bluuebunny/crossref_metadata_2025 huggingface dataset:
The effectiveness of Project-based Learning on students’ science process skills: a literature review
Authors: Andriyani R , Shimizu K , Widiyatmoko A
Published: November 2019

The aim of this literature review is to analyse the effectiveness of project-based learning on students’ science process skills (SPS). Project-based learning as the learning method, which is recommended by the Indonesian curriculum, supposed to improve students’ skills. Indonesian curriculum emphasizes the achievement of students’ competencies, namely spiritual, social, knowledge and skills. SPS are the part of skills competency that will improve in science learning process. The method used in this study is a literature review. First, the researcher provides the definition of project-based learning. Next step is to find information about how to conduct project-based learning and the important things to do in project-based learning. Then, the researcher synthesizes some information about work had been done to improve SPS in the previous study and make a connection with project-based learning. Based on the literature review, students’ SPS will improve through clear instructions which involve students to design the science learning activities. The finding indicated that project-based learning activities effective to improve students’ SPS.
The development of Assessment of Science Instruction in English (ASIE) to assess teaching skill in English of prospective science teacher
Authors: Wusqo I U , Pamelasari S D , Hardianti R D
Published: November 2019

This research is a research that aims to develop an assessment of Science Instruction in English (ASIE) and its implementation to assess valid and effective science teaching skills in English. The research design used was Research and Development. This design uses the ADDIE model. Data collection in this study using the method of observation, questionnaire and documentation. Data from the research results were analysed using quantitative descriptive analysis methods. The feasibility of the instrument is determined based on the feasibility test assessed using a validation sheet. The conclusions obtained were successfully developed in English (ASIE) Assessment of content instruction using ADDIE design, with very valid criteria with a score of 83.95 and practical with score 90.28%, and useful in measuring teaching ability in English as an effort to prepare prospective reputable teacher candidates with 90% of students getting grades B and 95% of user responses in good and very good categories.
The Value of Next-Generation Sequencing in the Screening and Evaluation of Hematologic Neoplasms in Clinical Practice
Authors: Northrup Victoria , Maybank Allison , Carson Nancy , Rahmeh Tarek
Published: November 2019

Objectives

The implementation of next-generation sequencing (NGS) in routine clinical hematology practice remains limited. We evaluate the clinical value of NGS in the screening, diagnosis, and follow-up in hematologic neoplasms.

Methods

A targeted NGS panel was used to assess a total of 178 patients for questionable or previously diagnosed myeloid neoplasms.

Results

Gene variants were identified in 53% of patients. Novel variants were identified in 29% of patients and variants of unknown significance in 34%. Bone marrow samples yielded a higher number of variants than in peripheral blood. NGS is a more sensitive test than conventional cytogenetics. In several cases, NGS played a key role in the screening, diagnostics, prognostic stratification, and the clinical follow-up of a wide variety of myeloid neoplasms.

Conclusions

NGS is an effective tool in the evaluation of suspected and confirmed hematologic neoplasms and could become part of the routine workup of patients.
Vocal characteristics of prairie dog alarm calls across an urban noise gradient
Authors: Shannon Graeme , McKenna Megan F , Wilson-Henjum Grete E , Angeloni Lisa M , Crooks Kevin R , Wittemyer George
Published: November 2019

Increasing anthropogenic noise is having a global impact on wildlife, particularly due to the masking of crucial acoustical communication. However, there have been few studies examining the impacts of noise exposure on communication in free-ranging terrestrial mammals. We studied alarm calls of black-tailed prairie dogs (Cynomys ludovicianus) across an urban gradient to explore vocal adjustment relative to different levels of noise exposure. There was no change in the frequency 5%, peak frequency, or duration of the alarm calls across the noise gradient. However, the minimum frequency—a commonly used, yet potentially compromised metric—did indeed show a positive relationship with noise exposure. We suspect this is a result of masking of observable call properties by noise, rather than behavioral adjustment. In addition, the proximity of conspecifics and the distance to the perceived threat (observer) did affect the frequency 5% of alarm calls. These results reveal that prairie dogs do not appear to be adjusting their alarm calls in noisy environments but likely do in relation to their social context and the proximity of a predatory threat. Anthropogenic noise can elicit a range of behavioral and physiological responses across taxa, but elucidating the specific mechanisms driving these responses can be challenging, particularly as these are not necessarily mutually exclusive. Our research sheds light on how prairie dogs appear to respond to noise as a source of increased risk, rather than as a distraction or through acoustical masking as shown in other commonly studied species (e.g., fish, songbirds, marine mammals).
Population genomics of Bombus terrestris reveals high but unstructured genetic diversity in a potential glacial refugium
Authors: Silva Sara E , Seabra Sofia G , Carvalheiro Luísa G , Nunes Vera L , Marabuto Eduardo , Mendes Raquel , Rodrigues Ana S B , Pina-Martins Francisco , Yurtsever Selçuk , Laurentino Telma G , Figueiredo Elisabete , Rebelo Maria T , Paulo Octávio S
Published: November 2019

