bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time resolved alkali silicate decondensation by sodium hydroxide solution
Authors: Dupuis Romain , Gomes Rodrigues Donatien , Champenois Jean-Baptiste , Pellenq Roland J-M , Poulesquen Arnaud 
Published: November 2019

AbstractSilica is by far the chemical compound the most widespread and used around the world: as a raw product in the buildings and roads industry, as concrete, or as a processed product in the manufacture of glass, ceramics or zeolites. In alkali silicate solutions—often used to synthesize those materials—a complex interplay of decondensation and condensation processes leads to the restructuring of silicate clusters at the atomic scale on a short time-scale. We were able to deconvolute these effects by combining time resolved small angle x-ray scattering, nuclear magnetic resonance, and parallel tempering simulations. We investigated the impact of a dilution by pure water or by a sodium hydroxide solution on the speciation and size of the dissolved silicates in solution. Herein, we show that the silicate clusters are not affected by dilution, suggesting that sodium cations protect the silicate clusters from hydrolysis. Decondensation is triggered by hydroxide ions that weaken and break Si–O bonds. Alongside the decondensation, the evolution of the computed protonation state of the silica species indicates a change in the interaction potential. Our results pave the way towards the investigation at the atomic scale of more complex systems implying alkali silicate solutions in condensation process by the addition of calcium or aluminum to synthesize aluminosilicate binders, hydrogels or zeolites.
The Pleasure of Its Company: Of One Blood and the Potentials of Plagiarism
Authors: Sanborn Geoffrey 
Published: November 2019

Abstract
In this essay, Sanborn extends his earlier work on Pauline Hopkins’s plagiarism by showing that Hopkins plagiarized a total of 143 passages from 36 texts in her novel Of One Blood and that at least 10,492 of the roughly 52,730 words in the novel—20%—were imported from other people’s publications. Sanborn argues that plagiarism is, for Hopkins, not a canny subversion or artful transmutation of another writer’s work; it is a means by which she can hold her text internally open to other voices and temporalities. It does not point us backward to a critique of the texts from which she drew—texts that she could not have imagined anyone discovering—but forward to the pleasurable possibility of a profoundly mixed-voice world. Like Marvel’s The Black Panther (2018), Of One Blood offers its audience a series of resources for dreaming, a series of larger-and-stranger-than-life scenarios capable of being used in self-transformational ways.
Phylonium: fast estimation of evolutionary distances from large samples of similar genomes
Authors: Klötzl Fabian , Haubold Bernhard 
Published: November 2019

Abstract

Motivation
Tracking disease outbreaks by whole-genome sequencing leads to the collection of large samples of closely related sequences. Five years ago, we published a method to accurately compute all pairwise distances for such samples by indexing each sequence. Since indexing is slow, we now ask whether it is possible to achieve similar accuracy when indexing only a single sequence.

Results
We have implemented this idea in the program phylonium and show that it is as accurate as its predecessor and roughly 100 times faster when applied to all 2678 Escherichia coli genomes contained in ENSEMBL. One of the best published programs for rapidly computing pairwise distances, mash, analyzes the same dataset four times faster but, with default settings, it is less accurate than phylonium.

Availability and implementation
Phylonium runs under the UNIX command line; its C++ sources and documentation are available from github.com/evolbioinf/phylonium.

Supplementary information
Supplementary data are available at Bioinformatics online.
MTA1 promotes tumorigenesis and development of esophageal squamous cell carcinoma via activating the MEK/ERK/p90RSK signaling pathway
Authors: Nan Peng , Wang Ting , Li Chunxiao , Li Hui , Wang Jinsong , Zhang Jingyao , Dou Na , Zhan Qimin , Ma Fei , Wang Haijuan , Qian Haili 
Published: November 2019

