bluuebunny/crossref_metadata_2025_split huggingface dataset:
SOMSpec as a General Purpose Validated Self-Organising Map Tool for Rapid Protein Secondary Structure Prediction From Infrared Absorbance Data
Authors: Pinto Corujo Marco , Olamoyesan Adewale , Tukova Anastasiia , Ang Dale , Goormaghtigh Erik , Peterson Jason , Sharov Victor , Chmel Nikola , Rodger Alison 
Published: January 2022

A protein’s structure is the key to its function. As protein structure can vary with environment, it is important to be able to determine it over a wide range of concentrations, temperatures, formulation vehicles, and states. Robust reproducible validated methods are required for applications including batch-batch comparisons of biopharmaceutical products. Circular dichroism is widely used for this purpose, but an alternative is required for concentrations above 10 mg/mL or for solutions with chiral buffer components that absorb far UV light. Infrared (IR) protein absorbance spectra of the Amide I region (1,600–1700 cm−1) contain information about secondary structure and require higher concentrations than circular dichroism often with complementary spectral windows. In this paper, we consider a number of approaches to extract structural information from a protein infrared spectrum and determine their reliability for regulatory and research purpose. In particular, we compare direct and second derivative band-fitting with a self-organising map (SOM) approach applied to a number of different reference sets. The self-organising map (SOM) approach proved significantly more accurate than the band-fitting approaches for solution spectra. As there is no validated benchmark method available for infrared structure fitting, SOMSpec was implemented in a leave-one-out validation (LOOV) approach for solid-state transmission and thin-film attenuated total reflectance (ATR) reference sets. We then tested SOMSpec and the thin-film ATR reference set against 68 solution spectra and found the average prediction error for helix (α + 310) and β-sheet was less than 6% for proteins with less than 40% helix. This is quantitatively better than other available approaches. The visual output format of SOMSpec aids identification of poor predictions. We also demonstrated how to convert aqueous ATR spectra to and from transmission spectra for structure fitting. Fourier self-deconvolution did not improve the average structure predictions.
Efficient Room-Temperature Phosphorescence from Discrete Molecules Based on Thianthrene Derivatives for Oxygen Sensing and Detection
Authors: Yang Zhiqiang , Zhao Shuaiqiang , Zhang Xiangyu , Liu Meng , Liu Haichao , Yang Bing 
Published: January 2022

In this work, two thianthrene (TA) derivatives, 1-phenylthianthrene (TA1P) and 2-phenylthianthrene (TA2P), were synthesized with single-phenyl modification for pure organic discrete-molecule room-temperature phosphorescence (RTP). They both show the dual emission of fluorescence and RTP in amorphous polymer matrix after deoxygenation, as a result of a new mechanism of folding-induced spin-orbit coupling (SOC) enhancement. Compared with TA1P, TA2P exhibits a higher RTP efficiency and a larger spectral separation between fluorescence and RTP, which is ascribed to the substituent effect of TA at the 2-position. With decreasing oxygen concentration from 1.61% to 0%, the discrete-molecule TA2P shows an about 18-fold increase in RTP intensity and an almost constant fluorescence intensity, which can make TA2P as a self-reference ratiometric optical oxygen sensing probe at low oxygen concentrations. The oxygen quenching constant (KSV) of TA2P is estimated as high as 10.22 KPa−1 for polymethyl methacrylate (PMMA)-doped film, and even reach up to 111.86 KPa−1 for Zeonex®-doped film, which demonstrates a very high sensitivity in oxygen sensing and detection. This work provides a new idea to design pure organic discrete-molecule RTP materials with high efficiency, and TA derivatives show a potential to be applied in quantitative detection of oxygen as a new-generation optical oxygen-sensing material.
Comparison of Clinical Outcomes Between Ticagrelor and Clopidogrel in Acute Coronary Syndrome: A Comprehensive Meta-Analysis
Authors: Sun Mengyi , Cui Weichen , Li Linping 
Published: January 2022

