bluuebunny/crossref_metadata_2025_split huggingface dataset:
Malodorous biogenic amines in Escherichia coli-caused urinary tract infections in women—a metabolomics approach
Authors: Puebla-Barragan Scarlett , Renaud Justin , Sumarah Mark , Reid Gregor 
Published: June 2020

AbstractMany women suffer from urinary tract infections (UTIs). In addition to pain and increased urgency to urinate, malodour is a significant issue for these patients. The specific factors causing this malodour are unclear, and there are no targeted treatment options to counteract it effectively. We used a metabolomics approach to compare the chemical composition of metabolites in the urine of women withE. coliUTIs (n = 15)and those who are healthy (n = 10). The biogenic amines trimethylamine and putrescine, which cause malodour in other urogenital conditions, were significantly increased in UTI patients. Conversely, the precursor of trimethylamine, trimethylamineN-oxide, was lower. To further confirm the source of the malodorous compounds,in vitroexperiments were conducted by incubating strains of uropathogenicE. coliin sterilized urine from healthy women. All tested strains accumulated trimethylamine and putrescine. Notably, cadaverine was also produced byE. colistrainsin vitro;however, it was not significantly different between both groups. We confirmed that the malodorous amines TMA and putrescine are found in higher concentrations in the urine of patients with anE.coli-caused UTI.
Spatial Association Effect of Haze Pollution in Cheng-Yu Urban Agglomeration
Authors: Zhang Degang , Lu Yuanquan , Tian Yuan 
Published: June 2020

AbstractThis study takes a network perspective to examine the spatial spillover effects of haze pollution in Cheng-Yu urban agglomeration which is the fourth largest urban agglomeration and a comprehensive demonstration zone of new urbanization in China. Firstly, we use Granger causality test to construct haze pollution spatial association network, and then we apply social network analysis to reveal the structural characteristics of this network. The results show that: haze pollution in Cheng-Yu urban agglomeration is a complex multithreaded network. Chongqing, Chengdu, Guang’an, Luzhou, Deyang and Nanchong are the centers of the network, sending and transmitting the most relationships. The haze pollution spatial association network can be divided into net beneficiary block, net overflow block, bilateral overflow block and broker block. These four blocks present obvious geographical distribution characteristics and are partly related to the difference of urbanization. The above results contribute by illustrating the current spatial spillover situation of haze pollution and provide a theoretical foundation for the government that it should simultaneously consider cities’ statues and their spatial spillover effects in the network rather than simple geographic proximity when formulating future haze pollution control policies in urban agglomeration.
Metal-matrix nanocomposites under compressive loading: Towards an understanding of how twinning formation can enhance their plastic deformation
Authors: Kardani A. , Montazeri A. 
Published: June 2020

AbstractRecently, Cu-Ag nanocomposites (NCs) have been extensively used as medical implants and surgical instruments due to their antibacterial properties. Consequently, mechanical behavior analysis of these NCs is of crucial importance with emphasis on their plastic deformation mechanisms. From the materials science perspective, dislocations slip at the room temperature and high strain rates conditions is hindered. However, copper and silver, as two metals with low stacking fault energy are prone to twin formation. Since microstructural changes in these nanostructured composites occur at the atomic scale, molecular dynamics (MD) simulation is undoubtedly a great tool to use. Accordingly, in the present research, first, the deformation mechanism of perfect copper-silver NCs under uniaxial compression is deeply analyzed employing MD. This is followed by inspection of the voids effect on their plastic deformation process. The results show that twinning is the dominant mechanism governing their deformation under uniaxial compressive loading conditions. It is revealed that twins are created by the conversion of internal stacking faults to their external counterparts. Also, investigation of the microstructural evolution demonstrates that the presence of voids within NC samples provides new sites for nucleation of Shockley dislocations in addition to the interface zone. Finally, to address the effect of interfacial coherency on the results, copper-based NCs infused with gold and nickel nanoparticles are also thoroughly examined.
Occurrence and seasonal variability of Dense Shelf Water Cascades along Australian continental shelves
Authors: Mahjabin Tanziha , Pattiaratchi Charitha , Hetzel Yasha 
Published: June 2020