AbstractMetastasis-associated protein 1 (MTA1) is upregulated in multiple malignancies and promotes cancer proliferation and metastasis, but whether and how MTA1 promotes esophageal squamous cell carcinoma (ESCC) tumorigenesis remain unanswered. Here, we established an ESCC model in MTA1 transgenic mice induced by the chemical carcinogen 4-nitroquinoline 1-oxide (4-NQO) and found that MTA1 promotes ESCC tumorigenesis in mice. MTA1 overexpression was observed in ESCC cells and clinical ESCC samples. Overexpressed MTA1 increased colony formation and the invasiveness and migration of ESCC cells, whereas knock down of MTA1 in ESCC cells significantly decreased colony formation, invasion and migration in vitro and inhibited the growth of xenograft tumors in vivo. RNA sequencing (RNA-seq) analysis combined with western blot assays revealed that MTA1 promotes carcinogenesis by enhancing MEK/ERK/p90RSK signaling. The phosphorylation of MEK, ERK and their downstream target p90RSK was significantly decreased after MTA1 knockdown in ESCC cells and was increased in MTA1-overexpressing cells. Moreover, colony formation, invasion and migration potential were dramatically suppressed when cells overexpressing MTA1 were treated with MEK (PD0325901) or ERK (SCH772948) inhibitors. In conclusion, MTA1 plays a pivotal oncogenic role in ESCC tumorigenesis and development through activating the MEK/ERK/p90RSK pathway.
Clinical Factors Associated With Congenital Cytomegalovirus Infection: A Cohort Study of Pregnant Women and Newborns
Authors: Uchida Akiko , Tanimura Kenji , Morizane Mayumi , Fujioka Kazumichi , Morioka Ichiro , Oohashi Masanobu , Minematsu Toshio , Yamada Hideto 
Published: November 2019

Abstract

Background
The aim of this prospective cohort study was to determine clinical factors associated with the occurrence of congenital cytomegalovirus infection (cCMV) in pregnant women.

Methods
Between March 2009 and November 2017, newborns born at a primary maternity hospital received polymerase chain reaction (PCR) analyses for CMV DNA in their urine with informed consent of the mothers at a low risk. Clinical data, including age, gravidity, parity, body mass index, occupation, maternal fever/flulike symptoms, pregnancy complications, gestational weeks at delivery, birth weight, and automated auditory brainstem response, were collected. Logistic regression analyses were performed to determine clinical factors associated with cCMV.

Results
cCMV was diagnosed by positive PCR results of neonatal urine in 9 of 4125 pregnancies. Univariate and multivariable analyses revealed that the presence of fever/flulike symptoms (odds ratio [OR], 17.9; 95% confidence interval [CI], 3.7–86.7; P &lt; .001) and threatened miscarriage/premature labor in the second trimester (OR, 6.0; 95% CI, 1.6–22.8; P &lt; .01) were independent clinical factors associated with cCMV. Maternal fever/flulike symptoms or threatened miscarriage/premature labor in the second trimester had 100% sensitivity, 53.2% specificity, and a maximum Youden index of .85.

Conclusions
This cohort study for the first time demonstrated that these clinical factors of pregnant women and newborns were associated with the occurrence of cCMV. This is useful information for targeted screening to assess risks of cCMV in low-risk mothers, irrespective of primary or nonprimary CMV infection.
Postexposure Prophylaxis With rVSV-ZEBOV Following Exposure to a Patient With Ebola Virus Disease Relapse in the United Kingdom: An Operational, Safety, and Immunogenicity Report
Authors: Davis Chris , Tipton Tom , Sabir Suleman , Aitken Celia , Bennett Susan , Becker Stephan , Evans Tom , Fehling Sarah Katharina , Gunson Rory , Hall Yper , Jackson Celia , Johanssen Ingolfur , Kieny Marie Paule , Mcmenamin Jim , Spence Elizabeth , Strecker Thomas , Sykes Catie , Templeton Kate , Thorburn Fiona , Peters Erica , Henao Restrepo Ana Maria , White Beth , Zambon Maria , Carroll Miles W , Thomson Emma C 
Published: November 2019

Abstract

Background
In October 2015, 65 people came into direct contact with a healthcare worker presenting with a late reactivation of Ebola virus disease (EVD) in the United Kingdom. Vaccination was offered to 45 individuals with an initial assessment of high exposure risk.

Methods
Approval for rapid expanded access to the recombinant vesicular stomatitis virus–Zaire Ebola virus (rVSV-ZEBOV) vaccine as an unlicensed emergency medicine was obtained from the relevant authorities. An observational follow-up study was carried out for 1 year following vaccination.

Results
Twenty-six of 45 individuals elected to receive vaccination between 10 and 11 October 2015 following written informed consent. By day 14, 39% had seroconverted, increasing to 87% by day 28 and 100% by 3 months, although these responses were not always sustained. Neutralizing antibody responses were detectable in 36% by day 14 and 73% at 12 months. Common side effects included fatigue, myalgia, headache, arthralgia, and fever. These were positively associated with glycoprotein-specific T-cell but not immunoglobulin (Ig) M or IgG antibody responses. No severe vaccine-related adverse events were reported. No one exposed to the virus became infected.

