bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple clones of colistin-resistantSalmonella entericacarryingmcr-1plasmids in meat products and patients in Northern Thailand
Authors: Patchanee Prapas , Chokesajjawatee Nipa , Santiyanont Pannita , Chuammitri Phongsakorn , Deeudom Manu , Monteith William , Sheppard Samuel K. , Pascoe Ben , Prasertsee Teerarat 
Published: December 2020

AbstractSalmonellaspp. is an important foodborne pathogen associated with consumption of contaminated food, especially livestock products. Antimicrobial resistance (AMR) inSalmonellahas been reported globally and increasing AMR in food production is a major public health issue worldwide. The objective of this study was to describe the genetic relatedness amongSalmonella entericaisolates, which displayed identical DNA fingerprint profiles. TenS. entericaisolates were selected from meat and human cases with an identical rep-PCR profile of serovars Rissen (n=4), Weltevreden (n=4), and Stanley (n=2). We used long-read whole genome sequencing (WGS) on the MinION sequencing platform to type isolates and investigatein silicothe presence of specific AMR genes. Antimicrobial susceptibility testing was tested by disk diffusion and gradient diffusion method to corroborate the AMR phenotype. Multidrug resistance and resistance to more than one antimicrobial agent were observed in eight and nine isolates, respectively. Resistance to colistin with an accompanyingmcr-1 gene was observed among theSalmonellaisolates. The analysis of core genome and whole genome MLST revealed that theSalmonellafrom meat and human salmonellosis were closely genetic related. Hence, it could be concluded that meat is one of the important sources forSalmonellainfection in human.HighlightsColistin resistance detected in 2 clones from 2 differentSalmonella entericaserovars (Rissen and Weltevreden) with accompanying plasmid-bornemcr-1 gene from the food production chain and human clinical salmonellosis.High prevalence of multidrug resistant isolates and resistance to more than one antimicrobial agent.MinION has potential for mobile, rapid and accurate application in veterinary genomic epidemiology studies.
Moving pictures: Reassessing docking experiments with a dynamic view of protein interfaces
Authors: Prévost Chantal , Sacquin-Mora Sophie 
Published: December 2020

AbstractThe modeling of protein assemblies at the atomic level remains a central issue in structural biology, as protein interactions play a key role in numerous cellular processes. This problem is traditionally addressed using docking tools, where the quality of the models is based on their similarity to a single reference experimental structure. However, using a static reference does not take into account the dynamic quality of the protein interface. Here, we used all-atom classical Molecular Dynamics simulations to investigate the stability of the reference interface for three complexes that previously served as targets in the CAPRI competition. For each one of these targets, we also ran MD simulations for ten models that are distributed over the High, Medium and Acceptable accuracy categories. To assess the quality of these models from a dynamic perspective, we set up new criteria which take into account the stability of the reference experimental protein interface. We show that, when the protein interfaces are allowed to evolve along time, the original ranking based on the static CAPRI criteria no longer holds as over 50% of the docking models undergo a category change (which can be either toward a better or a lower accuracy group) when reassessing their quality using dynamic information.
Large- and multi-scale networks in the rodent brain during novelty exploration
Authors: Cohen Michael X , Englitz Bernhard , França Arthur S C 
Published: December 2020

AbstractNeural activity is coordinated across multiple spatial and temporal scales, and these patterns of coordination are implicated in both healthy and impaired cognitive operations. However, empirical cross-scale investigations are relatively infrequent, due to limited data availability and to the difficulty of analyzing rich multivariate datasets. Here we applied frequency-resolved multivariate source-separation analyses to characterize a large-scale dataset comprising spiking and local field potential activity recorded simultaneously in three brain regions (prefrontal cortex, parietal cortex, hippocampus) in freely-moving mice. We identified a constellation of multidimensional, inter-regional networks across a range of frequencies (2-200 Hz). These networks were reproducible within animals across different recording sessions, but varied across different animals, suggesting individual variability in network architecture. The theta band (~4-10 Hz) networks had several prominent features, including roughly equal contribution from all regions and strong inter-network synchronization. Overall, these findings demonstrate a multidimensional landscape of large-scale functional activations of cortical networks operating across multiple spatial, spectral, and temporal scales during open-field exploration.Significance statementNeural activity is synchronized over space, time, and frequency. To characterize the dynamics of large-scale networks spanning multiple brain regions, we recorded data from the prefrontal cortex, parietal cortex, and hippocampus in awake behaving mice, and pooled data from spiking activity and local field potentials into one data matrix. Frequency-specific multivariate decomposition methods revealed a cornucopia of neural networks defined by coherent spatiotemporal patterns over time. These findings reveal a rich, dynamic, and multivariate landscape of large-scale neural activity patterns during foraging behavior.
Consequences of producing DNA gyrase from a syntheticgyrBAoperon inSalmonella entericaserovar Typhimurium
Authors: Pozdeev German , Mogre Aalap , Dorman Charles J 
Published: December 2020

