bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mining data from legacy taxonomic literature and application for sampling spiders of the Teutamus group (Araneae; Liocranidae) in Southeast Asia
Authors: Rivera-Quiroz F. Andres , Petcharad Booppa , Miller Jeremy A. 
Published: September 2020

AbstractTaxonomic literature contains information about virtually ever known species on Earth. In many cases, all that is known about a taxon is contained in this kind of literature, particularly for the most diverse and understudied groups. Taxonomic publications in the aggregate have documented a vast amount of specimen data. Among other things, these data constitute evidence of the existence of a particular taxon within a spatial and temporal context. When knowledge about a particular taxonomic group is rudimentary, investigators motivated to contribute new knowledge can use legacy records to guide them in their search for new specimens in the field. However, these legacy data are in the form of unstructured text, making it difficult to extract and analyze without a human interpreter. Here, we used a combination of semi-automatic tools to extract and categorize specimen data from taxonomic literature of one family of ground spiders (Liocranidae). We tested the application of these data on fieldwork optimization, using the relative abundance of adult specimens reported in literature as a proxy to find the best times and places for collecting the species (Teutamus politus) and its relatives (Teutamus group, TG) within Southeast Asia. Based on these analyses we decided to collect in three provinces in Thailand during the months of June and August. With our approach, we were able to collect more specimens of T. politus (188 specimens, 95 adults) than all the previous records in literature combined (102 specimens). Our approach was also effective for sampling other representatives of the TG, yielding at least one representative of every TG genus previously reported for Thailand. In total, our samples contributed 231 specimens (134 adults) to the 351 specimens previously reported in the literature for this country. Our results exemplify one application of mined literature data that allows investigators to more efficiently allocate effort and resources for the study of neglected, endangered, or interesting taxa and geographic areas. Furthermore, the integrative workflow demonstrated here shares specimen data with global online resources like Plazi and GBIF, meaning that others can freely reuse these data and contribute to them in the future. The contributions of the present study represent an increase of more than 35% on the taxonomic coverage of the TG in GBIF based on the number of species. Also, our extracted data represents 72% of the occurrences now available through GBIF for the TG and more than 85% of occurrences of T. politus. Taxonomic literature is a key source of undigitized biodiversity data for taxonomic groups that are underrepresented in the current biodiversity data sphere. Mobilizing these data is key to understanding and protecting some of the less well-known domains of biodiversity.
Multi-pulse laser-induced bubble formation and nanoparticle aggregation using MoS2 nanoparticles
Authors: Ko Brian , Lu Weigang , Sokolov Alexei V. , Lee Ho Wai Howard , Scully Marlan O. , Zhang Zhenrong 
Published: September 2020

AbstractUnderstanding of how particles and light interact in a liquid environment is vital for optical and biological applications. MoS2 has been shown to enhance nonlinear optical phenomena due to the presence of a direct excitonic resonance. Its use in biological applications is predicated on knowledge of how MoS2 interacts with ultrafast (< 1 ps) pulses. In this experiment, the interaction between two femtosecond pulses and MoS2 nanoparticles suspended in liquid is studied. We found that the laser pulses induce bubble formation on the surface of a nanoparticle and a nanoparticle aggregate then forms on the surface of the trapped bubble. The processes of formation of the bubble and the nanoparticle aggregation are intertwined.
Extracellular vesicles shuttle protective messages against heat stress in bovine granulosa cells
Authors: Gebremedhn Samuel , Gad Ahmed , Aglan Hoda Samir , Laurincik Jozef , Prochazka Radek , Salilew-Wondim Dessie , Hoelker Michael , Schellander Karl , Tesfaye Dawit 
Published: September 2020