AbstractTransport of water between the coast and the deeper ocean, across the continental shelf, is an important process for the distribution of biota, nutrients, suspended and dissolved material on the shelf. Presence of denser water on the inner continental shelf results in a cross-shelf density gradient that drives a gravitational circulation with offshore transport of denser water along the sea bed that is defined as Dense Shelf Water Cascade (DSWC). Analysis of field data, collected from multiple ocean glider data missions around Australia, confirmed that under a range of wind and tidal conditions, DSWC was a regular occurrence during autumn and winter months over a coastline spanning > 10,000 km. It is shown that even in the presence of relatively high wind- and tidal-induced vertical mixing, DSWCs were present due to the strength of the cross-shelf density gradient. The occurrence of DSWC around Australia is unique with continental scale forcing through air-sea fluxes that overcome local wind and tidal forcing. It is shown that DSWC acts as a conduit to transport suspended material across the continental shelf and is a critical process that influences water quality on the inner continental shelf.
Genetic aetiology of self-harm ideation and behaviour
Authors: Campos Adrian I. , Verweij Karin J. H. , Statham Dixie J. , Madden Pamela A. F. , Maciejewski Dominique F. , Davis Katrina A. S. , John Ann , Hotopf Matthew , Heath Andrew C. , Martin Nicholas G. , Rentería Miguel E. 
Published: June 2020

AbstractFamily studies have identified a heritable component to self-harm that is partially independent from comorbid psychiatric disorders. However, the genetic aetiology of broad sense (non-suicidal and suicidal) self-harm has not been characterised on the molecular level. In addition, controversy exists about the degree to which suicidal and non-suicidal self-harm share a common genetic aetiology. In the present study, we conduct genome-wide association studies (GWAS) on lifetime self-harm ideation and self-harm behaviour (i.e. any lifetime self-harm act regardless of suicidal intent) using data from the UK Biobank (n > 156,000). We also perform genome wide gene-based tests and characterize the SNP heritability and genetic correlations between these traits. Finally, we test whether polygenic risk scores (PRS) for self-harm ideation and self-harm behaviour predict suicide attempt, suicide thoughts and non-suicidal self-harm (NSSH) in an independent target sample of 8,703 Australian adults. Our GWAS results identified one genome-wide significant locus associated with each of the two phenotypes. SNP heritability (hsnp2) estimates were ~10%, and both traits were highly genetically correlated (LDSC rg > 0.8). Gene-based tests identified seven genes associated with self-harm ideation and four with self-harm behaviour. Furthermore, in the target sample, PRS for self-harm ideation were significantly associated with suicide thoughts and NSSH, and PRS for self-harm behaviour predicted suicide thoughts and suicide attempt. Follow up regressions identified a shared genetic aetiology between NSSH and suicide thoughts, and between suicide thoughts and suicide attempt. Evidence for shared genetic aetiology between NSSH and suicide attempt was not statistically significant.
Assessment of Luminal and Basal Phenotypes in Bladder Cancer
Authors: Guo Charles C. , Bondaruk Jolanta , Yao Hui , Wang Ziqiao , Zhang Li , Lee Sangkyou , Lee June-Goo , Cogdell David , Zhang Miao , Yang Guoliang , Dadhania Vipulkumar , Choi Woonyoung , Wei Peng , Gao Jianjun , Theodorescu Dan , Logothetis Christopher , Dinney Colin , Kimmel Marek , Weinstein John N. , McConkey David J. , Czerniak Bogdan 
Published: June 2020

AbstractGenomic profiling studies have demonstrated that bladder cancer can be divided into two molecular subtypes referred to as luminal and basal with distinct clinical behaviors and sensitivities to frontline chemotherapy. We analyzed the mRNA expressions of signature luminal and basal genes in bladder cancer tumor samples from publicly available and MD Anderson Cancer Center cohorts. We developed a quantitative classifier referred to as basal to luminal transition (BLT) score which identified the molecular subtypes of bladder cancer with 80–94% sensitivity and 83–93% specificity. In order to facilitate molecular subtyping of bladder cancer in primary care centers, we analyzed the protein expressions of signature luminal (GATA3) and basal (KRT5/6) markers by immunohistochemistry, which identified molecular subtypes in over 80% of the cases. In conclusion, we provide a tool for assessment of molecular subtypes of bladder cancer in routine clinical practice.
Mutations in the C1 element of the insulin promoter lead to diabetic phenotypes in homozygous mice
Authors: Noguchi Hirofumi , Miyagi-Shiohira Chika , Nakashima Yoshiki , Kinjo Takao , Saitoh Issei , Watanabe Masami 
Published: June 2020