Conclusions
This paper reports the use of the rVSV-ZEBOV vaccine given as an emergency intervention to individuals exposed to a patient presenting with a late reactivation of EVD. The vaccine was relatively well tolerated, but a high percentage developed a fever ≥37.5°C, necessitating urgent screening for Ebola virus, and a small number developed persistent arthralgia.
A Phase 2b, Randomized, Double-blind, Placebo-Controlled Multicenter Study Evaluating Antiviral Effects, Pharmacokinetics, Safety, and Tolerability of Presatovir in Hematopoietic Cell Transplant Recipients with Respiratory Syncytial Virus Infection of the Lower Respiratory Tract
Authors: Marty Francisco M , Chemaly Roy F , Mullane Kathleen M , Lee Dong-Gun , Hirsch Hans H , Small Catherine B , Bergeron Anne , Shoham Shmuel , Ljungman Per , Waghmare Alpana , Blanchard Elodie , Kim Yae-Jean , McKevitt Matt , Porter Danielle P , Jordan Robert , Guo Ying , German Polina , Boeckh Michael , Watkins Timothy R , Chien Jason W , Dadwal Sanjeet S 
Published: November 2019

Abstract

Background
Presatovir significantly reduced nasal viral load, signs, and symptoms of respiratory syncytial virus (RSV) infection in a human challenge study. We evaluated presatovir in hematopoietic-cell transplant (HCT) recipients with RSV lower respiratory tract infection (LRTI).

Methods
Patients with confirmed RSV in upper and lower respiratory tract and new chest X-ray abnormalities were randomized (1:1), stratified by supplemental oxygen and ribavirin use, to receive oral presatovir 200 mg or placebo every 4 days for 5 doses. The primary endpoint was time-weighted average change in nasal RSV viral load through day 9. Secondary endpoints included supplemental oxygen-free days, incident respiratory failure requiring mechanical ventilation, and all-cause mortality.

Results
From January 31, 2015, to March 20, 2017, 60 patients from 17 centers were randomized (31 presatovir, 29 placebo); 59 received study treatment (50 allogeneic, 9 autologous HCT). In the efficacy population (29 presatovir, 28 placebo), presatovir treatment did not significantly reduce time-weighted average change in viral load (−1.12 vs −1.09 log10 copies/mL; treatment difference −0.02 log10 copies/mL, 95% confidence interval: −.62, .57; P = .94), median supplemental oxygen-free days (26 vs 28 days, P = .84), incident respiratory failure (10.3 vs 10.7%, P = .98), or all-cause mortality (0 vs 7.1%, P = .19) versus placebo. Adverse events were similar between arms (presatovir 80%, placebo 79%). Resistance-associated substitutions in RSV fusion protein emerged in 6/29 presatovir-treated patients.

Conclusions
Presatovir treatment was well tolerated in HCT patients with RSV LRTI but did not improve virologic or clinical outcomes versus placebo.

Clinical Trials Registration
www.clinicaltrials.gov, NCT02254421; EudraCT, #2014-002475-29
Mitigation of lampricide toxicity to juvenile lake sturgeon: the importance of water alkalinity and life stage
Authors: Hepditch Scott L J , Tessier Laura R , Wilson Jonathan M , Birceanu Oana , O’Connor Lisa M , Wilkie Michael P 
Published: November 2019

Lay SummaryYoung-of-the-year lake sturgeon living in waters of high alkalinity are susceptible to mortality when exposed to 3-trifluoromethyl-4-nitrophenol (TFM), a pesticide used to control invasive sea lamprey in the Great Lakes. This risk may be reduced, however, by delaying TFM treatments to late-summer/fall, when sturgeon are larger and accumulate TFM more slowly.
Distal esophagus is the most commonly involved site for strictures in patients with eosinophilic esophagitis
Authors: Eluri Swathi , Tappata Manaswita , Huang Kevin Z , Koutlas Nathaniel T , Robey Benjamin S , Fan Claire , Reed Craig C , Shaheen Nicholas J , Dellon Evan S 
Published: November 2019