Ongoing climate change is expected to cause an increase in temperature and a reduction of precipitation levels in the Mediterranean region, which might cause changes in many species distributions. These effects negatively influence species gene pools, decreasing genetic variability and adaptive potential. Here, we use mitochondrial DNA and RADseq to analyse population genetic structure and genetic diversity of the bumblebee species Bombus terrestris (subspecies Bombus terrestris lusitanicus), in the Iberian Peninsula. Although this subspecies shows a panmictic pattern of population structure across Iberia and beyond, we found differentiation between subspecies B. t. lusitanicus and B. t. africanus, probably caused by the existence of barriers to gene flow between Iberia and North Africa. Furthermore, the results revealed that the Iberian Peninsula harbours a large fraction of B. terrestris intraspecific genetic variation, with the highest number of mitochondrial haplotypes found when compared with any other region in Europe studied so far, suggesting a potential role for the Iberian Peninsula as a glacial refugium. Our findings strengthen the idea that Iberia is a very important source of diversity for the global genetic pool of this species, because rare alleles might play a role in population resilience against human- or climate-mediated changes.
Glutathione S-transferase omega 2 regulates cell growth and the expression of E-cadherin via post-transcriptional down-regulation of β-catenin in human esophageal squamous cells
Authors: Terayama Masayoshi , Yamada Kazuhiko , Hagiwara Teruki , Inazuka Fumika , Sezaki Takuhito , Igari Toru , Yokoi Chizu , Nohara Kyoko , Soma Daisuke , Dohi Taeko , Kawamura Yuki I
Published: November 2019

Glutathione S-transferase omega 2 (GSTO2), which belongs to the superfamily of GST omega class, lacks any appreciable GST activity. Although GSTO2 exhibits thioltransferase and glutathione dehydrogenase activities, its precise expression and physiological functions are still unclear. In the present study, we found that GSTO2 is exclusively expressed in the basal cell layer in Ki67-negative non-proliferative cells in the human esophageal mucosa. GSTO2 overexpression in esophageal squamous cell carcinoma (ESCC) cell lines inhibited cell growth and colony formation, and GSTO2-transfected cells formed smaller tumors in nude mice compared with mock-transfected cells. Interestingly, GSTO2 induction suppressed the expressions of E-cadherin and β-catenin at the cell–cell contact site. We quantified the phosphorylation levels of key proteins of MAPK signaling pathway and identified phosphorylation of p38. Additionally, HSP27, a downstream molecule of p38, was accelerated in GSTO2-transfected cells, unlike in mock-transfected cells. When GSTO2-transfected cells were treated with a p38 inhibitor, the expression of β-catenin and the membrane localization of E-cadherin was recovered. We next examined GSTO2 expression in 61 ESCC tissues using quantitative reverse transcription polymerase chain reaction and immunostaining. The results showed that GSTO2 mRNA and protein were significantly reduced in ESCC compared with normal tissues. When human ESCC cell lines were treated with 5-aza-2′-deoxycytidine, a DNA-methyltransferase inhibitor, GSTO2 transcription was induced, suggesting that aberrant hypermethylation is the cause of the down-regulated expression. Our results indicate that GSTO2 expression inhibits the membrane localization of E-cadherin, probably by modulation of the p38 signaling pathway. Down-regulation of GSTO2 by DNA hypermethylation contributes to the growth and progression of ESCC.
Metal-containing Particulate Matter and Associated Reduced Olfactory Identification Ability in Children from an Area of High Atmospheric Exposure in Mexico City
Authors: Guarneros Marco , López-Rivera Cristina , Gonsebatt María Eugenia , Alcaraz-Zubeldia Mireya , Hummel Thomas , Schriever Valentin A , Valdez Bertha , Hudson Robyn
Published: November 2019

Air pollution has been linked to poor olfactory function in human adults. Among pollutants, particulate matter (PM) is especially relevant, as it may contain toxic metal ions that can reach the brain via olfactory pathways. Our purpose was to investigate the relation between atmospheric PM and olfactory identification performance in children. Using a validated method, we tested the olfactory identification performance of 120 children, 6–12 years old, from two locations in Mexico City: a focal group (n = 60) from a region with high PM levels and a control group of equal size and similar socioeconomic level from a region with markedly lower PM concentrations. Groups were matched for age and sex. Concentrations of manganese and lead in the hair of participants were determined as biomarkers of exposure. Daily outdoor PM levels were obtained from official records, and indoor PM levels were measured in the children’s classrooms. Official records confirmed higher levels of outdoor PM in the focal region during the days of testing. We also found higher classroom PM concentrations at the focal site. Children from the focal site had on average significantly lower olfactory identification scores than controls, and hair analysis showed significantly higher levels of manganese for the focal children but no difference in lead. Children appear to be vulnerable to the effects of air pollution on olfactory identification performance, and metal-containing particles likely play a role in this. Olfactory tests provide a sensitive, noninvasive means to assess central nervous function in populations facing poor air quality.
Antibiotic Duration, but Not Abscess Size, Impacts Clinical Cure of Limited Skin and Soft Tissue Infection After Incision and Drainage
Authors: Lake Jason G , Miller Loren G , Fritz Stephanie A
Published: November 2019

Antibiotics are frequently prescribed following incision and drainage of cutaneous abscesses. In subgroup analyses from a recent clinical trial, we observed higher likelihood of cure with antibiotic courses beyond 5 or 7 days (up to 10). Among this cohort, for abscesses ≤5 cm, size did not modify the antibiotic effect.
Mediating Syria’s Strangers Through Levinas: Communication Ethics and the Visuals of Children
Authors: Irom Bimbisar
Published: November 2019