BackgroundTicagrelor is currently recommended for patients with the acute coronary syndrome (ACS). However, recent studies have yielded controversial results.ObjectiveTo compare the clinical outcomes between ticagrelor and clopidogrel in patients with ACS.MethodsThree electronic databases were queried until April 25, 2021. We defined major adverse cardiovascular events (MACEs) as the primary efficacy endpoint. The secondary efficacy endpoints included stroke, stent thrombosis, cardiovascular death, all-cause death, and myocardial infarction. The safety endpoints were (major and minor) bleeding. Odds ratios (ORs) and 95% CIs were calculated to represent the estimated effect sizes.ResultsA total of 270,937 patients with ACS from 10 clinical trials and 18 observational studies were included. No significant difference was detected in MACE (OR 0.81, 95% CI 0.60–1.08, p = 0.15, I2 = 64.83%). However, ticagrelor introduced a higher risk of bleeding (1.46, 1.17–1.83, 0.00, 61.66%) and minor bleeding (1.71, 1.33–2.21, 0.00, 4.65%) in clinical trials. The results of secondary efficacy endpoints differed in the clinical trials and observational studies. Subgroup analysis demonstrated that ticagrelor showed better therapeutic effects in patients who underwent the percutaneous coronary intervention (PCI) (0.38, 0.23–0.63, 0.00, 0) than those intended for PCI (1.03, 0.76–1.38, 0.87, 64.26%). Meanwhile, ticagrelor showed different therapeutic effects on patients with ACS of different ethnicities and different countries.ConclusionThis meta-analysis demonstrated that ticagrelor is not superior to clopidogrel in MACE but is associated with a higher risk of bleeding in patients with ACS. Different PCI strategies, ethnicities, and countries may be the factors that contribute to different therapeutic effects of ticagrelor.Systematic Review RegistrationThis study is registered with PROSPERO (CRD42021251212).
Serum IL-1, Pyroptosis and Intracranial Aneurysm Wall Enhancement: Analysis Integrating Radiology, Serum Cytokines and Histology
Authors: Liu Qingyuan , Zhang Yisen , Zhu Chengcheng , Liu Weiqi , Ma Xuesheng , Chen Jingang , Mo Shaohua , Dong Linggen , Wang Nuochuan , Wu Jun , Liu Peng , He Hongwei , Wang Shuo 
Published: January 2022

Background and PurposeAneurysm wall enhancement (AWE) is correlated with the rupture and growth risk of unruptured intracranial aneurysms (UIAs). Pyroptosis is a proinflammation mode of lytic cell death, mediated by pyroptosis-related proteins, i.e., gasdermin D and interleukin 1 β (IL-1β). Integrating serum cytokines and histology, this study aimed to investigate the correlation between AWE and pyroptosis in UIAs.MethodsUIA patients receiving microsurgical clipping were prospectively enrolled from January 2017 and June 2020. UIA samples were collected, as well as the corresponding blood samples. In this study, high-resolution magnetic resonance was employed to identify the AWE. The serum 46-cytokines examination and the histological analysis were conducted to determine pyroptosis, CD68 and MMP2. The IL-1 ra/beta ratio was determined by complying with the serum IL-1β and IL-1.ra. A comparison was drawn in the differences between UIAs with and without AWE. Lastly, the correlation between inflammation in UIA samples and serums was investigated.ResultsThis study included 34 UIA patients. The serum proinflammatory cytokines [IL-1β (P &lt; 0.001) and TNF-α (P &lt; 0.001)] were up-regulated, and serum anti-inflammatory cytokine (IL-1.ra, P = 0.042) were down-regulated in patients with AWE UIAs. The patients with AWE UIAs achieved a higher IL-1.ra/beta ratio (P &lt; 0.001). The multivariate logistic analysis demonstrated IL-1β [odds ratio (OR), 1.15; 95% confidence interval (CI), 1.02–1.30; P = 0.028] and IL-1.ra (OR, 0.998; 95% CI, 0.997–1.000; P = 0.017) as the risk factors correlated with the AWE. IL-1.ra/beta ratio achieved the highest predictive accuracy [area under the curve (AUC), 0.96] for AWE, followed by IL-1.ra (AUC, 0.90), IL-1β (AUC, 0.88) and TNF-α (AUC, 0.85). As compared with the UIAs without AWE, the AWE UIAs were manifested as a severer wall remodeling, with higher relative levels of pyroptosis-related proteins, CD68 and MMP2. The serum IL-1β, IL-1.ra and IL-1.ra/beta ratio had a positive correlation with the relative levels of pyroptosis-related proteins, CD68 and MMP2 in UIA tissues.ConclusionThe serum IL-1β and IL-1.ra were correlated with the AWE. More pyroptosis-related proteins were identified in UIAs with AWE. The serum IL-1β and IL-1.ra were correlated with the pyroptosis-related proteins in aneurysm tissues.
A ∼28-kyr Continuous Lacustrine Paleoseismic Record of the Intraplate, Slow-Slipping Fuyun Fault in Northwest China
Authors: Fan Jiawei , Xu Hongyan , Shi Wei , Guo Qiaoqiao , Zhang Siqi , Wei Xiaotong , Cai Minggang , Huang Shuaitang , Wang Jiangyong , Xiao Jule 
Published: January 2022

