bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of hydroxylysine-O-glycosylation on the structure of type I collagen molecule: A computational study
Authors: Tang Ming , Wang Xiaocong , Gandhi Neha S , Foley Bethany Lachele , Burrage Kevin , Woods Robert J , Gu YuanTong 
Published: March 2020

AbstractCollagen undergoes many types of post-translational modifications (PTMs), including intracellular modifications and extracellular modifications. Among these PTMs, glycosylation of hydroxylysine (Hyl) is the most complicated. Experimental studies demonstrated that this PTM ceases once the collagen triple helix is formed and that Hyl-O-glycosylation modulates collagen fibrillogenesis. However, the underlying atomic-level mechanisms of these phenomena remain unclear. In this study, we first adapted the force field parameters for O-linkages between Hyl and carbohydrates and then investigated the influence of Hyl-O-glycosylation on the structure of type I collagen molecule, by performing comprehensive molecular dynamic simulations in explicit solvent of collagen molecule segment with and without the glycosylation of Hyl. Data analysis demonstrated that (i) collagen triple helices remain in a triple-helical structure upon glycosylation of Hyl; (ii) glycosylation of Hyl modulates the peptide backbone conformation and their solvation environment in the vicinity and (iii) the attached sugars are arranged such that their hydrophilic faces are well exposed to the solvent, while their hydrophobic faces point towards the hydrophobic portions of collagen. The adapted force field parameters for O-linkages between Hyl and carbohydrates will aid future computational studies on proteins with Hyl-O-glycosylation. In addition, this work, for the first time, presents the detailed effect of Hyl-O-glycosylation on the structure of human type I collagen at the atomic level, which may provide insights into the design and manufacture of collagenous biomaterials and the development of biomedical therapies for collagen-related diseases.
Neural Basis of Smoking-Related Difficulties in Emotion Regulation
Authors: Faulkner Paul , Dean Andy C , Ghahremani Dara G , London Edythe D 
Published: March 2020

Abstract

Background
Negative emotional states contribute to cigarette smoking, and difficulties in regulating these states can hinder smoking cessation. Understanding the neural bases of these difficulties in smokers may facilitate development of novel therapies for Tobacco Use Disorder.

Methods
Thirty-seven participants (18 smokers, 19 nonsmokers; 16–21 years old) completed the Difficulties in Emotion Regulation Scale (DERS), which is comprised of 6 subscales (lack of emotional clarity, lack of emotional awareness, limited access to emotion regulation strategies, nonacceptance of emotional responses, difficulties engaging in goal-directed behaviors, and impulse control difficulties) that combine to provide a total score. Participants also underwent functional magnetic resonance imaging to determine resting-state functional connectivity of the amygdala. Separate ANOVAs were used to determine group differences in self-reports on the DERS. Voxel-wise linear mixed models were performed to determine whether group influenced relationships between whole-brain functional connectivity of the amygdala and scores on the DERS.

Results
Compared with nonsmokers, smokers reported greater difficulties in emotion regulation, denoted by higher total scores on the DERS. Group differences were observed on a subscale of lack of emotional clarity, but no other subscale differences on the DERS were observed. Nonsmokers exhibited a greater negative correlation than smokers between lack of emotional clarity scores and connectivity of the amygdala with the left inferior frontal gyrus. Finally, this amygdala-to-left inferior frontal gyrus connectivity was weaker in smokers than in nonsmokers.

Conclusions
These findings suggest that difficulties in emotion regulation in smokers are at least partially due to lack of emotional clarity. Given the role of the inferior frontal gyrus in understanding emotional states, strengthening connectivity between the amygdala and the inferior frontal gyrus may improve emotional clarity to help smokers regulate their negative emotions, thereby improving their ability to quit smoking.
Full-Rank Valuations and Toric Initial Ideals
Authors: Bossinger Lara 
Published: March 2020