This paper investigates how the visuals of two children affected by the Syrian conflict, Alan Kurdi and Omran Daqneesh, circulate within the humanitarian imaginary. I argue that these communication artifacts offer us an opportunity to explore the links between two areas not often thought of in conjunction: ethical theory and mediation. The goal is to contribute to our understanding of the relationships between communication ethics and the mediated representations of subjects who are perceived as “Others.” The visuals of Alan and Omran are appropriate for this investigation, given their evident Otherness as Syrians to a predominantly Western audience. Exploring these visuals in the light of Emmanuel Levinas’ ethical call of the Other and the mediated visibility of sufferers will further our understanding of the connections between communication ethics and mediation as textual and social/ethical practice.
The Issue Niche Theory of Nongovernmental and Nonprofit Organizations’ Interorganizational Network Ecology
Authors: Yang Aimei
Published: November 2019

Societies are filled with numerous issues. Issues are contestable matters of concerns regarding facts, values, or policies, of which resolutions may affect social change. Some issues—such as climate change, gun rights, health care, and gender inequality—are extensively covered in the news and often become the center of public discourse and debates. Issues sometimes pose imminent threats to communities and even entire countries, and such conditions often call for the mobilization of considerable social resources and require collaborations of individuals and organizations from different social sectors and across countries.
Expanding Advice Response Theory by Incorporating Goal Inference: College Students’ Perceptions of Parental Exercise Advice
Authors: Guntzviller Lisa M , Ratcliff Chelsea L , Pusateri Kimberly B
Published: November 2019

We expanded Advice Response Theory (ART) by proposing that recipient perceptions of advisor characteristics can be distal (e.g., parenting style) and proximal (e.g., goal inference). We examined how the recipient’s inference of the advisor’s goals (confirmation, change, and novelty) mediates associations between distal characteristics and message feature evaluations and outcomes. As predicted, positive associations occurred between perceptions of parenting style, confirmation goal inference, advice efficacy and positive facework, and desirable advice outcomes. Counter to predictions, inferring change and novelty goals did not have uniformly undesirable effects. An inference of the change goal was associated with higher efficacy ratings and the recipient changing plans following the conversation. Our findings support conceptualizing ART advisor characteristics as distal and proximal, and advisor goal inference as a relevant proximal characteristic.
In patients undergoing video-assisted thoracic surgery for lung resection, does three-dimensional endoscopic vision provide superior clinical outcomes?
Authors: Chandarana Karishma , Caruana Edward J
Published: November 2019

A best evidence topic in thoracic surgery was written according to a structured protocol. The question addressed was whether the use of 3-dimensional endoscopic vision provides superior clinical outcomes to patients undergoing video-assisted thoracic surgery for lung resection. Altogether 231 unique papers were found using the reported search, of which 6 represented the best evidence to answer the clinical question. The authors, journal, date and country of publication, patient group studied, study type, relevant outcomes and results of these papers are tabulated. Four of the 6 papers demonstrated a statistically significant reduction in operative time, although this difference may not be of sufficient magnitude to be relevant clinically. There was no difference in any other outcomes assessed. We therefore conclude that, in patients undergoing video-assisted thoracic surgery for lung resection, 3-dimensional endoscopic vision has no demonstrable impact on perioperative or oncological outcomes, or cost, although it may reduce operative time.
Allegiance, Ability, and Achievement in the American Civil War: Commander Traits and Battlefield Military Effectiveness
Authors: Arnold Jeffrey B , Chatagnier J Tyson , Hollibaugh Gary E
Published: November 2019

How do the characteristics of military leaders relate to battlefield outcomes? To answer this question, we employ original battle-level data and biographical information on hundreds of commanders in more than 250 battles in the American Civil War. We examine the relationship between two common measures of battlefield success (victory and casualties) and two latent features of commanders—competence and loyalty—that have long been seen as important in the broader study of executive appointments. We find that competent commanders are associated with more successful battlefield outcomes, as are more loyal Confederate commanders. More broadly, our analysis suggests that focusing on the relationship between military appointments and battlefield outcomes—with the latter's relatively clear definition of “success”—allows for direct examination of the relationship between appointee traits and organizational performance. As such, our results have implications for the study of conflict as well as bureaucratic politics.
Specific staphylococcal cassette chromosome mec (SCCmec) types and clonal complexes are associated with low-level amoxicillin/clavulanic acid and cefalotin resistance in methicillin-resistant Staphylococcus pseudintermedius
Authors: Wegener Alice , Damborg Peter , Guardabassi Luca , Moodley Arshnee , Mughini-Gras Lapo , Duim Birgitta , Wagenaar Jaap A , Broens Els M
Published: November 2019

Background

Staphylococcus pseudintermedius is a common pathogen in dogs and methicillin resistance has emerged over recent decades. According to the current guidelines, S. pseudintermedius displaying oxacillin resistance should be reported as resistant to all β-lactams.

Objectives

To identify possible associations between β-lactam resistance levels and clonal complexes (CCs) and/or staphylococcal cassette chromosome mec (SCCmec) types in methicillin-resistant S. pseudintermedius (MRSP).

Methods

MICs of oxacillin, penicillin, ampicillin, amoxicillin/clavulanic acid and cefalotin were determined by broth microdilution for 86 clinical canine MRSP isolates from Denmark and the Netherlands. PCR and sequencing were used for SCCmec typing and MLST.

Results

Isolates belonged to CC71 (n = 36), CC258 (n = 33), CC45 (n = 11), CC68 (n = 1) and five singleton STs. SCCmecII-III was exclusively found in CC71 and SCCmecIV was significantly associated with CC258. SCCmecV and non-typeable SCCmec types occurred in 4 and 14 isolates, respectively. SCCmecIV was associated with lower MICs of oxacillin (<2 mg/L), ampicillin (<8 mg/L) and amoxicillin/clavulanic acid (<4 mg/L) and with susceptibility to cefalotin (<4 mg/L). All isolates harbouring SCCmecV were susceptible to cefalotin as well.