AbstractGenome editing technologies such as CRISPR–Cas9 are widely used to establish causal associations between mutations and phenotypes. However, CRISPR–Cas9 is rarely used to analyze promoter regions. The insulin promoter region (approximately 1,000 bp) directs β cell-specific expression of insulin, which in vitro studies show is regulated by ubiquitous, as well as pancreatic, β cell-specific transcription factors. However, we are unaware of any confirmatory in vivo studies. Here, we used CRISPR–Cas9 technology to generate mice with mutations in the promoter regions of the insulin I (Ins1) and II (Ins2) genes. We generated 4 homozygous diabetic mice with 2 distinct mutations in the highly conserved C1 elements in each of the Ins1 and Ins2 promoters (3 deletions and 1 replacement in total). Remarkably, all mice with homozygous or heterozygous mutations in other loci were not diabetic. Thus, the C1 element in mice is required for Ins transcription in vivo.
Chemogenomic profiling of breast cancer patient-derived xenografts reveals targetable vulnerabilities for difficult-to-treat tumors
Authors: Savage Paul , Pacis Alain , Kuasne Hellen , Liu Leah , Lai Daniel , Wan Adrian , Dankner Matthew , Martinez Constanza , Muñoz-Ramos Valentina , Pilon Virginie , Monast Anie , Zhao Hong , Souleimanova Margarita , Annis Matthew G. , Aguilar-Mahecha Adriana , Lafleur Josiane , Bertos Nicholas R. , Asselah Jamil , Bouganim Nathaniel , Petrecca Kevin , Siegel Peter M. , Omeroglu Atilla , Shah Sohrab P. , Aparicio Samuel , Basik Mark , Meterissian Sarkis , Park Morag 
Published: June 2020

AbstractSubsets of breast tumors present major clinical challenges, including triple-negative, metastatic/recurrent disease and rare histologies. Here, we developed 37 patient-derived xenografts (PDX) from these difficult-to-treat cancers to interrogate their molecular composition and functional biology. Whole-genome and transcriptome sequencing and reverse-phase protein arrays revealed that PDXs conserve the molecular landscape of their corresponding patient tumors. Metastatic potential varied between PDXs, where low-penetrance lung micrometastases were most common, though a subset of models displayed high rates of dissemination in organotropic or diffuse patterns consistent with what was observed clinically. Chemosensitivity profiling was performed in vivo with standard-of-care agents, where multi-drug chemoresistance was retained upon xenotransplantation. Consolidating chemogenomic data identified actionable features in the majority of PDXs, and marked regressions were observed in a subset that was evaluated in vivo. Together, this clinically-annotated PDX library with comprehensive molecular and phenotypic profiling serves as a resource for preclinical studies on difficult-to-treat breast tumors.
The clinical diagnostic value of Xpert MTB/RIF for the detection of Mycobacterium tuberculosis in gastric aspirates
Authors: Tan Hong-Kun , Fan Shu-Jin , Xu Yu-Cheng , Zhou Jiong-Jiong , Chen Yuan-Zhi , Xie Tian-Ao , Pan Zhi-Yong , Xia Yong , Guo Xu-Guang 
Published: June 2020