Abstract
Let $V(I)$ be a polarized projective variety or a subvariety of a product of projective spaces, and let $A$ be its (multi-)homogeneous coordinate ring. To a full-rank valuation ${\mathfrak{v}}$ on $A$ we associate a weight vector $w_{\mathfrak{v}}$. Our main result is that the value semi-group of ${\mathfrak{v}}$ is generated by the images of the generators of $A$ if and only if the initial ideal of $I$ with respect to $w_{\mathfrak{v}}$ is prime. As application, we prove a conjecture by [ 7] connecting the Minkowski property of string polytopes to the tropical flag variety. For Rietsch-Williams’ valuation for Grassmannians, we identify a class of plabic graphs with non-integral associated Newton–Okounkov polytope (for ${\operatorname *{Gr}}_k(\mathbb C^n)$ with $n\ge 6$ and $k\ge 3$).
Results from the Survey of Antibiotic Resistance (SOAR) 2015–17 in the Middle East (Kuwait, Lebanon and Saudi Arabia): data based on CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints
Authors: Torumkuney D , Mokaddas E , Jiman-Fatani A , Ageel A , Daoud Z , Bouferraa Y , Zerdan M B , Morrissey I 
Published: March 2020

Abstract

Objectives
To determine antibiotic susceptibility of Streptococcus pneumoniae and Haemophilus influenzae isolates from community-acquired respiratory tract infections (CA-RTIs) collected in 2015–17 from Kuwait, Lebanon and Saudi Arabia.

Methods
MICs were determined by CLSI broth microdilution and susceptibility was assessed using CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints.

Results
A total of 139 S. pneumoniae isolates were collected from four centres in Kuwait, Lebanon and Saudi Arabia in 2015–17 and 55 H. influenzae isolates were collected and analysed from Saudi Arabia over the same time period. Pneumococci from all three countries were commonly non-susceptible to penicillin based on CLSI oral or low-dose IV penicillin using EUCAST breakpoints (39% in Kuwait to 57.1% in Lebanon) but by CLSI IV and EUCAST high-dose breakpoints most isolates were susceptible (∼90% in Kuwait and Saudi Arabia, and 100% in Lebanon). Isolates from Lebanon were highly susceptible to most other antibiotics (&gt;90%) except cefaclor, oral cefuroxime and cefpodoxime (EUCAST breakpoints only). Overall, susceptibility was significantly lower in Kuwait and Saudi Arabia than Lebanon. Although all H. influenzae isolates (Saudi Arabia only) were β-lactamase negative, 3.6% and 12.7% were ampicillin resistant by CLSI and EUCAST breakpoints, respectively. Otherwise susceptibility was high in H. influenzae. The application of different EUCAST breakpoints for low and higher doses for some of the antibiotics (amoxicillin, amoxicillin/clavulanic acid, ampicillin, penicillin, ceftriaxone, clarithromycin, erythromycin, levofloxacin and trimethoprim/sulfamethoxazole) allowed, for the first time in a SOAR study, the effect of raising the dosage on susceptibility to be quantified.

Conclusions
Relatively low antibiotic susceptibility was observed in S. pneumoniae from Kuwait and Saudi Arabia in contrast to Lebanon, where rates of susceptibility were generally higher. Isolates of H. influenzae from Saudi Arabia were susceptible to most antibiotics. These factors are important in decision making for empirical therapy of CA-RTIs.
Results from the Survey of Antibiotic Resistance (SOAR) 2015–17 in Turkey: data based on CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints
Authors: Torumkuney D , Tunger A , Sancak B , Bıçakçıgil A , Altun B , Aktas Z , Kayacan C , Morrissey I 
Published: March 2020

Abstract

Objectives
To determine antibiotic susceptibility of Streptococcus pneumoniae and Haemophilus influenzae isolates from community-acquired respiratory tract infections (CA-RTIs) collected in 2015–17 from Turkey.

Methods
MICs were determined by CLSI broth microdilution and susceptibility was assessed using CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints.

