bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monte Carlo calculated detector-specific correction factors for Elekta radiosurgery cones
Authors: Renil Mon P S , Meena Devi V N , Bhasi Saju , Nair Sneha S 
Published: February 2021

Abstract
A radiation field is considered small if its dimension is lower than the range of secondary electrons and the collimating devices partially occlude the source. Different detector types, such as unshielded diodes, diamond detectors, and small-volume ion chambers, are used for small-field measurements. Although the active volumes of these detectors are small, their non-water equivalent materials cause response variations. Herein, we aim to calculate the correction factors for our clinical detectors, EDGE detector (Sun Nuclear), 60017 diode (PTW), and CC01 ion chamber (IBA), for stereotactic radiosurgery cones of diameters of 5–15 mm in an Elekta Synergy linear accelerator using a Monte Carlo simulation. An Elekta Synergy linear accelerator treatment head was simulated using BEAMnrc Monte Carlo code as per the manufacturer specification. All three detectors were simulated as per the manufacturer specification. Three EGSnrc user codes were used for the detector simulation based on the detector geometry. The Monte Carlo model of the treatment head was validated against the measured data for a standard field size of 10 × 10 cm2. The off-axis profile, percentage depth dose, and tissue phantom ratio

TPR

10

20

were verified in the validation procedure. The measured and Monte Carlo calculated relative output factors (ROFs) were not consistent. In a 5 mm field size, EDGE diode overestimated the ROF by 7.06%, and 60017 diode to 4.611%. In a 7.5 mm field size, the variations were 4.295% and 3.691% for EDGE and 60017 diodes, respectively. CC01 ion chamber under-responded up to 10% because of its low-density active volume. The maximum corrections were obtained in the smallest field size, which were 0.939(0.007), 0.962(0.006), and 1.117(0.008) for EDGE, PTW T60017, and CC01 detectors, respectively. After applying the Monte Carlo calculated correction factor to the measured ROF, it became consistent with the Monte Carlo calculated ROF.
Nanoscale differentiation of surfaces and cores for olivine phosphate particles—a key characteristic of practical battery materials
Authors: Zhang Y , Alarco J A , Khosravi M , Mackinnon I D R 
Published: February 2021

Abstract
We provide a review of our recent studies on the surface chemistries and electronic structures of olivine phosphate cathode materials LiMPO4 (M = Mn, Fe, Co, Ni). Li-depletion and mixed oxidation for the transition metal ions have been detected on particle surfaces, across the family of metal phosphate cathode materials. The effects of surface Li-depletion on optical properties and electronic band structures are discussed. LiFePO4 doped with metals or ions that are reported in the literature as beneficial for rate capability enhancement show more pronounced surface Li-depletion and mixed oxidation compared to undoped material. This outcome, among others, indicates that the dopant resides predominantly on, and influences, the surface of cathode materials.
Retention of activity and secondary structure of hyperthermophilic laccase adsorbed on carbon black
Authors: Tamaki Takanori , Sugiyama Tomoharu , Oshiba Yuhei , Yamaguchi Takeo 
Published: February 2021

AbstractFurther increases in the current density of biofuel cells are partly limited by the deactivation of enzymes upon adsorption on hydrophobic carbon materials. A hyperthermophilic enzyme, hyperthermophilic laccase, was employed in the present study and the change in the activities and secondary structures upon adsorption on carbon black (CB) were evaluated by the oxidation rate of 2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonate) and by Fourier transform infrared spectroscopy, respectively, in comparison with the mesophilic enzymes, laccase fromTrametes versicolor(denoted as mesophilic laccase), and glucose oxidase (GOx). Hyperthermophilic laccase retained its specific activities and secondary structures upon adsorption on CB compared with the other two enzymes mesophilic laccase and GOx.
Experimental determination of Li diffusivity in LLZO using isotopic exchange and FIB-SIMS
Authors: Brugge Rowena H , Chater Richard J , Kilner John A , Aguadero Ainara 
Published: February 2021