AbstractDNA gyrase is an essential type II topoisomerase that is composed of two subunits, GyrA and GyrB and has an A2B2structure. Although both subunits are required in equal proportions to form DNA gyrase, thegyrAandgyrBgenes that encode them inSalmonella(and in many other bacteria) are at widely separated locations on the chromosome, are under separate transcriptional control and are present in different copy numbers in rapidly growing bacteria (gyrAis near the terminus of chromosome replication whilegyrBis near the origin). We generated a syntheticgyrBAoperon at theoriC-proximal location ofgyrBto test the significance of the gyrase gene position forSalmonellaphysiology. Producing gyrase from an operon did not alter growth kinetics, cell morphology, competitive fitness index, or sensitivity to some gyrase-inhibiting antibiotics. However, the operon strain had altered DNA supercoiling set points, its SPI-2 virulence genes were expressed at a reduced level and its survival was reduced in macrophage. ThegyrBgene could not be deleted from itsoriC-proximal location, even in agyrBmerodiploid strain. We discuss the physiological significance of the differentgyrAandgyrBgene arrangements found naturally inSalmonellaand other bacteria.
Co-creation of a food marketing offer by final purchasers in the context of their lifestyles
Authors: Baruk Agnieszka Izabela 
Published: December 2020

PurposeThis article is theoretical and empirical in nature. Its purpose is to determine whether a lifestyle resulting from a particular personality type is significant for elements of a food marketing offer, which final purchasers would like to co-create with offerors.Design/methodology/approachA cognitive-critical analysis of the world literature on the subject was used to prepare the theoretical section. The results of the analysis indicate a cognitive and research gap in analyzing the above aspects. In order to reduce the gap, empirical studies were conducted in which a questionnaire was used to gather primary data. The data were subjected to quantitative analysis using statistical analysis including exploratory factor analysis, Pearson chi-square independence test, V-Cramer coefficient analysis, Kruskal–Wallis test and cluster analysis.FindingsThe results of the statistical analysis allowed three research hypotheses to be verified. It was found that there is dependence between respondents' lifestyles and elements of a marketing offer which they would like to co-create with offerors. It was also found that a lifestyle is a feature differentiating both material and non-material elements of a marketing offer which respondents would like to co-create with offerors. Such dependence was identified for, respectively, a material product, service and brand, regardless of whether these considered a company or a product. Thus, research hypotheses were proved to be valid for respondents.Research limitations/implicationsThe results obtained from the research have a cognitive and applicability value. They contribute to the theory, including marketing and customer behavior. They can also facilitate the shaping of good mutual relationships between offerors and final purchasers as important partners cooperating in the process of creating marketing values.Originality/valueThe originality of the approach presented is confirmed by the fact that until now elements of a marketing offer which purchasers would like to co-create with offerors have not been analyzed in the context of a lifestyle either in theory or in practice.
Non‐technical skills for emergency incident management teams: A literature review
Authors: Hayes Peter , Bearman Chris , Butler Philip , Owen Christine 
Published: December 2020