AbstractElevated summer temperature is reported to be the leading cause of stress in dairy and beef cows, which negatively affects various reproductive functions. Follicular cells respond to heat stress (HS) by activating the expression of heat shock family proteins (HSPs) and other antioxidants. HS is reported to negatively affect the bi-directional communication between the follicular cells and the oocyte, which is partly mediated by follicular fluid extracellular vesicles (EVs) released from surrounding cells. As carriers of bioactive molecules (DNA, RNA, protein, and lipids), the involvement of EVs in mediating the stress response in follicular cells is not fully understood. Here we used an in vitro model to decipher the cellular and EV-coupled miRNAs of bovine granulosa cells in response to HS. Moreover, the protective role of stress-related EVs against subsequent HS was assessed. For this, bovine granulosa cells from smaller follicles were cultured in vitro and after sub-confluency, cells were either kept at 37 °C or subjected to HS (42 °C). Results showed that granulosa cells exposed to HS increased the accumulation of ROS, total oxidized protein, apoptosis, and the expression of HSPs and antioxidants, while the viability of cells was reduced. Moreover, 14 and 6 miRNAs were differentially expressed in heat-stressed granulosa cells and the corresponding EVs, respectively. Supplementation of stress-related EVs in cultured granulosa cells has induced adaptive response to subsequent HS. However, this potential was not pronounced when the cells were kept under 37 °C. Taking together, EVs generated from granulosa cells exposed to HS has the potential to shuttle bioactive molecules to recipient cells and make them robust to subsequent HS.
Homogenization of Maxwell’s equations in a layered system beyond the static approximation
Authors: Merzlikin Alexander M. , Puzko Roman S. 
Published: September 2020

AbstractThe propagation of electromagnetic waves through a disordered layered system is considered in the paradigm of the homogenization of Maxwell’s equations. Although the accuracy of the effective dielectric permittivity and/or magnetic permeability is still unclear outside the static approximation, we show that the effective wave vector can be correctly introduced even in high-frequency cases. It is demonstrated that both the real and imaginary parts of the effective wave vector are self-averaging quantities connected by the Kramers–Kronig relations. We provide a unified approach to describe the propagation and localization of electromagnetic waves in terms of the effective wave vector. We show that the effective wave vector plays the same role in describing composite materials in electrodynamics as the effective dielectric permittivity does in statics.
Treatment patterns and clinical outcomes of chemotherapy treatment in patients with muscle-invasive or metastatic bladder cancer in the Netherlands
Authors: Reesink Daan J. , van de Garde Ewoudt M. W. , Peters Bas. J. M. , van der Nat Paul B. , Los Maartje , Horenblas Simon , van Melick Harm H. E. 
Published: September 2020

AbstractThis retrospective study was performed to evaluate real-world oncological outcomes of patients treated with chemo-based therapy for muscle-invasive or metastatic bladder cancer (MIBC/mBC) and compare results to data from RCTs and other cohorts. Among 1578 patients diagnosed, 470 (30%) had MIBC/mBC. Median overall survival (mOS) for RC alone (47 months), first-line (13 months) and second-line (7 months) chemotherapy, and chemotherapy for recurrent disease (8 months) were similar to literature. Treatment with neoadjuvant and induction chemotherapy (NAIC) was only utilized in 9% of patients, and often in patients with poor disease status, resulting in a lower mOS compared to literature (35 and 20 months, respectively). Patients treated with chemotherapy had many adversities to treatment, with only 50%, 13%, 18% and 7% of patients in NAIC, first-line, salvage after RC, and second-line setting completing the full pre-planned chemotherapy treatment. Real-world data shows NAIC before RC is underutilized. Adversities during chemotherapy treatment are frequent, with many patients requiring dose reduction or early treatment termination, resulting in poor treatment response. Although treatment efficacy between RCTs and real-world patients is quite similar, there are large differences in baseline characteristics and treatment patterns. Possibly, results from retrospective studies on real-world data can deliver missing evidence on efficacy of chemotherapy treatment on older and ‘unfit’ patients.
Skeletal age prediction model from percentage of adult height in children and adolescents
Authors: Olivares Luis Alberto Flores , De León Lidia G. , Fragoso Maria Isabel 
Published: September 2020