Abstract
Current lithium ion battery technology makes use of flammable liquid electrolytes and so the development of solid ceramic electrolytes for the next generation of all-solid-state batteries can offer a safer alternative. However, the lithium diffusion behaviour in these solid electrolytes is not yet well characterised, despite the importance of this information for optimising cell performance. Similarly, the transport properties at the metal anode interface are critically important, but not well understood. We propose a methodology for obtaining lithium diffusion coefficients of bulk solid ceramic garnet-type Li7La3Zr2O12 (LLZO) electrolytes by coupling dense pellets with isotopically labelled lithium metal, followed by analysis with focused-ion-beam secondary ion mass spectrometry. We report room temperature lithium diffusivities of 2–8 × 10−13 m2 s−1 for doped LLZO using an estimate of the lithium diffusion length in good agreement with electrochemical impedance spectroscopy. Simultaneous detection of positive and negative secondary ion species by SIMS enables correlation of layered interfaces consisting of metallic lithium, corrosion/surface degradation products and bulk LLZO during depth profiling. Charging of the ceramic during ion sputtering is investigated and shown to have a minimal effect on the obtained lithium isotopic fractions in the current setup. Additionally, the effect of the presence of corrosion products at the surface of garnets as a result of air-exposure is investigated. This method could be extended to any Li-metal stable solid electrolyte, or with a reactive solid electrolyte coupled with a stable interlayer. As such, this work sets the basis of a methodology for further quantitative diffusion analyses for Li-conducting solid ceramic electrolytes and their interfaces with electrodes, as used in both solid-state lithium batteries and hybrid systems coupling solid and liquid electrolytes.
A Broad Safety Assessment of the 9-Valent Human Papillomavirus Vaccine
Authors: Yih W Katherine , Kulldorff Martin , Dashevsky Inna , Maro Judith C 
Published: February 2021

Abstract
Parents indicate that safety is their top concern about human papillomavirus (HPV) vaccination. A data-mining method not requiring prespecification of health outcome(s) or postexposure period(s) of potentially increased risk can be used to identify possible associations between an exposure and any of thousands of medically attended health outcomes; this method was applied to data on the 9-valent HPV vaccine (HPV9) to detect potential safety problems. Data on 9- to 26-year-olds who had received HPV9 vaccine between November 4, 2016, and August 5, 2018, inclusive, were extracted from the MarketScan database and analyzed for statistically significant clustering of incident diagnoses within the hierarchy of diagnoses coded using the International Classification of Diseases and temporally within the 1 year after vaccination, using the self-controlled tree-temporal scan statistic and TreeScan software. Only 56 days of postvaccination enrollment was required; subsequent follow-up was censored at disenrollment. Multiple testing was adjusted for. The analysis included 493,089 doses of HPV9. Almost all signals resulted from temporal confounding, not unexpected with a 1-year follow-up period. The only plausible signals were for nonspecific adverse events (e.g., injection-site reactions, headache) on days 1–2 after vaccination, with attributable risks as low as 1 per 100,000 vaccinees. Considering the broad scope of the evaluation and the high statistical power, the findings of no specific serious adverse events should provide reassurance about this vaccine’s safety.
Association Between Nocturnal Blood Pressure Dipping and Chronic Kidney Disease Among Patients With Controlled Office Blood Pressure
Authors: Cho So Mi J , Lee Hokyou , Yoo Tae-Hyun , Jhee Jong Hyun , Park Sungha , Kim Hyeon Chang 
Published: February 2021

Abstract

BACKGROUND
Although abnormal blood pressure (BP) patterns are associated with adverse cardiorenal outcomes, their associations are yet unquantified by nocturnal dipping status. We examined the association of nocturnal BP dipping pattern with albuminuria and kidney function among participants with controlled hypertension without prior advanced kidney disease.

METHODS
Ambulatory BP (ABP) measurements were collected from 995 middle-aged, cardiology clinic patients with controlled office BP (OBP) (&lt;140/90 mm Hg). The magnitude of dipping was calculated as the difference between daytime and nighttime systolic BP (SBP) divided by daytime SBP. Accordingly, the participants were categorized as extreme-dipper (≥20%), dipper (10% to &lt;20%), non-dipper (0% to &lt;10%), or reverse-dipper (&lt;0%). We analyzed the cross-sectional associations of dipping with albuminuria (urine albumin-to-creatinine ratio ≥30 mg/g) and decreased estimated glomerular filtration rate (&lt;60 ml/min/1.73 m2), adjusting for OBP/ABP, antihypertensive class, body mass index, total cholesterol, fasting glucose, socioeconomic status, and health behavior.