AbstractEvery year, incident management teams (IMTs) coordinate the response to hundreds of emergency events across Australasia. Larger scale emergencies such as a storms, floods, wildfires, oil spills and chemical explosions can place a lot of pressure on an IMT. Non‐technical skills play a central role in the performance of these teams. This article reviewed the broader non‐technical skills (NTS) literature before focusing on the NTS required for emergency management. It was found that most NTS frameworks share four to five common skill categories, although there were greater differences at the element and behavioural marker level. A variety of issues were identified in the literature that highlight that emergency management is very different from other domains where NTS systems have been developed. The literature on NTS in conjunction with this set of issues was used to develop a proposed NTS framework for emergency IMTs. This framework comprises 7 skill categories (i.e. communication, coordination, cooperation, decision‐making, situation awareness, leadership and coping, stress and fatigue management). The 7 skills can be further delineated into 16 elements and 44 behavioural markers. The framework provides a prototype that can form the basis for further research in this area.
Soil chemistry dynamics of Sus scrofa carcasses with and without delayed Diptera colonization
Authors: Heo Chong C. , Tomberlin Jeffery K. , Aitkenhead‐Peterson Jacqueline A. 
Published: December 2020

AbstractUnder normal circumstances, insects such as blow flies will oviposit and larvae will colonize a carcass as soon as possible. However, insect colonization on a carcass may be delayed due to the effects of wrapping, shallow burial, addition of lime derivatives to mitigate scavenging and odor, or extreme weather. The impacts of delayed insect colonization on carcass decomposition and its subsequent effect on soil chemistry profiles have not been examined to date. The objectives of this study were to determine soil chemistry dynamics associated with porcine carcasses experiencing delayed insect colonization for 7‐day or 14‐day. Soil chemistry profiles such as ammonium‐N (NH4‐N), orthophosphate‐P (PO4‐P), and dissolved organic carbon (DOC) were significantly different among treatments: insect inclusion (immediate access of blow fly colonization on porcine carcasses), 7‐day insect exclusion and 14‐day insect exclusion (blow fly access was delayed up to 7‐day and 14‐day). Furthermore, significant differences of soil chemical profiles were detected between days of decomposition and soil regions. Soil moisture, NH4‐N, PO4‐P, and DOC were significantly higher when insects were excluded from the porcine carcass suggesting loss of tissue from larval feeding reduced the mass of nutrients entering the soil. This study provides useful information for forensic science in cases where insect colonization is delayed for a period of time postmortem and soil chemistry in the cadaver decomposition island is considered for estimating postmortem interval.
Identification of determinants of pollen donor fecundity using the hierarchical neighborhood model
Authors: Chybicki Igor J. , Oleksa Andrzej , Dering Monika 
Published: December 2020

AbstractIndividual differences in male reproductive success drive genetic drift and natural selection, altering genetic variation and phenotypic trait distributions in future generations. Therefore, identifying the determinants of reproductive success is important for understanding the ecology and evolution of plants. Here, based on the spatially explicit mating model (the neighborhood model), we develop a hierarchical probability model that links co‐dominant genotypes of offspring and candidate parents with phenotypic determinants of male reproductive success. The model accounts for pollen dispersal, genotyping errors as well as individual variation in selfing, pollen immigration, and differentiation of immigrant pollen pools. Unlike the classic neighborhood model approach, our approach is specially designed to account for excessive variation (overdispersion) in male fecundity. We implemented a Bayesian estimation method (the Windows computer program available at: https://www.ukw.edu.pl/pracownicy/plik/igor_chybicki/1806/) that, among others, allows for selecting phenotypic variables important for male fecundity and assessing the fraction of variance in fecundity (R2) explained by selected variables. Simulations showed that our method outperforms both the classic neighborhood model and the two‐step approach, where fecundities and the effects of phenotypic variables are estimated separately. The analysis of two data examples showed that in wind‐pollinated trees, male fecundity depends on both the amount of produced pollen and the ability to pollen spread. However, despite that the tree size was positively correlated with male fecundity, it explained only a fraction of the total variance in fecundity, indicating the presence of additional factors. Finally, case studies highlighted the importance of accounting for pollen dispersal in the estimation of fecundity determinants.
Ore‐forming Fluid and Metallogenic Mechanism of Wolframite–Quartz Vein‐type Tungsten Deposits in South China
Authors: NI Pei , LI Wensheng , PAN Junyi 
Published: December 2020