Conclusions

SCCmec types were associated with different CCs and with either high- or low-level resistance to different β-lactams. The finding of amoxicillin/clavulanic acid (20%) and cefalotin (70%) in vitro susceptibility across all CCs might have clinical implications, since amoxicillin/clavulanic acid and first-generation cephalosporins are first-choice antibiotics for treatment of S. pseudintermedius infections. Pharmacokinetic/pharmacodynamic and clinical outcome studies are warranted to evaluate the in vivo efficacy of these β-lactams for treatment of MRSP infections.
Morphology and orientated growth of second-phase precipitates in a Eu2+-doped equimolar KCl:KBr solid solution: an epifluorescence microscopy study by using the doping ion as a fluorochrome
Authors: Cordero-Borboa Adolfo Ernesto , Unda-Angeles Rodrigo
Published: November 2019

The shape and orientation of second-phase precipitates in a Eu2+-doped equimolar KCl:KBr solid solution are reported in this paper as they were unveiled by epifluorescence microscopy. To make this, microscopy images of different optical cross sections of some precipitate fields and, also, of some representative precipitates in these fields, were recorded by using the Eu2+ ion itself as a fluorochrome. From these images, the corresponding precipitate fields and individual precipitates were electronically reconstructed into the host lattice space. Previously, the KCl:KBr:Eu2+ system was characterized by absorption and fluorescence optical spectrophotometry, to tailor properly the fluorescence mirror unit, as well as by powder and single-plate X-ray diffraction, to correlate the host lattice orientation with those of the observed precipitates. These are shaped as plates, with broad faces parallel to host lattice {100}, {110} or {120}planes (the {100}, {110} and {120} precipitates, respectively), and as rods, aligned with a host lattice ˂100> direction (the ˂100> precipitates). The {100}, {110}, {120}-precipitate broad faces are in the shapes of 72.6° rhomboids, rectangles and 59.5° rhomboids, with a side lying along host lattice <310>, <110> and <421> directions, respectively, and with another side lying along a <100> direction. A typical precipitate field and the spatial reconstructions of typical {100}, {110}, {120} and ˂100> precipitates, as well as their corresponding electronic 3D-geometrical models, are described in detail. It is discussed that four different europium precipitation states are responsible for the precipitation and that the precipitate lattices are spatially coherent with the host lattice.
Oversampling of Minority Populations Through Dual-Frame Surveys
Authors: Chen Sixia , Stubblefield Alexander , Stoner Julie A
Published: November 2019

Previous studies have shown disparities in health conditions and behaviors among different ethnic groups. Sampling designs that do not consider oversampling certain minority populations, such as American Indians or African Americans, may not produce sufficient sample sizes for estimating health parameters for minority populations. Oversampling is one of the most common approaches that researchers use to achieve required precision levels for small domain estimation. However, it has not been rigorously investigated in dual-frame survey settings. To take advantage of extra information for minority populations in the Marketing Systems Group database, we propose a novel optimal oversampling strategy that minimizes the domain variance subject to total cost restriction or vice versa. We further extend the method to oversample multiple minorities simultaneously. Empirical study using a population-based community survey shows the benefits of our proposed methods compared with traditional methods in terms of statistical efficiency and cost balance.
X-ray study of the double source plane gravitational lens system Eye of Horus observed with XMM–Newton
Authors: Tanaka Keigo , Tsuji Ayumi , Akamatsu Hiroki , Chan J H H , Coupon Jean , Egami Eiichi , Finet Francois , Fujimoto Ryuichi , Ichinohe Yuto , Jaelani Anton T , Lee Chien-Hsiu , Mitsuishi Ikuyuki , More Anupreeta , More Surhud , Oguri Masamune , Okabe Nobuhiro , Ota Naomi , Rusu Cristian E , Sonnenfeld Alessandro , Tanaka Masayuki , Ueda Shutaro , Wong Kenneth C
Published: November 2019

A double source plane (DSP) system is a precious probe for the density profile of distant galaxies and cosmological parameters. However, these measurements could be affected by the surrounding environment of the lens galaxy. Thus, it is important to evaluate the cluster-scale mass for detailed mass modelling. We observed the Eye of Horus, a DSP system discovered by the Hyper Suprime-Cam Subaru Strategic Survey (HSC–SSP), with XMM–Newton. We detected two X-ray extended emissions, originating from two clusters, one centred at the Eye of Horus, and the other located ∼100 arcsec north-east to the Eye of Horus. We determined the dynamical mass assuming hydrostatic equilibrium, and evaluated their contributions to the lens mass interior of the Einstein radius. The contribution of the former cluster is $1.1^{+1.2}_{-0.5}\times 10^{12}\, \mathrm{M}_{\odot }$, which is $21\!-\!76{{\ \rm per\ cent}}$ of the total mass within the Einstein radius. The discrepancy is likely due to the complex gravitational structure along the line of sight. On the other hand, the contribution of the latter cluster is only $\sim 2{{\ \rm per\ cent}}$ on the Eye of Horus. Therefore, the influence associated with this cluster can be ignored.
3D Modeling of absorption by various species for hot jupiter HD209458b
Authors: Shaikhislamov I F , Khodachenko M L , Lammer H , Berezutsky A G , Miroshnichenko I B , Rumenskikh M S
Published: November 2019