Results
A total of 179 S. pneumoniae and 239 H. influenzae isolates were collected. Few (27.9%) pneumococci were penicillin susceptible by CLSI oral or EUCAST low-dose breakpoints, but by EUCAST high-dose or CLSI IV breakpoints 84.4% were susceptible. The most active antibiotics (excluding penicillin IV) by CLSI breakpoints were fluoroquinolones (98.9% of isolates susceptible), ceftriaxone (83.2%), amoxicillin (78.8%) and amoxicillin/clavulanic acid (78.8%). Pneumococcal susceptibility to amoxicillin and amoxicillin/clavulanic acid was lower using EUCAST low-dose breakpoints (49.7%), although susceptibility increased when using EUCAST high-dose (57.0%–58.1%) and PK/PD (78.8%–87.7%) breakpoints. Twenty-three H. influenzae isolates were β-lactamase positive, with 11 characterized as β-lactamase negative and ampicillin resistant following EUCAST criteria and 5 by CLSI criteria. Generally antibiotic susceptibility was high using CLSI breakpoints: ≥92.9% for all antibiotics except ampicillin (87% by CLSI and EUCAST breakpoints) and trimethoprim/sulfamethoxazole (67.4% and 72% by CLSI and EUCAST breakpoints, respectively). Susceptibility using EUCAST breakpoints (where these are published) was similar, except for cefuroxime (oral) with 3.8% of isolates susceptible. PK/PD breakpoints indicated low susceptibility to macrolides (5.9%–10%) and cefaclor (13%). The application of different EUCAST breakpoints for low and higher doses for some of the antibiotics (amoxicillin, amoxicillin/clavulanic acid, ampicillin, penicillin, ceftriaxone, clarithromycin, erythromycin, levofloxacin and trimethoprim/sulfamethoxazole) allowed, for the first time in a SOAR study, the effect of raising the dosage on susceptibility to be quantified.

Conclusions
Antibiotic susceptibility of S. pneumoniae was generally low, which is in keeping with evidence of inappropriate and high antibiotic use in Turkey. H. influenzae susceptibility was high. These data are important for empirical therapy of CA-RTIs.
Fluoroquinolone resistance in Escherichia coli isolates after exposure to non-fluoroquinolone antibiotics: a retrospective case–control study
Authors: Chaname Pinedo Linda E , Bruyndonckx Robin , Catry Boudewijn , Latour Katrien , Goossens Herman , Abrams Steven , Coenen Samuel 
Published: March 2020

Abstract

Objectives
To investigate whether prior exposure to non-fluoroquinolone antibiotics increases the risk of fluoroquinolone resistance in Escherichia coli.

Methods
This was a secondary analysis of data collected retrospectively in a case–control study linking microbiological test results (isolated bacteria and their susceptibility) of urine samples routinely collected from primary, secondary and tertiary care patients in Belgium with information on prior antibiotic use at the patient level up to 1 year previously.

Results
In urine samples from 6125 patients, 7204 E. coli isolates were retrieved [1949 fluoroquinolone-resistant isolates (cases) and 5255 fluoroquinolone-susceptible isolates (controls)]. After adjusting for potential confounders (including fluoroquinolone use) and correcting for multiple testing there were lower odds of fluoroquinolone resistance in E. coli isolates after exposure to cefazolin (OR = 0.65; 95% CI = 0.52–0.81; P = 0.00014) and higher odds after exposure to trimethoprim/sulfamethoxazole (OR = 1.56; 95% CI = 1.23–1.97; P =0.00020) or nitrofurantoin (OR = 1.50; 95% CI = 1.23–1.84; P =0.000083). A sensitivity analysis excluding samples with antibiotic use during the 6 months prior to the sampling date confirmed the higher odds of fluoroquinolone resistance after exposure to trimethoprim/sulfamethoxazole and nitrofurantoin.

Conclusions
Assuming no residual confounding or other biases, this study suggests that exposure to non-fluoroquinolone antibiotics, i.e. trimethoprim/sulfamethoxazole and nitrofurantoin, might be causally related to fluoroquinolone resistance in E. coli isolates from urinary samples. Future prospective research is needed to confirm non-fluoroquinolone antibiotics as potential drivers of fluoroquinolone resistance.
Recovery and Sporicidal Resistance of Various B. subtilis Spore Preparations on Porcelain Penicylinders Compared with Results from AOAC Test Methods
Authors: Danielson James W , Zuroski Kristine E , Twohy Christine , Thompson Richard D , Bell Ellis , McClure Foster 
Published: March 2020