AbstractSkeletal age (SA) is considered the gold standard to assess the degree of maturation and has been widely used in sports, education and public health areas; however, it requires sophisticated equipment and well-trained technicians. Therefore, it is important to develop non-invasive methods for its evaluation. The aim was to develop an equation to predict SA using the percentage of adult height. SA was measured by Tanner-Whitehouse-3 method, and the percentage of adult height was estimated by two methodologies: Tanner-Whitehouse-3 method (P-TW3) and Khamis-Roche method (P-KR) using 839 schoolchildren of both sexes. Linear regression was used for predicting SA from P-TW3; then P-TW3 was replaced in the equation for P-KR value. Bland–Altman graphs, interclass correlation coefficient and Kappa index were used as validation tests. Model showed a SA predictive capacity of 93.2% in boys and 96.8% in girls. The average differences between SA measured and SA predicted by P-TW3 was 0.0504 (± 0.664) in boys and 0.0144 (± 0.435) in girls (P = 0.229 and 0.667, respectively). When P-TW3 was replaced for P-KR value in the equation, the average differences were − 0.0532 in boys and 0.0850 in girls (P = 0.509 and 0.167 respectively). The present model, based on the percentage of adult height, showed an adequate estimation of SA in children and adolescents and it can be used in the absence of bone X-ray equipment, in healthy boys aged 9 to 15 and girls 8 to 13.
Analytical formulas representing track-structure simulations on DNA damage induced by protons and light ions at radiotherapy-relevant energies
Authors: Kundrát Pavel , Friedland Werner , Becker Janine , Eidemüller Markus , Ottolenghi Andrea , Baiocco Giorgio 
Published: September 2020

AbstractTrack structure based simulations valuably complement experimental research on biological effects of ionizing radiation. They provide information at the highest level of detail on initial DNA damage induced by diverse types of radiation. Simulations with the biophysical Monte Carlo code PARTRAC have been used for testing working hypotheses on radiation action mechanisms, for benchmarking other damage codes and as input for modelling subsequent biological processes. To facilitate such applications and in particular to enable extending the simulations to mixed radiation field conditions, we present analytical formulas that capture PARTRAC simulation results on DNA single- and double-strand breaks and their clusters induced in cells irradiated by ions ranging from hydrogen to neon at energies from 0.5 GeV/u down to their stopping. These functions offer a means by which radiation transport codes at the macroscopic scale could easily be extended to predict biological effects, exploiting a large database of results from micro-/nanoscale simulations, without having to deal with the coupling of spatial scales and running full track-structure calculations.
Intravenously administeredd-mannitol-coated maghemite nanoparticles cause elemental anomalies in selected rat organs
Authors: Matusiak Katarzyna , Drozdz Agnieszka , Setkowicz Zuzanna , Kubala-Kukus Aldona , Stabrawa Ilona , Ciarach Małgorzata , Janeczko Krzysztof , Horak Daniel , Babic Michal , Chwiej Joanna 
Published: September 2020

AbstractIn this study novel d-mannitol coated maghemite nanoparticles (MIONPs) are presented in terms of their influence on elemental homeostasis of living organisms and for this purpose highly sensitive total reflection X-ray fluorescence was used. Because of the biological indifference of d-mannitol and presumed lower toxicity of maghemite, compared to the most commonly used magnetite in nanomedicine, such nanoparticles seem to be promising candidates for biomedical applications. The examined dose of MIONPs was comparable with one of the lowest doses used in medical diagnostics. However, it should be emphasized that the amount of iron injected in this form is still significant compared to its total content in organs, especially in kidneys or the heart, and may easily disrupt their elemental homeostasis. The aim of the present study was to evaluate the elemental changes occurring in selected rat organs after injecting a low dose of MIONPs. The results were compared with those obtained for previously examined PEG-coated nanoparticles with magnetite cores. In the light of our findings the elemental changes observed after exposure to MIONPs were less extensive than those following PEG-coated magnetite nanoparticle administration.
Forsythoside A protects against lipopolysaccharide-induced acute lung injury through up-regulating microRNA-124
Authors: Lu Zibin , Yang Huayi , Cao Huihui , Huo Chuying , Chen Yuyao , Liu Dongyi , Xie Pei , Zhou Hongling , Liu Junshan , Yu Linzhong 
Published: September 2020