Abstract
Background: At present, the infection and prevalence rates of tuberculosis (TB) are still high in worldwide. The Xpert MTB/RIF technology has improved the diagnosis speed of Mycobacterium tuberculosis (MTB) and facilitated the rapid treatment of TB patients.
Methods: We searched experimental data derived from Xpert MTB/RIF for detecting MTB in gastric aspirates in PubMed, Embase, Web Of Science, and the Cochrane Library databases between January 2012 to April 2019. A summary receiver operating characteristic curve (SROC curve) was used to analyze the pooled sensitivity, pooled specificity, PLR, NLR, and DOR for determining the accuracy of the test.
Results: Our database search resulted in 10 relevant articles. The pooled sensitivity of Xpert MTB/RIF for detecting TB in GA was 86% (95% CI, 83–89%), and I2 = 93.4%. The pooled specificity was 92% (95% CI, 90–93%) and I2 = 97.8%. In addition, the positive LR was 12.12 (95% CI, 5.60–26.21), negative LR was 0.20 (95% CI, 0.11–0.36), and the diagnostic odds ratio (DOR) was 147.04 (95% CI, 37.20–581.19). Using the SROC curve, the AUC was 0.9730 and Q* was 0.9248 (SE = 0.0261). The publication bias was P=0.517 (P&gt;0.05).
Conclusions: The Xpert MTB/RIF for detecting MTB in gastric aspirates was highly accurate. In addition, we observed that the publication bias in the present study was low. Hence, the Xpert MTB/RIF technology is highly accurate and has the advantage of rapid testing for MTB in clinical samples.
Discourse Prosody in Children's Rhyme Speech Produced by Prelingually Deaf Mandarin-Speaking Children With Cochlear Implants
Authors: Yu Jue , Liao Yiyuan , Wu Shengyi , Li Yun , Huang Meiping 
Published: June 2020

PurposeThis study aimed to obtain a comprehensive understanding about how Mandarin-speaking children with cochlear implants (CIs) performed speech prosody in a connected discourse and to what extent their prosodic scenario differed from those normal-hearing (NH) peers.MethodFifteen prelingually deaf Mandarin-speaking children with unilateral multichannel CIs were chosen and 15 age-matched NH controls were recruited. Speech samples were spontaneously elicited by children's rhyme speech genre and subject to phonetic annotation. Acoustic analysis was conducted on all speech samples, mainly focusing on the measurements of duration and fundamental frequency (F0). Tempo measures included temporal fluency, syllable-lengthening, and rhythm metrics, whereas melodic measures included both local and global F0 variations under different prosodic domains.ResultsThe CI children generally achieved compatible temporal performance with the NH children in spontaneous discourse, except that they were somewhat arbitrary when operationalizing lengthening strategy and pausing strategy at different prosodic boundaries. With regard to melodic performance, CI children may not sufficiently modulate local phonetic nuances of F0 variation, and meanwhile, they performed atypically in the global F0 declination pattern and overall F0 resetting pattern, failing to signal the specific structure of children's rhyme discourse. Early age at implantation and longer CI experience did not play a significant role in the temporal performance of the CI children but did facilitate their articulation of dynamic pitch variation in the spontaneous discourse to some extent.ConclusionCI children did exhibit atypical prosodic patterns in discourse context, especially the overall mapping between the prosodic manifestation and the discourse structure.
Is the primary CoRoT target HD 43587 under a Maunder minimum phase?
Authors: Ferreira R. R. , Barbosa R. , Castro M. , Guerrero G. , de Almeida L. , Boumier P. , do Nascimento J.-D. 
Published: June 2020

Context. One of the most enigmatic phenomena related to solar activity is the so-called Maunder minimum phase. It consists in the lowest sunspot count ever registered for the Sun and has not been confirmed for other stars to date. Since the spectroscopic observations of stellar activity at the Mount Wilson Observatory, the solar analog HD 43587 has shown a very low and apparently invariant activity level, which makes it a Maunder minimum candidate.
Aims. We aim to analyze the chromospheric activity evolution of HD 43587 and its evolutive status, with the intention of unraveling the reasons for this low and flat activity.
Methods. We used an activity measurements dataset available in the literature, and computed the S-index from HARPS and NARVAL spectra to infer a cycle period. Additionally, we analyzed the CoRoT light curve of HD 43587, and applied gyrochronology and activity calibrations to determine its rotation period. Finally, based on an evolutionary model and the inferred rotation period, we used the EULAG-MHD code to perform global MHD simulations of HD 43587 to get some insight into its dynamo process.
Results. We confirm the almost flat activity profile, with a cycle period Pcyc = 10.44 ± 3.03 yr deduced from the S-index time series, and a long-term trend that might be a period of more than 50 yr. It was impossible to define a rotation period from the light curve, however gyrochronology and activity calibrations allow us to infer an indirect estimate of ¯Prot = 22.6 ± 1.9 d. Furthermore, the MHD simulations confirm an oscillatory dynamo with a cycle period in good agreement with the observations and a low level of surface magnetic activity.
Conclusions. We conclude that this object might be experiencing a “natural” decrease in magnetic activity as a consequence of its age. Nevertheless, the possibility that HD 43587 is in a Maunder minimum phase cannot be ruled out.
Taking apart the dynamical clock
Authors: Pasquato Mario , Di Cintio Pierfrancesco 
Published: June 2020