The Fuyun Fault is a typical intraplate, slow-slipping fault, but has been repeatedly ruptured by surface wave magnitude (Ms) ≥ 8.0 earthquakes. The 11 August 1931 Ms 8.0 Fuyun earthquake resulted in more than 10,000 casualties in the sparsely populated Fuyun area. Cosmogenic 10Be dating of offset landforms produced by prehistoric Ms ≥ 8.0 earthquakes yields an average recurrence interval of 9,700 ± 3,300 years, much longer than previously estimated 2,000–4,500 years, clouding our understanding of the timing and recurrence behavior of past earthquakes originating from the Fuyun Fault. Reflection seismic data reveal widely distributed subaquatic faults in Yileimu Lake, implying high sensitivity of the lake sediments to paleoearthquakes originating from the Fuyun Fault. Two new long sediment cores (Y20A: 267 cm; Y20B: 890 cm) together with previously published two short cores (Y19: 71 cm; Y20: 31.5 cm) from the depocenter and nearshore zone of Yileimu Lake are used for stratigraphic correlations and analyses of sedimentary structures, grain-size distributions, magnetic susceptibility, elemental composition and carbon content. The mass-wasting deposits with underlying soft-sediment deformation structures (SSDS) in the Y20B core indicate six siliciclastic-enriched sandy sediment fluxes from earthquake-triggered landslides of granitic rocks, and isolated SSDS record three additional earthquake-induced in situ deformations. Turbidite-like deposits with sorting indices &gt;3 and Si contents &gt;700 counts per second (cps) are comparable to those of the seismic mass-wasting deposits, and are thus interpreted as seismites from earthquake-induced re-deposition of nearshore sediments. There are a total of 20 seismic events recorded by the Y20B core. Seismic intensity calculation results, combined with historical seismic data, provide potential magnitudes of Ms ≥ 8.0, Ms ≥ 7.0, and Ms ≥ 5.5 for the earthquake-triggered mass-wasting deposits, SSDS, and turbidite-like seismites, respectively, in Yileimu Lake, generally consistent with previously published magnitude thresholds. Radiocarbon dating and stratigraphic correlations constrain the timing of these past earthquakes to ∼28 cal kyr BP. This unique, long lacustrine paleoseismic record suggests a weakly periodic pattern with recurrence intervals between 2,317 and 7,830 years and an average of 5,303 years for potential Ms ≥ 8.0 earthquakes, and reveals an unprecedented high frequency of potential Ms ≥ 7.0 earthquakes originating from the Fuyun Fault in the last 5 kyr, demonstrating the urgent need for an improved assessment of seismic hazards and risks in the Fuyun Fault zone.
Multiplex Antibody Analysis of IgM, IgA and IgG to SARS-CoV-2 in Saliva and Serum From Infected Children and Their Close Contacts
Authors: Dobaño Carlota , Alonso Selena , Vidal Marta , Jiménez Alfons , Rubio Rocío , Santano Rebeca , Barrios Diana , Pons Tomas Gemma , Melé Casas María , Hernández García María , Girona-Alarcón Mònica , Puyol Laura , Baro Barbara , Millat-Martínez Pere , Ajanovic Sara , Balanza Núria , Arias Sara , Rodrigo Melero Natalia , Carolis Carlo , García-Miquel Aleix , Bonet-Carné Elisenda , Claverol Joana , Cubells Marta , Fortuny Claudia , Fumadó Victoria , Codina Anna , Bassat Quique , Muñoz-Almagro Carmen , Fernández de Sevilla Mariona , Gratacós Eduard , Izquierdo Luis , García-García Juan José , Aguilar Ruth , Jordan Iolanda , Moncunill Gemma 
Published: January 2022