RESULTS
The participants (mean age 60.2 years; 52.9% male) consisted of 13.5% extreme-dippers, 43.1% dippers, 34.7% non-dippers, and 8.7% reverse-dippers. In reference to dippers, odds ratios [95% confidence interval] for albuminuria were 1.73 [1.04–2.60] in reverse-dippers, 1.67 [1.20–2.32] in non-dippers, and 0.62 [0.38–1.04] in extreme-dippers. Likewise, abnormal dipping profile was associated with decreased kidney function: reverse-dipping, 2.02 [1.06–3.84]; non-dipping, 1.98 [1.07–3.08]; extreme-dipping, 0.69 [0.20–1.17]. The associations persisted among participants with more conservatively controlled OBP (&lt;130/80 mm Hg).

CONCLUSIONS
Monitoring diurnal and nocturnal BP may identify chronic kidney disease otherwise overlooked based on OBP.
Immunogenicity to Botulinum Toxin Type A: A Systematic Review With Meta-Analysis Across Therapeutic Indications
Authors: Rahman Eqram , Alhitmi Hitmi Khalifa , Mosahebi Afshin 
Published: February 2021

AbstractBackgroundBotulinum toxin A (BTX-A) is commonly employed as a neuromodulator in several neurological diseases and aesthetic indications. Formation of neutralizing antibodies (NAbs) after BTX-A injections may be responsible for treatment failure.ObjectivesThe authors sought to quantify the prevalence of NAbs following treatment with Abobotulinumtoxin A, Incobotulinumtoxin A, and Onabotulinumtoxin A for therapeutic indications.MethodsAn electronic systematic search (2000-2020) of PubMed, Scopus, Web of Science, and Embase was conducted. Original studies reporting prevalence of NAbs were included. Data analysis was carried out through open meta-analysis softwares.ResultsForty-three studies involving 8833 patients were included in this meta-analysis. The incidence of NAbs was 1.8% (summary estimate = 0.018, 95% CI [0.012, 0.023]); a meta-regression analysis revealed that BTX-A duration was significantly associated with increased incidence of NAbs (P = 0.007). Patients with dystonia had the highest incidence (7.4%) of NAbs against BTX-A (summary estimate = 0.074, 95% CI = [0.045, 0.103], I2 = 93.%, P &lt; 0.00) followed by patients with spasticity (6.7%) and urological indications (6.2%). Abobotulinumtoxin A was associated with the highest incidence of NAbs (7.4%) (summary estimate = 0.074, 95% CI = [0.053, 0.096], I2 = 97.24%, P &lt; 0.00) by the Incobotulinumtoxin A and Onabotulinumtoxin A 0.3% (summary estimate &lt;0.003%, 95% CI = [−0.001, 0.007], P &lt; 0.003).ConclusionsAlthough the overall incidence of NAbs following BTX-A injections is relatively low, patients with secondary nonresponse to BTX-A with no apparent causes should be investigated for NAbs. A consensus needs to be developed for the optimal management of such patients.Level of Evidence: 2
A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium
Authors: Warwicker Jim 
Published: February 2021

Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causative agent of the coronavirus disease 2019 (COVID-19) pandemic, is thought to release its RNA genome at either the cell surface or within endosomes, the balance being dependent on spike protein stability, and the complement of receptors, co-receptors and proteases. To investigate possible mediators of pH-dependence, pKa calculations have been made on a set of structures for spike protein ectodomain and fragments from SARS-CoV-2 and other coronaviruses. Dominating a heat map of the aggregated predictions, three histidine residues in S2 are consistently predicted as destabilizing in pre-fusion (all three) and post-fusion (two of the three) structures. Other predicted features include the more moderate energetics of surface salt–bridge interactions and sidechain–mainchain interactions. Two aspartic acid residues in partially buried salt-bridges (D290–R273 and R355–D398) have pKas that are calculated to be elevated and destabilizing in more open forms of the spike trimer. These aspartic acids are most stabilized in a tightly closed conformation that has been observed when linoleic acid is bound, and which also affects the interactions of D614. The D614G mutation is known to modulate the balance of closed to open trimer. It is suggested that D398 in particular contributes to a pH-dependence of the open/closed equilibrium, potentially coupled to the effects of linoleic acid binding and D614G mutation, and possibly also A570D mutation. These observations are discussed in the context of SARS-CoV-2 infection, mutagenesis studies, and other human coronaviruses.
An OMICs-based meta-analysis to support infection state stratification
Authors: Myall Ashleigh C , Perkins Simon , Rushton David , David Jonathan , Spencer Phillippa , Jones Andrew R , Antczak Philipp 
Published: February 2021