Abstract
Sporicidal test results obtained from carriers inoculated with 4 types of defined Bacillus subtilis spore preparations were compared with the standard AOAC sporicidal test using soil extract nutrient broth (SENB) B. subtilis 19659 spores. Recoveries of spores inoculated on penicylinders from B. subtilis clean spores (washed and suspended in water) and B. subtilis 19659 spores inoculated from culture filtrates according to the AOAC method were compared. Spores were exposed to 6 concentrations (0.5–3.0% w/v) of glutaraldehyde in phosphate buffer (pH 7.5) for 10 h. Concentrations were established by titrimetry and liquid chromatography. Recoveries of surviving spores were determined for 3 types of clean B. subtilis var. niger preparations, one clean B. subtilis 19659 preparation, and the SENB B. subtilis 19659 filtrates. Spore carriers, inoculated by the standard AOAC protocol, resulted in as much as a 2-log number difference in runs 1–12, but not more than 0.5 log number for each clean spore preparation. The SENB spores varied most in resistance to glutaraldehyde, with no growth in recovery media from 3 different batches of 1, 1.5, and 2% glutaraldehyde. Separate batches of SENB preparations of B. subtilis 19659 were resistant and destroyed by 1.0% glutaraldehyde, with 3.98 and 6.0 log numbers of spores on penicylinders, respectively. Clean spore preparations of B. subtilis 19659 on porcelain penicylinders were more resistant to glutaraldehyde than were SENB spores. Nutrient agar/Mg/Ca and nutrient agar/Mg spore preparations of B. subtilis var. niger showed the most uniform resistance to glutaraldehyde. Spores with calcium added showed increased resistance to glutaraldehyde. B. subtilis 19659 spores from the Columbia broth spore preparation were the most resistant and were recovered after exposure to 3.0% glutaraldehyde.
Element and Radionuclide Concentrations in Food: FDA Total Diet Study 1991–1996
Authors: Capar Stephen G , Cunningham William C 
Published: March 2020

Abstract
Foods purchased throughout the United States during 1991–1997 under the U.S. Food and Drug Administration's Total Diet Study (TDS) program were analyzed for elements and radionuclides. The program is described with emphasis on food analysis and quality control, including independent interlaboratory exercises. Analytical results are summarized for Cd, Pb, Ni, As, Hg, Se, Cu, Zn, Mn, Fe, Mg, Ca, P, K, and Na and for 137Cs, 131I, 106Ru, and 90Sr. Concentration data are provided to expand the information base used to support assessments of the safety and nutritive value of the U.S. food supply and for their potential use in food composition databases. For selected foods, comparisons were made with past TDS results and with those reported in the literature. An extensive listing of the analytical data is available on the FDA CFSAN Website.
Speciation of Iodide, Iodine, and Iodate in Environmental Matrixes by Inductively Coupled Plasma Atomic Emission Spectrometry Using in situ Chemical Manipulation
Authors: Anderson Kim A , Markowski Peter 
Published: March 2020

Abstract
Dissolved iodine, iodide, and iodate are determined in environmental matrixes by in situ chemical manipulation and inductively coupled plasma atomic emission spectrometry (ICPAES). The method uses equipment commonly available to most laboratories involved in environmental inorganic analysis. Total dissolved iodine, iodide, and iodate are determined by ICPAES using iodine vapor generation. Total iodine is determined directly by ICPAES after filtration. Total dissolved iodide (I−) is oxidized in situ to iodine by the addition of sodium nitrite in sulfuric acid in a simplified continuous flow manifold. Iodate is determined by prereduction at the instrument before analysis by the in situ oxidation ICPAES procedure. A standard nebulizer produces the gas–liquid separation of the total iodine, which is then quantified by ICPAES at 206.16 nm. The instrument detection limit for the iodine analysis was 0.04 μg/mL. Recoveries from seawater, saltwater, and freshwater standard reference materials ranged from 85 to 118% and averaged 98%. For samples containing both iodine and iodide, the total is determined with in situ oxidation, iodine is determined without the oxidizing reagents, and iodide is calculated from the difference. For samples containing all 3 species, pre-reduction is used and the iodine and iodide concentrations are subtracted for quantitation of iodate. The analysis is selective for these 3 species (I−, I2, and IO−3). A group of 20–30 samples may be analyzed and quantitated for all 3 individual, commonly occurring iodide species in less than 1 h. The procedure is considerably faster than any other reported techniques. This method is especially well-suited to the analysis of small environmental samples.
Comparative Photodegradation Study of Atrazine and Desethylatrazine in Water Samples Containing Titanium Dioxide/Hydrogen Peroxide and Ferric Chloride/Hydrogen Peroxide
Authors: Peñuela Gustavo A , Barceló Damià 
Published: March 2020