AbstractSouth China is endowed with copious wolframite–quartz vein‐type W deposits that provide a significant contribution to the world's tungsten production. Mineralization is spatially associated with highly evolved granites, which have been interpreted as products of ancient crustal anatexis. Ore veins are mainly hosted in low‐grade metamorphosed quartz sandstone, slate and granitic rocks. The ore minerals mainly comprise wolframite, cassiterite, scheelite and pyrite, with minor molybdenite, arsenopyrite and chalcopyrite. Typical steeply dipping veins can be divided into five zones from top to the bottom, namely: (I) thread, (II) veinlet, (III) moderate vein, (IV) thick vein, and (V) thin out zones. In general, three types of fluid inclusions at room temperature are commonly recognized in wolframite and/or quartz from these veins: two‐phase liquid‐rich (type L), two‐phase CO2‐bearing (type CB), and CO2‐rich (type C). Comparative microthermometry performed on fluid inclusions hosted in wolframite and associated quartz indicates that most wolframite was not co‐precipitated with the coexisting quartz. Detailed petrographic observation and cathodoluminescence (CL) imaging on coexisting wolframite and quartz of the Yaogangxian deposit, show repeated precipitation of quartz, wolframite, and muscovite, suggesting a more complex fluid process forming these veins. Previous studies of H‐O isotopes and fluid inclusions suggested that the main ore‐forming fluids forming the wolframite–quartz vein‐type deposits had a magmatic source, whereas an unresolved debate is centered on whether mantle material supplemented the ore‐forming fluids. The variable CO2 contents in the ore‐forming fluids also implies that CO2 might have had a positive effect on ore formation. Fluid inclusion studies indicate that wolframite was most likely deposited during cooling from an initial H2O + NaCl ± CO2 magmatic fluid. In addition, fluid‐phase separation and/or mixing with sedimentary fluid might also have played an important role in promoting wolframite deposition. We speculate that these processes determine the precipitation of W to varying degrees whereas the leading mechanistic cause remains an open question. Comprehensive studies on spatial variation of fluid inclusions show that both the steeply and gently dipping veins are consistent with the “five floors” model that may have broader applications to exploration of wolframite–quartz vein‐type deposits. Recent quantitative analysis of wolframite‐ and quartz‐hosted fluid inclusions by laser ablation inductively‐coupled plasma mass spectrometry shows enhanced advantages in revealing fluid evolution, tracing the fluid source and dissecting the ore precipitation process. Further studies on wolframite–quartz vein‐type W deposits to bring a deeper understanding on ore‐forming fluids and the metallogenic mechanism involved.
Rectifying the Neoproterozoic Stratigraphic Framework of Eastern Jiangnan Orogen, Southeast China
Authors: YU Xinqi , LIU Junlai , CHEN Ziwei , HU Jun , ZENG Yan , LIU Xiu , LIU Mengyan , HE Yu , MENG Linghui , WANG Zishen 
Published: December 2020

AbstractStudies on the metamorphic and related magmatic rocks within the Jiangnan Orogen, southern China, are important to understand the formation and evolution of this Neoproterozoic orogen because they can provide evidence for revealing the tectonic evolution of the South China Block. Following on from earlier attempts at stratigraphic correlation and creating a framework for the low‐grade metamorphosed basement, new first‐hand information on the composition and deformation of the East Jiangnan Orogen basement indicates that the sedimentary rocks in the north are composed of the sequential Shangxi Group (Gp) and the overlying Likou Gp, with a clear regional unconformity in between. The Likou Gp includes the Zhentou Formation (Fm.) and the Dengjia Fm., with the previously named Puling Fm. only basalt interbeds within the Dengjia Fm. The Xucun granodiorite pluton of ∼830 Ma intrudes the Shangxi Gp, thereby resulting in a 100 m‐wide hornfels zone within the wall rocks, indicating that the formation of the group occurred earlier than that of the pluton. By contrast, the southern metamorphic rocks of the Xikou Gp and the overlying Jingtan Fm. are flaky, disordered, and strongly deformed. The Jingtan Fm. is roughly equivalent to the Heshangzhen Gp and includes the Zhoujiacun conglomerates in the lower part and a rhyolite in the upper part with interbedded basalt. This assessment of Neoproterozoic stratigraphic sequences and magmatic rocks in the east of the Jiangnan Orogen differs from and rectifies previous studies, emphasizing that explanation of analytical results, particularly geochronology, should be consistent with facts gathered in the field.
Mineralogy and Geochemistry of Uraniferous Sandstones in Fault Zone, Wadi El Sahu Area, Southwestern Sinai, Egypt: Implications for Provenance, Weathering and Tectonic Setting
Authors: SALLAM Osama R. , MIRA Hamed I. , TOHAMY Amira M. El , ABBAS Abd Elhadi A. 
Published: December 2020