COVID-19 affects children to a lesser extent than adults but they can still get infected and transmit SARS-CoV-2 to their contacts. Field deployable non-invasive sensitive diagnostic techniques are needed to evaluate the infectivity dynamics of SARS-CoV-2 in pediatric populations and guide public health interventions, particularly if this population is not fully vaccinated. We evaluated the utility of high-throughput Luminex assays to quantify saliva IgM, IgA and IgG antibodies against five SARS-CoV-2 spike (S) and nucleocapsid (N) antigens in a contacts and infectivity longitudinal study in 122 individuals (52 children and 70 adults). We compared saliva versus serum/plasma samples in infected children and adults diagnosed by weekly RT-PCR over 35 days (n=62), and those who consistently tested negative over the same follow up period (n=60), in the Summer of 2020 in Barcelona, Spain. Saliva antibody levels in SARS-CoV-2 RT-PCR positive individuals were significantly higher than in negative individuals and correlated with those measured in sera/plasmas. Asymptomatic infected individuals had higher levels of anti-S IgG than symptomatic individuals, suggesting a protective anti-disease role for antibodies. Higher anti-S IgG and IgM levels in serum/plasma and saliva, respectively, in infected children compared to infected adults could also be related to stronger clinical immunity in them. Among infected children, males had higher levels of saliva IgG to N and RBD than females. Despite overall correlation, individual clustering analysis suggested that responses that may not be detected in blood could be patent in saliva, and vice versa.In conclusion, measurement of SARS-CoV-2-specific saliva antibodies should be considered as a complementary non-invasive assay to serum/plasma to determine COVID-19 prevalence and transmission in pediatric populations before and after vaccination campaigns.
Structure and Conductivity Correlation in NASICON Based Na3Al2P3O12 Glass: Effect of Na2SO4
Authors: Mandal Indrajeet , Chakraborty Saswata , Ghosh Manasi , Dey Krishna K. , Annapurna K. , Allu Amarnath R. 
Published: January 2022

Identifying the factors influencing the movement of sodium cations (Na+) in glasses accelerates the possible options of glass-based solid electrolyte materials for their applications as a promising electrolyte material in sodium-ion batteries. Nevertheless, due to the poor correlation between the structure and conductivity in glass materials, identifying the factors governing the conductivity still exists as a challenging task. Herein, we have investigated the DC-conductivity variations by correlating the structure and conductivity in sodium superionic conductor (NASICON) based Na3Al2P3O12 (NAP) glass (mol%: 37.5 P2O5—25.0 Al2O3—37.5 Na2O) due to the successive substitution of Na2SO4 for Al2O3. Structural variations have been identified using the Raman and magic-angle spinning nuclear magnetic resonance (MAS-NMR) (for 31P, 23Na, and 27Al nuclei) and conductivity measurements have been done using the impedance spectroscopy. From the ac-conductivity spectra, the correlations between mean square displacement (MSD) and dc-conductivity and between the Na+ concentration and dc-conductivity have also been evaluated. Raman spectra reveal that the increase in the Na2SO4 concentration increases the number of isolated SO42− sulfate groups that are charge compensated by the Na+ cations in the NAP glass. MAS-NMR spectra reveal that the increase in Na2SO4 concentration increases the concentration of non-bridging oxygens and further neither S-O-P nor S-O-Al bonds are formed. Impedance spectroscopy reveals that, at 373 K, the DC conductivity of the NAP glass increases with increasing the Na2SO4 up to 7.5 mol% and then decreases with the further increase. In the present study, we have shown that the mobility of sodium cations played a significant role in enhancing the ionic-conductivity. Further, we have shown that inter-ionic Coulombic interactions and the structural modification with the formation of SO42− units significantly influence the critical hopping length &lt; R2 (tp)&gt; of the sodium cations and consequently the mobility and the ionic conductivity. The present study clearly indicates that, based on the compositions, glass materials can also be treated as strong-electrolyte materials.
Which Is a Better Predictor of GFR Decline: 24-h Urine Protein or 24-h Protein–Creatinine Ratio? An Exploration of the MDRD Study Data
Authors: Ayoub Isabelle , Nagaraja Haikady N. , Kang Rima , Rovin Brad , Bhatt Udayan 
Published: January 2022

BackgroundProteinuria is a known risk factor for progression of chronic kidney disease. Proteinuria magnitude can be estimated by measuring spot urine protein-to-creatinine ratio (least accurate), 24-h urine collection for protein (24 P), or 24-h protein–creatinine ratio (24 PCR). The MDRD study found that 24 P measured at baseline was the strongest single predictor of the rate of GFR decline during study follow-up. However, predictive powers of 24 P and 24 PCR have not been compared in the literature. The current study addresses this question using the MDRD cohort data.MethodsThe study is a retrospective analysis of prospectively collected data from the MDRD cohort using simple and multiple regression models. Slope of measured GFR (mGFR) over time was used as the response and models that included baseline 24 PCR or 24 P were compared for the entire sample and for subgroups formed by restricting the values of 24-h creatinine and 24 P.ResultsLog 24 P and Log 24 PCR correlated almost equally with mGFR slope. However, in simple linear regression models and multivariable linear regression models adjusting for age and sex, the model with 24 PCR had a higher R2 than the corresponding one that had 24 P except for the subgroup 24 P &lt; 1 g.ConclusionWe observe that 24 PCR may be a better marker of proteinuria magnitude in predicting decline in kidney function compared to 24 P in particular for patients with 24 P ≥ 1. This finding needs validation in prospective clinical trials.
Management of Unruptured Small Multiple Intracranial Aneurysms in China: A Comparative Effectiveness Analysis Based on Real-World Data
Authors: Chen Jigang , Tong Xin , Feng Xin , Peng Fei , Niu Hao , Han Mingyang , Liu Lang , Zhao Yuanli , Wang Daming , Pan Yuesong , Liu Aihua 
Published: January 2022