SUMMARYWhile strictures are common in eosinophilic esophagitis (EoE), there are few data on stricture distribution and characteristics. Our primary aim was to characterize strictures by location in the esophagus in EoE and associated clinical, endoscopic, and histologic features. This was a retrospective study from the UNC EoE Clinicopathologic Database of subjects with esophageal strictures or narrowing from 2002 to 2017. Strictures were categorized as distal esophagus/gastroesophageal junction, mid-esophagus, proximal esophagus, or diffusely narrowed. Stricture location was assessed and compared with clinical, endoscopic, and histologic features, and also with treatment response to diet or topical steroids. Efficacy of combination therapy with dilation and intralesional steroid injection was assessed in a sub-group of patients with strictures. Of 776 EoE cases, 219 (28%) had strictures, 45% of which were distal, 30% were proximal, 5% were mid-esophageal, and 20% had diffuse narrowing. Those with mid-esophageal strictures were younger (P = 0.02) and had shorter symptom duration (P &lt; 0.01). Those with diffuse esophageal narrowing were more likely to be women (57%) and have abdominal pain (25%). There was no association between other clinical, endoscopic, and histologic findings and treatment response based on stricture location. Fourteen patients (8%) received intralesional triamcinolone injection and subsequently achieved a higher mean dilation diameter after injection (13.7 vs. 15.5 mm; P &lt; 0.01). In conclusion, almost half of strictures in EoE patients were in the distal esophagus. Therefore, EoE should be a diagnostic consideration in patients with focal distal strictures and not presumed to be secondary to gastroesophageal reflux disease.
How to be fooled searching for significant variations of the b-value
Authors: Marzocchi W , Spassiani I , Stallone A , Taroni M 
Published: November 2019

SUMMARYAn unbiased estimation of the b-value and of its variability is essential to verify empirically its physical contribution to the earthquake generation process, and the capability to improve earthquake forecasting and seismic hazard. Notwithstanding the vast literature on the b-value estimation, we note that some potential sources of bias that may lead to non-physical b-value variations are too often ignored in seismological common practice. The aim of this paper is to discuss some of them in detail, when the b-value is estimated through the popular Aki’s formula. Specifically, we describe how a finite data set can lead to biased evaluations of the b-value and its uncertainty, which are caused by the correlation between the b-value and the maximum magnitude of the data set; we quantify analytically the bias on the b-value caused by the magnitude binning; we show how departures from the exponential distribution of the magnitude, caused by a truncated Gutenberg–Richter law and by catalogue incompleteness, can affect the b-value estimation and the search for statistically significant variations; we derive explicitly the statistical distribution of the magnitude affected by random symmetrical error, showing that the magnitude error does not induce any further significant bias, at least for reasonable amplitude of the measurement error. Finally, we provide some recipes to minimize the impact of these potential sources of bias.
Estimated Burden of Community-Onset Respiratory Syncytial Virus–Associated Hospitalizations Among Children Aged &lt;2 Years in the United States, 2014–15
Authors: Arriola Carmen S , Kim Lindsay , Langley Gayle , Anderson Evan J , Openo Kyle , Martin Andrew M , Lynfield Ruth , Bye Erica , Como-Sabetti Kathy , Reingold Arthur , Chai Shua , Daily Pam , Thomas Ann , Crawford Courtney , Reed C , Garg S , Chaves Sandra S 
Published: November 2019

Abstract

Background
Respiratory syncytial virus (RSV) is a major cause of hospitalizations in young children. We estimated the burden of community-onset RSV-associated hospitalizations among US children aged &lt;2 years by extrapolating rates of RSV-confirmed hospitalizations in 4 surveillance states and using probabilistic multipliers to adjust for ascertainment biases.

Methods
From October 2014 through April 2015, clinician-ordered RSV tests identified laboratory-confirmed RSV hospitalizations among children aged &lt;2 years at 4 influenza hospitalization surveillance network sites. Surveillance populations were used to estimate age-specific rates of RSV-associated hospitalization, after adjusting for detection probabilities. We extrapolated these rates using US census data.

Results
We identified 1554 RSV-associated hospitalizations in children aged &lt;2 years. Of these, 27% were admitted to an intensive care unit, 6% needed mechanical ventilation, and 5 died. Most cases (1047/1554; 67%) had no underlying condition. Adjusted age-specific RSV hospitalization rates per 100 000 population were 1970 (95% confidence interval [CI],1787 to 2177), 897 (95% CI, 761 to 1073), 531 (95% CI, 459 to 624), and 358 (95% CI, 317 to 405) for ages 0–2, 3–5, 6–11, and 12–23 months, respectively. Extrapolating to the US population, an estimated 49 509–59 867 community-onset RSV-associated hospitalizations among children aged &lt;2 years occurred during the 2014–2015 season.