Abstract
Acute lung injury (ALI) is a life-threatening disease without effective pharmacotherapies, so far. Forsythia suspensa is frequently used in the treatment of lung infection in traditional Chinese medicine. In search for natural anti-inflammatory components, the activity and the underlying mechanism of Forsythoside A (FA) from Forsythia suspensa were explored. In the present paper, BALB/c mice and murine RAW 264.7 cells were stimulated by LPS to establish inflammation models. Data showed that FA inhibited the production of TNF-α and IL-6 and the activation of STAT3 in LPS-stimulated RAW 264.7 cells. Additionally, FA increased the expression level of microRNA-124 (miR-124). Furthermore, the inhibitory effect of FA on STAT3 was counteracted by the treatment of miR-124 inhibitor. Critically, FA ameliorated LPS-induced ALI pathological damage, the increase in lung water content and inflammatory cytokine, cells infiltration and activation of the STAT3 signaling pathway in BALB/c mice. Meanwhile, FA up-regulated the expression of miR-124 in lungs, while administration with miR-124 inhibitor attenuated the protective effects of FA. Our results indicated that FA alleviates LPS-induced inflammation through up-regulating miR-124 in vitro and in vivo. These findings indicate the potential of FA and miR-124 in the treatment of ALI.
Uncovering protein structure
Authors: Stollar Elliott J , Smith David P 
Published: September 2020

Abstract
Structural biology is the study of the molecular arrangement and dynamics of biological macromolecules, particularly proteins. The resulting structures are then used to help explain how proteins function. This article gives the reader an insight into protein structure and the underlying chemistry and physics that is used to uncover protein structure. We start with the chemistry of amino acids and how they interact within, and between proteins, we also explore the four levels of protein structure and how proteins fold into discrete domains. We consider the thermodynamics of protein folding and why proteins misfold. We look at protein dynamics and how proteins can take on a range of conformations and states. In the second part of this review, we describe the variety of methods biochemists use to uncover the structure and properties of proteins that were described in the first part. Protein structural biology is a relatively new and exciting field that promises to provide atomic-level detail to more and more of the molecules that are fundamental to life processes.
Associations Between Measures of Auditory Function and Brief Assessments of Cognition
Authors: Humes Larry E. 
Published: September 2020

Purpose
The two primary purposes of this report are (a) to compare the results of three brief cognitive screens in older adults and (b) to examine associations between performance on each of the screens and auditory function measured either concurrently or 9 years earlier.

Method
This was a prospective longitudinal study of 98 adults (66 women) with baseline ages ranging from 40 to 85 years. The mean interval between T1 baseline and T2 follow-up measurements was 8.8 years with a range from 7 to 11 years. Measures of hearing threshold, gap detection, and auditory temporal-order identification were completed at T1 and T2. The Mini-Mental State Examination was completed at T1 and T2, whereas the Montreal Cognitive Assessment (MoCA) and A Quick Test were completed at T2 only.

Results
Higher scores and pass rates were obtained for the Mini-Mental State Examination than for the MoCA or the A Quick Test. The measures were moderately correlated among themselves and with the Wechsler Adult Intelligence Scale–Third Edition. Significant associations emerged frequently between auditory and cognitive functions, most often for the auditory measure of temporal-order identification, including dichotic measures of this ability.

Conclusions
From this evaluation, the MoCA emerged as the preferred test for clinicians desiring a quick assessment of the cognitive function of their older patients. Auditory temporal-order identification is associated with cognitive function and explains about 10%–20% of the variation in cognitive function independent of age and hearing loss.

Supplemental Material

https://doi.org/10.23641/asha.12986021
Investigating episodic accretion in a very low-mass young stellar object
Authors: Stock C. , Caratti o Garatti A. , McGinnis P. , Garcia Lopez R. , Antoniucci S. , Fedriani R. , Ray T. P. 
Published: September 2020