The absorption of stellar radiation observed at transits of HD209458b in resonant lines of OI and CII has not yet been satisfactorily modeled. In our previous 2D simulations we have shown that hydrogen-dominated upper atmosphere of HD209458b, heated by XUV radiation, expands supersonically beyond the Roche lobe and drags heavier species along with it. Assuming solar abundances, OI and CII particles accelerated by tidal forces to velocities up to 50 km/s should produce the absorption due to Doppler resonance at the level of 6–10 per cent, consistent with the observations. Since the 2D geometry does not take into account the Coriolis force in a planet reference frame, the question remained to which extent the spiraling of escaping planetary material and actually achieved velocity may influence the conclusions made on basis of 2D modeling. In the present paper we apply for the first time in studies of HD209458b a global 3D hydrodynamic multi-fluid model. The results confirm our previous findings that the velocity of the planetary flow is sufficiently high to match the widths of OI and CII resonant lines. To match absorption in those lines, including HI, with observations, the mass loss rate of HD209458b should be about 2.5·1011 g/s which is 3.5 times larger than that revealed by the 2D model. The other novel finding is that matching of the absorption measured in MgII and SiIII lines requires at least 10 times lower abundances of these elements than the Solar values.
High-resolution reflection spectra for Proxima b and Trappist-1e models for ELT observations
Authors: Lin Z , Kaltenegger L
Published: November 2019

The closest stars that harbor potentially habitable planets are cool M-stars. Upcoming ground- and space-based telescopes will be able to search the atmosphere of such planets for a range of chemicals. To facilitate this search and to inform upcoming observations, we model the high-resolution reflection spectra of two of the closest potentially habitable exoplanets for a range of terrestrial atmospheres and surface pressures for active and inactive phases of their host stars for both oxic and anoxic conditions: Proxima b, the closest potentially habitable exoplanet, and Trappist-1e, one of 3 Earth-size planets orbiting in the Habitable Zone of Trappist-1. We find that atmospheric spectral features, including biosignatures like O2 in combination with a reduced gas like CH4 for oxic atmospheres, as well as climate indicators like CO2 and H2O for all atmospheres, show absorption features in the spectra of Proxima b and Trappist-1e models. However for some features like oxygen, high-resolution observations will be critical to identify them in a planet's reflected flux. Thus these two planets will be among the best targets for upcoming observations of potential Earth-like planets in reflected light with planned Extremely Large Telescopes.
rascalc: a jackknife approach to estimating single- and multitracer galaxy covariance matrices
Authors: Philcox Oliver H E , Eisenstein Daniel J , O’Connell Ross , Wiegand Alexander
Published: November 2019

To make use of clustering statistics from large cosmological surveys, accurate and precise covariance matrices are needed. We present a new code to estimate large-scale galaxy two-point correlation function (2PCF) covariances in arbitrary survey geometries that, due to new sampling techniques, runs ∼104 times faster than previous codes, computing finely binned covariance matrices with negligible noise in less than 100 CPU-hours. As in previous works, non-Gaussianity is approximated via a small rescaling of shot noise in the theoretical model, calibrated by comparing jackknife survey covariances to an associated jackknife model. The flexible code, rascalc, has been publicly released, and automatically takes care of all necessary pre- and post-processing, requiring only a single input data set (without a prior 2PCF model). Deviations between large-scale model covariances from a mock survey and those from a large suite of mocks are found to be indistinguishable from noise. In addition, the choice of input mock is shown to be irrelevant for desired noise levels below ∼105 mocks. Coupled with its generalization to multitracer data sets, this shows the algorithm to be an excellent tool for analysis, reducing the need for large numbers of mock simulations to be computed.
Towards a deeper understanding of the physics driving galaxy quenching – inferring trends in the gas content via extinction
Authors: Piotrowska Joanna M , Bluck Asa F L , Maiolino Roberto , Concas Alice , Peng Yingjie
Published: November 2019

In order to investigate the importance of different proposed quenching mechanisms, we use an indirect method to estimate gas masses for ∼62 000 SDSS DR7 galaxies. We infer gas surface densities from dust column densities as traced by extinction within the fibre, applying a metallicity correction to account for varying dust-to-gas ratios. We find that both gas fraction and star formation efficiency (SFE) decrease moving away from the star-forming main sequence (MS) towards quiescence for all galaxy masses. We further show that both quantities correlate similarly strongly with the departure from the MS, implying the need for any physical model of quenching to invoke a change in both gas fraction and SFE. Our results call for a better understanding of the physical processes driving the decrease in SFE, which has received relatively little attention in the theory of quenching until now.
STRIDE—a fluorescence method for direct, specific in situ detection of individual single- or double-strand DNA breaks in fixed cells
Authors: Kordon Magdalena M , Zarębski Mirosław , Solarczyk Kamil , Ma Hanhui , Pederson Thoru , Dobrucki Jurek W
Published: November 2019