Conclusions
Our findings highlight the importance of RSV as a cause of hospitalization, especially among children aged &lt;2 months. Our approach to estimating RSV-related hospitalizations could be used to provide a US baseline for assessing the impact of future interventions.
Accretion of small satellites and gas inflows in a disc galaxy
Authors: Ramón-Fox F G , Aceves Héctor 
Published: November 2019

ABSTRACT
Galaxy interactions can have an important effect in a galaxy’s evolution. Cosmological models predict a large number of small satellites around galaxies. It is important to study the effect that these small satellites can have on the host. The present work explores the effect of small N-body spherical satellites with total mass ratios in the range ≈ 1:1000-1:100 in inducing gas flows to the central regions of a disc galaxy with late-type morphology resembling the Milky Way. Two model galaxies are considered: barred and non-barred models; the latter one is motivated in order to isolate and understand better the effects of the satellite. Several circular and non-circular orbits are explored, considering both prograde and retrogade orientations. We show that satellites with such small mass ratios can still produce observable distortions in the gas and stellar components of the galaxy. In terms of gas flows, the prograde circular orbits are more favourable for producing gas flows, where in some cases up to $60{{\ \rm per\ cent}}$ of the gas of the galaxy is driven to the central region. We find, hence, that small satellites can induce significant gas flows to the central regions of a disc galaxy, which is relevant in the context of fuelling active galactic nuclei.
Mapping observations of complex organic molecules around Sagittarius B2 with the ARO 12 m telescope
Authors: Li Juan , Wang Junzhi , Qiao Haihua , Quan Donghui , Fang Min , Du Fujun , Li Fei , Shen Zhiqiang , Li Shanghuo , Li Di , Shi Yong , Zhang Zhiyu , Zhang Jiangshui 
Published: November 2019

ABSTRACT
We have performed high-sensitivity mapping observations of several complex organic molecules around Sagittarius B2 with the ARO 12 m telescope at 3 mm wavelength. Based on their spatial distribution, molecules can be classified as either ‘extended’, those detected not only in Sgr B2(N) and Sgr B2(M), or ‘compact’, those only detected toward or near Sgr B2(N) and Sgr B2(M). The ‘extended’ molecules include glycolaldehyde (CH2OHCHO), methyl formate (CH3OCHO), formic acid (t-HCOOH), ethanol (C2H5OH) and methyl amine (CH3NH2), while the ‘compact’ molecules include dimethyl ether (CH3OCH3), ethyl cyanide (C2H5CN), and amino acetonitrile (H2NCH2CN). These ‘compact’ molecules are likely produced under strong UV radiation, while the ‘extended’ molecules are likely formed at low temperatures, via gas-phase or grain-surface reactions. The spatial distribution of ‘warm’ CH2OHCHO at 89 GHz differs from the spatial distribution of ‘cold’ CH2OHCHO observed at 13 GHz. We found evidence for an overabundance of CH2OHCHO compared to that expected from the gas-phase model, which indicates that grain-surface reactions are necessary to explain the origin of CH2OHCHO in Sagittarius B2. Grain-surface reactions are also needed to explain the correlation between the abundances of ‘cold’ CH2OHCHO and C2H5OH. These results demonstrate the importance of grain-surface chemistry in the production of complex organic molecules.
The [α/Fe]–[Fe/H] relation in the E-MOSAICS simulations: its connection to the birth place of globular clusters and the fraction of globular cluster field stars in the bulge
Authors: Hughes Meghan E , Pfeffer Joel L , Martig Marie , Reina-Campos Marta , Bastian Nate , Crain Robert A , Kruijssen J M Diederik 
Published: November 2019

ABSTRACT
The α-element abundances of the globular cluster (GC) and field star populations of galaxies encode information about the formation of each of these components. We use the E-MOSAICS cosmological simulations of ∼L* galaxies and their GCs to investigate the [α/Fe]–[Fe/H] distribution of field stars and GCs in 25 Milky Way–mass galaxies. The [α/Fe]–[Fe/H] distribution of GCs largely follows that of the field stars and can also therefore be used as tracers of the [α/Fe]–[Fe/H] evolution of the galaxy. Due to the difference in their star formation histories, GCs associated with stellar streams (i.e. which have recently been accreted) have systematically lower [α/Fe] at fixed [Fe/H]. Therefore, if a GC is observed to have low [α/Fe] for its [Fe/H] there is an increased possibility that this GC was accreted recently alongside a dwarf galaxy. There is a wide range of shapes for the field star [α/Fe]–[Fe/H] distribution, with a notable subset of galaxies exhibiting bimodal distributions, in which the high [α/Fe] sequence is mostly comprised of stars in the bulge, a high fraction of which are from disrupted GCs. We calculate the contribution of disrupted GCs to the bulge component of the 25 simulated galaxies and find values between 0.3 and 14 per cent, where this fraction correlates with the galaxy’s formation time. The upper range of these fractions is compatible with observationally inferred measurements for the Milky Way, suggesting that in this respect the Milky Way is not typical of L*galaxies, having experienced a phase of unusually rapid growth at early times.