Abstract

Motivation
A fundamental problem for disease treatment is that while antibiotics are a powerful counter to bacteria, they are ineffective against viruses. Often, bacterial and viral infections are confused due to their similar symptoms and lack of rapid diagnostics. With many clinicians relying primarily on symptoms for diagnosis, overuse and misuse of modern antibiotics are rife, contributing to the growing pool of antibiotic resistance. To ensure an individual receives optimal treatment given their disease state and to reduce over-prescription of antibiotics, the host response can in theory be measured quickly to distinguish between the two states. To establish a predictive biomarker panel of disease state (viral/bacterial/no-infection), we conducted a meta-analysis of human blood infection studies using machine learning.

Results
We focused on publicly available gene expression data from two widely used platforms, Affymetrix and Illumina microarrays as they represented a significant proportion of the available data. We were able to develop multi-class models with high accuracies with our best model predicting 93% of bacterial and 89% viral samples correctly. To compare the selected features in each of the different technologies, we reverse-engineered the underlying molecular regulatory network and explored the neighbourhood of the selected features. The networks highlighted that although on the gene-level the models differed, they contained genes from the same areas of the network. Specifically, this convergence was to pathways including the Type I interferon Signalling Pathway, Chemotaxis, Apoptotic Processes and Inflammatory/Innate Response.

Availability
Data and code are available on the Gene Expression Omnibus and github.

Supplementary information
Supplementary data are available at Bioinformatics online.
orfipy: a fast and flexible tool for extracting ORFs
Authors: Singh Urminder , Wurtele Eve Syrkin 
Published: February 2021

Abstract

Summary
Searching for open reading frames is a routine task and a critical step prior to annotating protein coding regions in newly sequenced genomes or de novo transcriptome assemblies. With the tremendous increase in genomic and transcriptomic data, faster tools are needed to handle large input datasets. These tools should be versatile enough to fine-tune search criteria and allow efficient downstream analysis. Here we present a new python based tool, orfipy, which allows the user to flexibly search for open reading frames in genomic and transcriptomic sequences. The search is rapid and is fully customizable, with a choice of FASTA and BED output formats.

Availability and implementation
orfipy is implemented in python and is compatible with python v3.6 and higher. Source code: https://github.com/urmi-21/orfipy. Installation: from the source, or via PyPi (https://pypi.org/project/orfipy) or bioconda (https://anaconda.org/bioconda/orfipy).

Supplementary information
Supplementary data are available at Bioinformatics online.
Mechanical and oral antibiotic bowel preparation versus no bowel preparation in right and left colectomy: subgroup analysis of MOBILE trial
Authors: Koskenvuo L , Lehtonen T , Koskensalo S , Rasilainen S , Klintrup K , Ehrlich A , Pinta T , Scheinin T , Sallinen V 
Published: February 2021

Abstract

Background
In retrospective series, mechanical and oral antibiotic bowel preparation (MOABP) has been reported to reduce surgical-site infections (SSIs) after colectomy compared with no bowel preparation (NBP).

Method
This was a subgroup analysis of a multicentre randomized trial that included patients scheduled for elective colectomy. The MOABP group underwent mechanical bowel preparation, and took 2 g neomycin and 2 g metronidazole orally during the day before surgery. The NBP group did not undergo bowel preparation. Patients were categorized according to the side of resection (right versus left colectomy), and these subgroups compared for postoperative outcomes.