AbstractPaleozoic rocks in the Wadi El Sahu area are affected by many major faults in different directions. A reverse fault trending NE‐SW is exposed for about 300 m of its length as it cuts through the Abu Hamata and Adedia formations on the south side of Wadi El Sahu. A secondary ascending hydrothermal solution carrying heavy metals and radioactive minerals passed through the fault plain and the surrounding fractures, forming mineralized and radioactive zone. The mineralized zone thickness ranges from 60 cm to 200 cm along the fault plain. These rocks were analyzed radiometrically using a portable gamma‐ray spectrometer, chemically by employing ICP‐ES and ICP‐MS, as well as mineralogically by both binocular and Environmental Scanning Electron microscope. Gold content was also determined by fire assay. REE and U contents reached up to 2682 and 1216 ppm, respectively. Mineralogical investigations indicated the presence of uraninite, torbernite, autunite, sklodowskite, kasolite as uranium minerals, thorite as a thorium mineral, monazite, allanite and xenotime as REE‐bearing minerals, zircon and columbite as accessory minerals, gold and nickel as precious and base metals, in addition to cassiterite, chalcopyrite, chalcocite and chrysocolla. High REE and U contents are attributed to the circulation of epigenetic U and REE‐bearing hydrothermal solutions along the fault plain and its surrounding fractures. Hydrothermal alteration processes could then be confirmed by the presence of the M‐type tetrad effect in the REE‐patterns of the ferruginous sandstone. The non‐chondritic ratio of Nb/Ta, Zr/Hf and Y/Ho in the studied sandstone may be attributed to the tetrad effect. The Ce and Eu anomaly with unusual REE‐patterns was represented by the presence of conjugated M‐W tetrad effects, indicating either the dual effect of hydrothermal solutions or groundwater with seawater. The results clarify that the tetrad‐effects could be used as evidence for the environment of deposition and as an indication for gold mineralization.
Experiences of underrepresented faculty in pediatric emergency medicine
Authors: Nfonoyim Bianca , Martin Ashley , Ellison Angela , Wright Joseph L. , Johnson Tiffani J. 
Published: December 2020

AbstractObjectiveThe aim of this study is to elucidate the unique challenges faced by pediatric emergency medicine (PEM) physicians from racial/ethnic groups underrepresented in medicine (URiM).MethodsThis study is a subanalysis of data from 18 URiM faculty from a sample of 51 semistructured key informant interviews with PEM faculty in the top NIH‐funded pediatric departments and highest‐volume pediatric EDs in the country. Faculty are from eight hospitals representing a spectrum of geographic locations including the northeastern, midwestern, western, and southern regions of the country.ResultsOf 18 study participants, the majority were Black (72.2%) and female (83.3%). Three main thematic categories were identified: challenges related to race, support systems, and suggested strategies to improve diversity and inclusion in PEM. A common race‐related experience was microaggressions from colleagues and patients. Additionally, when attempting to lead and assert themselves, URiM women in particular were perceived as “angry” and “intimidating” in a way that non‐URiM peers were not. As a result of these negative experiences, participants described the need to go above and beyond to prove themselves. Such pressure produced stress and feelings of isolation. Participants combatted these stressors through resilience strategies such as formal mentorship and peer and family support. Participants indicated the need to increase diversity and create more inclusive work environments, which would benefit both URiM physician wellness and the diverse patients they serve.ConclusionThose URiM in PEM face subtle racial discrimination at an institutional, peer, and patient level. The stress caused by this discrimination may further contribute to physician burnout in PEM. While URiMs adopt individual resilience strategies, their unique challenges suggest the need for departmental and institutional efforts to promote greater diversity and inclusion for physician wellness, retention, and quality patient care.