We here describe a technique termed STRIDE (SensiTive Recognition of Individual DNA Ends), which enables highly sensitive, specific, direct in situ detection of single- or double-strand DNA breaks (sSTRIDE or dSTRIDE), in nuclei of single cells, using fluorescence microscopy. The sensitivity of STRIDE was tested using a specially developed CRISPR/Cas9 DNA damage induction system, capable of inducing small clusters or individual single- or double-strand breaks. STRIDE exhibits significantly higher sensitivity and specificity of detection of DNA breaks than the commonly used terminal deoxynucleotidyl transferase dUTP nick-end labeling assay or methods based on monitoring of recruitment of repair proteins or histone modifications at the damage site (e.g. γH2AX). Even individual genome site-specific DNA double-strand cuts induced by CRISPR/Cas9, as well as individual single-strand DNA scissions induced by the nickase version of Cas9, can be detected by STRIDE and precisely localized within the cell nucleus. We further show that STRIDE can detect low-level spontaneous DNA damage, including age-related DNA lesions, DNA breaks induced by several agents (bleomycin, doxorubicin, topotecan, hydrogen peroxide, UV, photosensitized reactions) and fragmentation of DNA in human spermatozoa. The STRIDE methods are potentially useful in studies of mechanisms of DNA damage induction and repair in cell lines and primary cultures, including cells with impaired repair mechanisms.
Supracerebellar Transtentorial Approach for Mesial Temporal Lobe Cavernous Malformation: 2-Dimensional Operative Video
Authors: Hendricks Benjamin K , Spetzler Robert F
Published: November 2019

Medial temporal cavernous malformations can involve transgression of eloquent parenchyma. For a tentorium-abutting temporal cavernous malformation, the supracerebellar transtentorial corridor is a suitable approach with minimal parenchymal insult. Using dynamic and gravity retraction, lighted bipolar forceps and suction, and stereotactic navigation, this trajectory provides a minimally invasive corridor. The patient in this case has a medial temporal cavernous malformation, with the lesion abutting the tentorial leaflet. The cavernous malformation is accessed and removed in a piecemeal manner. Complete removal of the lesion is achieved. The patient remained neurologically stable after the procedure. The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary. Used with permission from Barrow Neurological Institute, Phoenix, Arizona.
Alloxan Disintegrates the Plant Cytoskeleton and Suppresses mlo-Mediated Powdery Mildew Resistance
Authors: Wu Hongpo , Zhang Weiwei , Schuster Martin , Moch Marcin , Windoffer Reinhard , Steinberg Gero , Staiger Christopher J , Panstruga Ralph
Published: November 2019

Recessively inherited mutant alleles of Mlo genes (mlo) confer broad-spectrum penetration resistance to powdery mildew pathogens in angiosperm plants. Although a few components are known to be required for mlo resistance, the detailed molecular mechanism underlying this type of immunity remains elusive. In this study, we identified alloxan (5,5-dihydroxyl pyrimidine-2,4,6-trione) and some of its structural analogs as chemical suppressors of mlo-mediated resistance in monocotyledonous barley (Hordeum vulgare) and dicotyledonous Arabidopsis thaliana. Apart from mlo resistance, alloxan impairs nonhost resistance in Arabidopsis. Histological analysis revealed that the chemical reduces callose deposition and hydrogen peroxide accumulation at attempted fungal penetration sites. Fluorescence microscopy revealed that alloxan interferes with the motility of cellular organelles (peroxisomes, endosomes and the endoplasmic reticulum) and the pathogen-triggered redistribution of the PEN1/SYP121 t-SNARE protein. These cellular defects are likely the consequence of disassembly of actin filaments and microtubules upon alloxan treatment. Similar to the situation in animal cells, alloxan elicited the temporary accumulation of reactive oxygen species (ROS) in cotyledons and rosette leaves of Arabidopsis plants. Our results suggest that alloxan may destabilize cytoskeletal architecture via induction of an early transient ROS burst, further leading to the failure of molecular and cellular processes that are critical for plant immunity.
Amyloidogenicity and cytotoxicity of des-Lys-1 human amylin provides insight into amylin self-assembly and highlights the difficulties of defining amyloidogenicity
Authors: Lee Kyung-Hoon , Zhyvoloup Alexander , Raleigh Daniel
Published: November 2019

The polypeptide amylin is responsible for islet amyloid in type 2 diabetes, a process which contributes to β-cell death in the disease. The role of the N-terminal region of amylin in amyloid formation is relatively unexplored, although removal of the disulfide bridged loop between Cys-2 and Cys-7 accelerates amyloid formation. We examine the des Lys-1 variant of human amylin (h-amylin), a variant which is likely produced in vivo. Lys-1 is a region of high charge density in the h-amylin amyloid fiber. The des Lys-1 polypeptide forms amyloid on the same time scale as wild-type amylin in phosphate buffered saline, but does so more rapidly in Tris. The des Lys-1 variant is somewhat less toxic to cultured INS cells than wild type. The implications for the in vitro mechanism of amyloid formation and for comparative analysis of amyloidogenicity are discussed.
Predictor of enhanced mortality in patients with multimorbidity and atrial fibrillation in an acute hospital setting
Authors: Iñiguez Vázquez I , Matesanz Fernández M , Romay Lema E M , Seoane Pillado M T , Monte Secades R , Pértega Díaz S , Casariego Vales E
Published: November 2019

Background

Patients with atrial fibrillation (AF) admitted to hospital commonly have comorbidities. Few studies have attempted to determine factors prognostic of mortality in hospitalized AF patients with multimorbidity.

Aim

To identify factors associated with mortality in hospitalized AF patients.

Design

Retrospective cohort study.

Methods

Patients with multimorbidity (≥2 chronic diseases), with or without AF, discharged from Lugo hospital (Spain) between 1 January 2000 and 31 December 2015. Data were extracted from hospital medical records.

