration of nanoparticles for PBMCs was determined by MTT assay. The effect of TiO2 nanoparticles at concentrations of 25–100 μg/ml on DNA methylation of PBMCs was investigated by measuring the %5-mC alterations through an ELISA assay. The physicochemical analysis showed that the TiO2 nanoparticles were crystalline, pure and in the anatase phase. Peaks related to Ti-O tensile vibrations were observed in the range of 1510 cm−1. The size of nanoparticles was in the range of 39–74 nm with an average hydrodynamic diameter of 43.82 nm. According to the results of the MTT test, 100 μg/ml was found to be maximum non-toxic concentration. The %5-mC in treated PBMCs revealed that TiO2 nanoparticles could lead to DNA hypomethylation in PBMCs. The %5-mC difference compared with the negative control was found to be 2.07 ± 1.02% (P = 0.03). The difference of %5-mC between the 25 and 100 μg/ml concentration of nanoparticles was statistically significant (P = 0.02). The results of the current study show that the TiO2 nanoparticles cause DNA hypomethylation in PBMCs in a dose-response manner. Therefore, it is recommended to evaluate the effects of cytotoxicity and epigenotoxicity of commonly used nanoparticles before their use.
Changes in Pain Sensitivity and Conditioned Pain Modulation During Recovery From Whiplash-associated Disorders
Authors: Christensen Steffan W.M. , Bellosta-López Pablo , Doménech-García Víctor , Herrero Pablo , Palsson Thorvaldur S. 
Published: August 2021

Objective:
The objective of this study was to investigate the pain-sensory profile of patients with whiplash-associated disorders (WADs) prior and post 2 weeks of standardized rehabilitation and after a 6-month follow-up.

Materials and Methods:
Twenty-two WAD participants (grade II; 14 women) and 22 sex-matched and age-matched healthy pain-free controls were enrolled. Pressure pain thresholds (PPTs) were assessed at local and distal muscles. Conditioned pain modulation (CPM) of PPTs was assessed using cuff pressure around the upper arm. Referred area of pain following supra-threshold pressure stimulation of the infraspinatus muscle was recorded on a body chart. Psychometric variables (pain intensity, area of perceived pain, pain catastrophizing, kinesiophobia, sleep problems, and depression level) were assessed. WAD group additionally completed the Neck Disability Index.

Results:
The WAD group demonstrated lower local PPTs compared with controls at all time points (P<0.05) and lower distal PPTs at baseline and at 2 weeks when compared with 6 months (within-group) (P<0.05). The WAD group had a reduced CPM response and larger induced referred pain areas compared with controls (P<0.05), while no within-group changes were observed at any time point. The WAD group reported higher pain intensity and perceived area of pain compared with controls at all time points (P<0.05) and a mean Neck Disability Index score of 41% at baseline, 16% at 2 weeks, and 4% at 6 months. Furthermore, the WAD group reported improvements in all other psychometric variables (P<0.05), although only pain catastrophizing levels were comparable to controls at 2 weeks.

Discussion:
PPTs but not CPM improved in the WAD group and were comparable to controls following 2 weeks following standardized rehabilitation, indicating that normalization of CPM may not be required to recover from WAD.