Context. Very low-mass Class I protostars have been investigated very little thus far. Variability of these young stellar objects (YSOs) and whether or not they are capable of strong episodic accretion is also left relatively unstudied.
Aims. We investigate accretion variability in IRS 54 (YLW52), a Class I very low-mass protostar with a mass of M⋆ ∼ 0.1 − 0.2 M⊙.
Methods. We obtained spectroscopic and photometric data with VLT/ISAAC and VLT/SINFONI in the near-infrared (J, H, and K bands) across four epochs (2005, 2010, 2013, and 2014). We used accretion-tracing lines (Paβ and Brγ) and outflow-tracing lines (H2 and [Fe II]) to examine physical properties and kinematics of the object.
Results. A large increase in luminosity was found between the 2005 and 2013 epochs of more than 1 magnitude in the K band, followed in 2014 by a steep decrease. Consistently, the mass accretion rate (Ṁacc) rose by an order of magnitude from ∼10−8 M⊙ yr−1 to ∼10−7 M⊙ yr−1 between the two early epochs. The visual extinction (AV) has also increased from ∼15 mag in 2005 to ∼24 mag in 2013. This rise in AV in tandem with the increase in Ṁacc is explained by the lifting up of a large amount of dust from the disc of IRS 54, following the augmented accretion and ejection activity in the YSO, which intersects our line of sight due to the almost edge-on geometry of the disc. Because of the strength and timescales involved in this dramatic increase, this event is believed to have been an accretion burst possibly similar to bursts of EXor-type objects. IRS 54 is the lowest mass Class I source observed to have an accretion burst of this type, and therefore potentially one of the lowest mass EXor-type objects known so far.
Thermophysical model for icy cometary dust particles
Authors: Markkanen J. , Agarwal J. 
Published: September 2020

Context. Cometary dust particles are subjected to various forces after being lifted off the nucleus. These forces define the dynamics of dust, trajectories, alignment, and fragmentation, which, in turn, have a significant effect on the particle distribution in the coma.
Aims. We develop a numerical thermophysical model that is applicable to icy cometary dust to study the forces attributed to the sublimation of ice.
Methods. We extended the recently introduced synoptic model for ice-free dust particles to ice-containing dust. We introduced an additional source term to the energy balance equation accounting for the heat of sublimation and condensation. We use the direct simulation Monte Carlo approach with the dusty gas model to solve the mass balance equation and the energy balance equation simultaneously.
Results. The numerical tests show that the proposed method can be applied for dust particles covering the size range from tens of microns to centimetres with a moderate computational cost. We predict that for an assumed ice volume fraction of 0.05, particles with a radius, r ≫ 1 mm, at 1.35 AU, may disintegrate into mm-sized fragments due to internal pressure build-up. Particles with r < 1 cm lose their ice content within minutes. Hence, we expect that only particles with r > 1 cm may demonstrate sustained sublimation and the resulting outgassing forces.
R-matrix electron-impact excitation data for the N-like iso-electronic sequence
Authors: Mao Junjie , Badnell N. R. , Del Zanna G. 
Published: September 2020

Context. Spectral lines from N-like ions can be used to measure the temperature and density of various types of astrophysical plasmas. The atomic databases of astrophysical plasma modelling codes still have room for improvement in their electron-impact excitation data sets for N-like ions, especially for R-matrix data. This is particularly relevant for future observatories (e.g. Arcus), which will host high-resolution spectrometers.
Aims. We aim to obtain level-resolved effective collision strengths for all transitions up to nl = 5d over a wide range of temperatures for N-like ions from O II to Zn XXIV (i.e. O+ to Zn23+) and to assess the accuracy of the present work. We also examine the impact of our new data on plasma diagnostics by modelling solar observations with CHIANTI.
Methods. We carried out systematic R-matrix calculations for N-like ions, which included 725 fine-structure target levels in both the configuration interaction target and close-coupling collision expansions. The R-matrix intermediate coupling frame transformation method was used to calculate the collision strengths, while the AUTOSTRUCTURE code was used for the atomic structures.
Results. We compare the present results for selected ions with those in archival databases and the literature. The comparison covers energy levels, oscillator strengths, and effective collision strengths. We show examples of improved plasma diagnostics when compared to CHIANTI models, which use only distorted wave data as well as some using previous R-matrix data. The electron-impact excitation data are archived according to the Atomic Data and Analysis Structure (ADAS) data class adf04 and will be available in OPEN-ADAS. The data can be used to improve the atomic databases for astrophysical plasma diagnostics.