Results

Of 74 220 patients (170 978 hospitalizations), 52 939 had multimorbidity (14 181 had AF; 38 758 no AF) and were included in our study. Patients with AF were older (mean ± standard deviation 78.6 ± 10.0 vs. 71.9 ± 14.2 years) and had a higher mortality rate (27.1 vs. 20.5%) than those without AF. Gender (female), age, stroke and congestive heart failure (CHF), but not AF, were independently associated with mortality. AF significantly increased the mortality risk in women [relative risk (RR) 1.091; 95% confidence interval (CI) 1.021–1.165; P = 0.010] and in those aged >80 years (RR 1.153; 95% CI, 1.1–1.2; P < 0.001). CHF independently increased the risk of mortality across all age groups (RR 1.496; 95% CI 1.422–1.574; P < 0.001).

Conclusions

Hospitalized patients with AF have a higher mortality rate than those without AF. The prognostic significance of AF changes with age and gender while CHF is associated with the greatest risk of death.
Mechanisms of Metabolism Interaction Between p-Cresol and Mycophenolic Acid
Authors: Rong Yan , Kiang Tony K L
Published: November 2019

Mycophenolic acid (MPA) is commonly prescribed for preventing graft rejection after kidney transplantation. The primary metabolic pathways of MPA are hepatic glucuronidation through UDP-glucuronosyltransferase (UGT) enzymes in the formation of MPA-glucuronide (MPAG, major pathway) and MPA-acyl glucuronide (AcMPAG). p-Cresol, a potent uremic toxin known to accumulate in patients with renal dysfunction, can potentially interact with MPA via the inhibition of glucuronidation. We hypothesized that the interaction between MPA and p-cresol is clinically relevant and that the estimated exposure changes in the clinic are of toxicological significance. Using in vitro approaches (ie, human liver microsomes and recombinant enzymes), the potency and mechanisms of inhibition by p-cresol towards MPA glucuronidation were characterized. Inter-individual variabilities, effects of clinical co-variates, in vitro-in vivo prediction of likely changes in MPA exposure, and comparison to other toxins were determined for clinical relevance. p-Cresol inhibited MPAG formation in a potent and competitive manner (Ki=5.2 µM in pooled human liver microsomes) and the interaction was primarily mediated by UGT1A9. This interaction was estimated to increase plasma MPA exposure in patients by approximately 1.8-fold, which may result in MPA toxicity. The mechanism of inhibition for AcMPAG formation was noncompetitive (Ki=127.5 µM) and less likely to be clinically significant. p-Cresol was the most potent inhibitor of MPA-glucuronidation compared with other commonly studied uremic toxins (eg, indole-3-acetic acid, indoxyl sulfate, hippuric acid, kynurenic acid, and 3-carboxy-4-methyl-5-propyl-2-furanpropionic acid) and its metabolites (ie, p-cresol sulfate and p-cresol glucuronide). Our findings indicate that the interaction between p-cresol and MPA is of toxicological significance and warrants clinical investigation.
A Genome Resource for Several North American Venturia inaequalis Isolates with Multiple Fungicide Resistance Phenotypes
Authors: Lichtner Franz J. , Jurick Wayne M. , Ayer Katrin M. , Gaskins Verneta L. , Villani Sara M. , Cox Kerik D.
Published: November 2019

The apple scab pathogen, Venturia inaequalis, is among the most economically important fungal pathogens that affects apples. Fungicide applications are an essential part of disease management. Implementation of cultural practices and genetic sources of resistance in the host are vital components of scab management. This is the first presentation of multiple, high quality, well-annotated genomes of four North American V. inaequalis isolates having both sensitive and multiple fungicide resistance phenotypes. We envision that these isolates will enable investigations into fungicide resistance mechanisms, exploring fungal virulence factors and delineating phylogenomic relationships among apple scab isolates from around the world.
Rubrivivax albus sp. nov., isolated from a freshwater pond
Authors: Sheu Shih-Yi , Li Zhi-Hao , Young Chiu-Chung , Chen Wen-Ming
Published: November 2019

Strain ICH-3T, isolated from a freshwater pond in Taiwan 9ROC), was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that ICH-3Tis affiliated with the species in the genusRubrivivax. ICH-3Twas most closely related toRubrivivax benzoatilyticusJA2TandRubrivivax gelatinosusNCIB 8290Twith 97.5 and 97.4 % 16S rRNA gene sequence similarity. The average nucleotide identity and digital DNA–DNA hybridization identity between ICH-3Tand the two closely related strains were 77.3 and 20.9–21.0 %, respectively, indicating that ICH-3Trepresents a novel species of the genusRubrivivax. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and formed white colonies. Optimal growth occurred at 30 °C, pH 7.5–8.0 and with 0.5 % NaCl. The major fatty acids (>20 %) of ICH-3Twere summed feature 3 (comprising C16 : 1ω7cand/or C16 : 1ω6c) and C16 : 0. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminophospholipid and two uncharacterized phospholipids. The major isoprenoid quinone was Q-8. The genomic DNA G+C content of ICH-3Twas 70.3 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain ICH-3Tshould be classified as representing a novel species of the genusRubrivivax, for which the nameRubrivivax albussp. nov. is proposed. The type strain is ICH-3T(=BCRC 81155T=LMG 30930T=KCTC 62866T).
Pseudomonas saxonica sp. nov., isolated from raw milk and skimmed milk concentrate
Authors: Hofmann Katharina , Huptas Christopher , Doll Etienne V. , Scherer Siegfried , Wenning Mareike
Published: November 2019

A polyphasic approach was used to investigate the taxonomic status of two bacterial strains, WS 5072T and WS 5092, isolated from skimmed milk concentrate and raw cow’s milk. The 16S rRNA and rpoD gene sequences affiliated the strains to the same, hitherto unknown,