Abstract
Results are reported for a comparative photodegradation study of atrazine and desethylatrazine in water using TiO2/H2O2, FeCl3/H2O2, and photolysis. Deionized water and ground water spiked with atrazine or desethylatrazine at 36 μg/L were irradiated by using a xenon arc lamp and/or sunlight. After irradiation, the water samples containing the spiked pesticides were preconcentrated by using C18 solid-phase extraction disks and analyzed by gas chromatography with nitrogen–phosphorus and mass spectrometric detection. A relative percentage of 7% desethylatrazine was detected in samples removed after 20 and 4 min of sensitized photodegradation with TiO2 and Fe3+, respectively. Atrazine and desethylatrazine did not degrade when solar irradiation (in winter) and deionized water were used. Atrazine degraded faster than desethylatrazine when a xenon arc lamp or sunlight plus FeCl3 was used, with half-lives varying from 5 to 11 min and from 19 to 26 min, respectively. In other photodegradation experiments, the degradation of atrazine was slightly higher than that of desethylatrazine. This study shows that desethylatrazine has slightly higher stability than atrazine in environmental water samples; this stability accounts for the frequent detection of desethylatrazine together with atrazine in natural waters.
Second transurethral resection for high-risk non-muscle invasive bladder cancer patients: a propensity score matched analysis
Authors: Matsushita Yuto , Watanabe Kyohei , Watanabe Hiromitsu , Tamura Keita , Motoyama Daisuke , Ito Toshiki , Sugiyama Takayuki , Otsuka Atsushi , Miyake Hideaki 
Published: March 2020

Abstract

Objectives
Second transurethral resection is recommended for patients diagnosed with high-risk non-muscle invasive bladder cancer; however, there have been several studies showing conflicting findings regarding the advantage of second transurethral resection. The objective of this study was to investigate the prognostic significance of second transurethral resection using propensity score matched analysis.

Patients and Methods
This study retrospectively included 164 consecutive patients who underwent initial transurethral resection and were diagnosed with high-risk non-muscle invasive bladder cancer. Of these, 56 subsequently received second transurethral resection, and the remaining 108 underwent initial transurethral resection alone.

Results
After adjusting patient variables by propensity score matching, 44 patients were included in each group. There was no significant difference in recurrence-free, progression-free or overall survival between these two groups.

Conclusions
These findings suggested no significant impact of second transurethral resection on the prognosis of high-risk non-muscle invasive bladder cancer patients; therefore, it may be necessary to perform a reassessment focusing on the indication for second transurethral resection by conducting a large-scale prospective study.
The Word on the Street or the Number from the State? Government-Provided Information and Americans’ Opinions of Schools
Authors: Valant Jon , Newark Daniel A 
Published: March 2020

AbstractPublic institutions seeking to facilitate effective decision making by boundedly rational constituents often must determine what information to provide and in what form to provide it. Ideally, this determination would reflect an understanding of how different kinds, forms, and sources of information are processed by constituents and influence constituents’ beliefs. However, research on this topic—especially in the context of educational institutions, and with a focus on official numerical information versus electronic word of mouth—has been minimal. Considering the case of state governments wishing to inform citizens about their schools, we examine how parents and the US public evaluate schools after receiving two increasingly abundant kinds of school quality information: numerical government ratings and online parent comments. Using an online survey experiment with a nationally representative sample, we find that perceptions of school quality are heavily influenced by parent comments even when these comments appear alongside official ratings. By contrast, the effects of official numerical ratings appear modest. Additional findings suggest that the comments’ influence results from preferences for the information’s source (parents over government) and style (narrative over numerical), and that nonprofit organizations are more trusted messengers of performance information than state governments. These results advance our theoretical understanding of the effects of different kinds of information on belief, and we conclude the article by discussing their implications for how public institutions disseminate information to their constituents.