Results
Among 217 patients undergoing right colectomy (106 in MOABP and 111 in NBP group), SSI was detected in seven (7 per cent) and 10 (9 per cent) patients (odds ratio (OR) 0.71, 95 per cent c.i. 0.26 to 1.95; P = 0.510), anastomotic dehiscence in two (2 per cent) and two (2 per cent) patients (OR 1.05, 0.15 to 7.58; P = 1.000), and the mean(s.d.) Comprehensive Complication Index (CCI) score was 9.4(12.9) and 10.5(18.0) (mean difference –1.09; 95 per cent c.i. –5.29 to 3.11; P = 0.608) in the MOABP and NBP groups respectively. Among 164 patients undergoing left colectomy (84 in MOABP and 80 in NBP group), SSI was detected in five (6 per cent) and eight (10 per cent) patients (OR 0.57, 0.18 to 1.82; P = 0.338), anastomotic dehiscence in four (5 per cent) and five (6 per cent) patients (OR 0.75, 0.19 to 2.90; P = 0.742), and the CCI score was 10.2(13.1) and 6.5(11.0) (mean difference 3.68, –0.06 to 7.42; P = 0.053) in the MOABP and NBP groups respectively.

Conclusions
MOABP did not decrease the rate of SSI or complications in patients undergoing either right or left colectomy compared with NBP.
Tracing the origins of hybrids through history: monstrous cultivars and Napoléon Bonaparte’s exiled paper daisies (Asteraceae; Gnaphalieae)
Authors: Collins Timothy L , Bruhl Jeremy J , Schmidt-Lebuhn Alexander N , Telford Ian R H , Andrew Rose L 
Published: February 2021

AbstractGolden everlasting paper daisies (Xerochrysum, Gnaphalieae, Asteraceae) were some of the earliest Australian native plants to be cultivated in Europe. Reputedly a favourite of Napoléon Bonaparte and Empress Joséphine, X. bracteatum is thought to have been introduced to the island of St Helena in the South Atlantic during Napoléon’s exile there. Colourful cultivars were developed in the 1850s, and there is a widely held view that these were produced by crossing Xerochrysum with African or Asian Helichrysum spp. Recent molecular phylogenetic analyses and subtribal classification of Gnaphalieae cast doubt on this idea. Using single-nucleotide polymorphism (SNP) data, we looked for evidence of gene flow between modern cultivars, naturalized paper daisies from St Helena and four Xerochrysum spp. recorded in Europe in the 1800s. There was strong support for gene flow between cultivars and X. macranthum. Paper daisies from St Helena were genotypically congruent with X. bracteatum and showed no indications of ancestry from other species or from the cultivars, consistent with the continuous occurrence of naturalized paper daisies introduced by Joséphine and Napoléon. We also present new evidence for the origin of colourful Xerochrysum cultivars and hybridization of congeners in Europe from Australian collections.
Diminished antiproteinuric effect of the angiotensin receptor blocker losartan during high potassium intake in patients with CKD
Authors: Wouda Rosa D , Waanders Femke , de Zeeuw Dick , Navis Gerjan , Vogt Liffert ,   the K+ Consortium
Published: February 2021

Abstract

Background
Angiotensin II type 1 receptor blockers (ARBs) lower blood pressure (BP) and proteinuria and reduce renal disease progression in many—but not all—patients. Reduction of dietary sodium intake improves these effects of ARBs. Dietary potassium intake affects BP and proteinuria. We set out to address the effect of potassium intake on BP and proteinuria response to losartan in non-diabetic proteinuric chronic kidney disease (CKD) patients.

Methods
We performed a post hoc analysis of a placebo-controlled interventional cross-over study in 33 non-diabetic proteinuric patients (baseline mean arterial pressure and proteinuria: 105 mmHg and 3.8 g/day, respectively). Patients were treated for 6 weeks with placebo, losartan and losartan/hydrochlorothiazide (HCT), combined with a habitual (∼200 mmol/day) and low-sodium (LS) diet (&lt;100 mmol/day), in randomized order. To analyse the effects of potassium intake, we categorized patients based on median split of 24-h urinary potassium excretion, reflecting potassium intake.

Results
Mean potassium intake was stable during all six treatment periods. Losartan and losartan/HCT lowered BP and proteinuria in all treatment groups. Patients with high potassium intake showed no difference in the BP effects compared with patients with low potassium intake. The antiproteinuric response to losartan monotherapy and losartan combined with HCT during the habitual sodium diet was significantly diminished in patients with high potassium intake (20% versus 41%, P = 0.011; and 48% versus 64%, P = 0.036). These differences in antiproteinuric response abolished when shifting to the LS diet.

Conclusions
In proteinuric CKD patients, the proteinuria, but not BP-lowering response to losartan during a habitual high-sodium diet was hampered during high potassium intake. Differences disappeared after sodium status change by LS diet.