Pseudomonas

species. Further examinations of the draft genomes based on multilocus sequence analysis and average nucleotide identity confirmed the presence of a novel

Pseudomonas

species. It was most closely related to

Pseudomonas fragi

DSM 3456T with 86.3 % ANIm. The DNA G+C content of strain WS 5072T was 56.3 mol%. Cells were aerobic, Gram-negative, catalase and oxidase positive, rod-shaped and motile. Growth occurred at 4–34 °C, pH 5.5–8.0 and with salt concentrations of up to 7 %. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The dominating quinone was Q-9 with 94 %, with noticeable amounts of Q-8 (5 %) and traces of Q-7 and Q-10. Fatty acid profiles showed a composition common for

Pseudomonas

with the major component C16 : 0. Based on these results, the novel species Pseudomonas saxonica sp. nov. is proposed, with the type strain WS 5072T (=DSM 108989T=LMG 31234T) and the additional strain WS 5092 (=DSM 108990=LMG 31235).
Flavobacterium microcysteis sp. nov., isolated from a culture of Microcystis aeruginosa
Authors: Seo Ye Lin , Jeong Sang Eun , Jin Hyun Mi , Jeon Che Ok
Published: November 2019

A Gram-stain-negative, yellow-pigmented, strictly aerobic bacterium, designated strain MaA-Y11T, was isolated from a culture of

Microcystis aeruginosa

in the Republic of Korea. Cells were non-motile rods showing catalase- and oxidase-positive reactions. Growth of strain MaA-Y11T was observed at 25–37 °C (optimum, 30 °C) and pH 6.0–9.0 (optimum, 7.0) and in the presence of 0–1.0 % (w/v) NaCl (optimum, 0 %). Strain MaA-Y11T did not produce flexirubin-type pigments. Strain MaA-Y11T contained iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as major cellular fatty acids and menaquinone-6 as the sole isoprenoid quinone. Phosphatidylethanolamine, three unidentified aminolipids and four unidentified lipids were detected as the major polar lipids. The G+C content of the genomic DNA was 37.0 mol%. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain MaA-Y11T formed a phyletic lineage with

Flavobacterium lindanitolerans

IP-10T within the genus

Flavobacterium

. Strain MaA-Y11T was most closely related to

Flavobacterium lindanitolerans

IP-10T, with a 98.85 % 16S rRNA gene sequence similarity, and shared less than 93.87 % sequence similarities with other type strains. Average nucleotide identity and in silico DNA–DNA hybridization values between strain MaA-Y11T and the type strain of

F. lindanitolerans

were 87.0 and 32.3 %, respectively. Here, we conclude that strain MaA-Y11T represents a new species of the genus

Flavobacterium

, for which the name Flavobacterium microcysteis sp. nov. is proposed. The type strain is MaA-Y11T (=KACC 21225T=JCM 33501T).
The role of IgM testing in the diagnosis and post-treatment follow-up of syphilis: a prospective cohort study
Authors: Osbak Kara K. , Tsoumanis Achilleas , De Baetselier Irith , Van Esbroek Marjan , Smet Hilde , Kenyon Chris R. , Crucitti Tania
Published: November 2019

Objectives

The diagnosis of repeat syphilis and its follow-up remains challenging. We aimed to investigate if IgM testing may assist in the diagnosis of syphilis reinfection/relapse and its treatment follow-up.

Methods

Sera were collected from 120 individuals with a new diagnosis of syphilis (72 with repeat infections) and 30 syphilis negative controls during a cohort study investigating syphilis biomarkers conducted at a STI/HIV clinic in Antwerp, Belgium. Syphilis was diagnosed based on a simultaneous positive treponemal and non-treponemal assay result and/or positive serum PCR targeting polA. Specimens collected at visit of diagnosis, and 3 and 6 months post-treatment were tested by two enzyme immuno assays (EIAs), recomWell (Mikrogen; MI) and Euroimmun (EU), to detect anti-treponemal IgM. Baseline specimens were also tested for anti-treponemal IgM using a line immuno assay (LIA) recomLine (Mikrogen). Quantitative kinetic decay curves were constructed from the longitudinal quantitative EIA results.

Results

An overall sensitivity for the diagnosis of syphilis of 59.8 % (95 % confidence interval (CI): 50.3-68.7), 75.0 % (95 %(CI): 66.1-82.3) and 64.2 % (95 %(CI): 54.8-72.6) was obtained for the EU, MI EIAs, and MI LIA, respectively. When only considering repeat syphilis, the diagnostic sensitivity decreased to 45.7 % (95 %(CI): 33.9-58.0), 63.9 % (95 %(CI): 51.7-74.6) and 47.2 % (95 %(CI): 35.5-59.3), respectively. IgM seroreverted in most cases 6 months after treatment. Post-treatment IgM concentrations decreased 30 % faster for initial syphilis compared to repeat infection. The IgM EIAs and IgM LIA agreed from fairly to moderately (Cohen’s kappa (κ): 0.36 [EU EIA]; κ: 0.53 [MI EIA]; κ: 0.40 [MI LIA]) with the diagnosis of syphilis.

Conclusions

IgM detection was not a sensitive method to diagnose syphilis and was even poorer in the diagnosis of syphilis repeat infections, but might play a role in treatment follow-up.

KEY MESSAGE BOX

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IgM detection was not a sensitive method to diagnose syphilis and was even poorer in the diagnosis of syphilis repeat infections

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IgM serorevert in most cases 6 months after treatment

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In repeat episodes of syphilis, IgM concentrations decline faster post-treatment