BackgroundUnruptured small aneurysms with a size of &lt;7 mm were often followed conservatively. However, it is unknown whether unruptured small multiple intracranial aneurysms (MIAs) are better to be prophylactically treated or conservatively followed.ObjectiveWe aim to compare the effectiveness of different strategies regarding their management.MethodsA decision-analytic Markov model was built over a entire life cycle. The compared strategies include natural history, treat one aneurysm, treat both aneurysms, annual follow-up, biennial follow-up, and follow-up every 5 years. The inputs for the model were obtained from real-world data and related medical literature. Outcomes were measured in terms of quality-adjusted life-years (QALYs).ResultsTreat both aneurysms had the highest effectiveness of 15.36 QALYs and treat one aneurysm had the second-highest effectiveness of 15.11 QALYs. Probabilistic sensitivity analysis with 10,000 iterations showed that treat both aneurysms and treat one aneurysm were optimal in 67.28 and 17.91% of all cases, respectively. One-way and two-way sensitivity analyses showed that the result was sensitive to the proportion of moderate to severe disability after treating two aneurysms, mortality after treating two aneurysms, proportion of moderate to severe disability after treating one aneurysm, and rupture rate of small growing aneurysm. Either treat both aneurysms or treat one aneurysm would be the optimal strategy under most of the circumstances with the variations of these parameters.ConclusionFor patients with small unruptured MIAs, prophylactic coiling was superior to conservative management and at least one aneurysm should be treated.
Potato Consumption and Risk of Cardiovascular Mortality and Type 2 Diabetes After Myocardial Infarction: A Prospective Analysis in the Alpha Omega Cohort
Authors: Cruijsen Esther , Indyk Indira M. , Simon Anne W. E. , Busstra Maria C. , Geleijnse Johanna M. 
Published: January 2022

BackgroundHigher potato intake, especially French fries, was unfavorably associated with cardiometabolic endpoints in population-based studies. Little is known about this in patients with ischemic heart disease (IHD).ObjectiveTotal and boiled potatoes and French fries intake were examined in relation to cardiovascular disease (CVD) mortality, all-cause mortality, and type 2 diabetes mellitus (T2DM) risk in Dutch post-myocardial infarction (MI) patients of the Alpha Omega Cohort.MethodsWe analyzed 3,401 patients (60–80 years, 78% male), free from T2DM at baseline, with an MI ≤ 10 years before enrolment. Diet was assessed at baseline (2002–2006) using a 203-item validated Food Frequency Questionnaire (FFQ) that includes potato preparation methods. Cause-specific mortality was monitored through December 2018, and T2DM incidence (self-reported physician diagnosis and/or prescribed anti-diabetes medication) was monitored during the first 40 months of follow-up. Multivariable Cox models were used to obtain hazard ratios (HRs) for fatal endpoints and incident T2DM in tertiles of potato intake.ResultsPatients had a median total potato intake (mainly boiled) of 111 g/d, 96% consumed &gt;1 serving (200 g) per week. French fries were consumed by 48% of the patients (median of 6 g/d among consumers). During &gt;12 years of follow-up (38,987 person-years), 1,476 deaths occurred of which 641 were from CVD, 394 were from IHD, and 119 were from a stroke. Total and boiled potatoes were not associated with CVD mortality, but a higher risk of all-cause mortality was observed (HR: 1.07; 95% CI: 1.01, 1.14; per 50 g/d). Potato consumption tended to be positively associated with incident T2DM (186 cases; HR: 1.11, 95% CI: 0.94, 1.32; per 50 g/d). Results for French fries were inconsistent for all outcomes.ConclusionIn Dutch post-MI patients, potatoes (mainly boiled) were not associated with CVD mortality but possibly adversely associated with all-cause mortality and T2DM risk. These findings warrant confirmation in other IHD patient cohorts. The Alpha Omega Cohort is registered at ClinicalTrials.gov as NCT03192410.