Context. In globular clusters (GCs), blue straggler stars (BSS) are heavier than the average star, so dynamical friction strongly affects them. The radial distribution of BSS, normalized to a reference population, appears bimodal in a fraction of Galactic GCs, with a density peak in the core, a prominent zone of avoidance at intermediate radii, and again higher density in the outskirts. The zone of avoidance appears to be located at larger radii the more relaxed the host cluster, acting as a sort of dynamical clock.
Aims. We use a new method to compute the evolution of the BSS radial distribution under dynamical friction and diffusion.
Methods. We evolve our BSS in the mean cluster potential under dynamical friction plus a random fluctuating force, solving the Langevin equation with the Mannella quasi symplectic scheme. This is a new simulation method that is much faster and simpler than direct N-body codes, but retains their main feature: diffusion powered by strong, if infrequent, kicks.
Results. We compute the radial distribution of initially unsegregated BSS normalized to a reference population as a function of time. We trace the evolution of its minimum, corresponding to the zone of avoidance. We compare the evolution under kicks extracted from a Gaussian distribution to that obtained using a Holtsmark distribution. The latter is a fat-tailed distribution which correctly models the effects of close gravitational encounters. We find that the zone of avoidance moves outwards over time, as expected based on observations, only when using the Holtsmark distribution. Thus, the correct representation of near encounters is crucial to reproduce the dynamics of the system.
Conclusions. We confirm and extend earlier results that showed how the dynamical clock indicator depends on dynamical friction and on effective diffusion powered by dynamical encounters. We demonstrated the high sensitivity of the clock to the details of the mechanism underlying diffusion, which may explain the difficulties in reproducing the motion of the zone of avoidance across different simulation methods.
Magnetohydrostatic modeling of AR11768 based on a SUNRISE/IMaX vector magnetogram
Authors: Zhu X. , Wiegelmann T. , Solanki S K. 
Published: June 2020

Context. High-resolution magnetic field measurements are routinely only done in the solar photosphere. Higher layers, such as the chromosphere and corona, can be modeled by extrapolating these photospheric magnetic field vectors upward. In the solar corona, plasma forces can be neglected and the Lorentz force vanishes. This is not the case in the upper photosphere and chromosphere where magnetic and nonmagnetic forces are equally important. One way to deal with this problem is to compute the plasma and magnetic field self-consistently, in lowest order with a magnetohydrostatic (MHS) model. The non-force-free layer is rather thin and MHS models require high-resolution photospheric magnetic field measurements as the lower boundary condition.
Aims. We aim to derive the magnetic field, plasma pressure, and density of AR11768 by applying the newly developed extrapolation technique to the SUNRISE/IMaX data embedded in SDO/HMI magnetogram.
Methods. We used an optimization method for the MHS modeling. The initial conditions consist of a nonlinear force-free field (NLFFF) and a gravity-stratified atmosphere. During the optimization procedure, the magnetic field, plasma pressure, and density are computed self-consistently.
Results. In the non-force-free layer, which is spatially resolved by the new code, Lorentz forces are effectively balanced by the gas pressure gradient force and gravity force. The pressure and density are depleted in strong field regions, which is consistent with observations. Denser plasma, however, is also observed at some parts of the active region edges. In the chromosphere, the fibril-like plasma structures trace the magnetic field nicely. Bright points in SUNRISE/SuFI 3000 Å images are often accompanied by the plasma pressure and electric current concentrations. In addition, the average of angle between MHS field lines and the selected chromospheric fibrils is 11.8°, which is smaller than those computed from the NLFFF model (15.7°) and linear MHS model (20.9°). This indicates that the MHS solution provides a better representation of the magnetic field in the chromosphere.