bluuebunny/crossref_metadata_2025_split huggingface dataset:
ViMRT: a text-mining tool and search engine for automated virus mutation recognition
Authors: Tong Yuantao , Tan Fanglin , Huang Honglian , Zhang Zeyu , Zong Hui , Xie Yujia , Huang Danqi , Cheng Shiyang , Wei Ziyi , Fang Meng , Crabbe M James C , Wang Ying , Zhang Xiaoyan 
Published: November 2022

AbstractMotivationVirus mutation is one of the most important research issues which plays a critical role in disease progression and has prompted substantial scientific publications. Mutation extraction from published literature has become an increasingly important task, benefiting many downstream applications such as vaccine design and drug usage. However, most existing approaches have low performances in extracting virus mutation due to both lack of precise virus mutation information and their development based on human gene mutations.ResultsWe developed ViMRT, a text-mining tool and search engine for automated virus mutation recognition using natural language processing. ViMRT mainly developed 8 optimized rules and 12 regular expressions based on a development dataset comprising 830 papers of 5 human severe disease-related viruses. It achieved higher performance than other tools in a test dataset (1662 papers, 99.17% in F1-score) and has been applied well to two other viruses, influenza virus and severe acute respiratory syndrome coronavirus-2 (212 papers, 96.99% in F1-score). These results indicate that ViMRT is a high-performance method for the extraction of virus mutation from the biomedical literature. Besides, we present a search engine for researchers to quickly find and accurately search virus mutation-related information including virus genes and related diseases.Availability and implementationViMRT software is freely available at http://bmtongji.cn:1225/mutation/index.
Histopathological tumour response scoring in resected pancreatic cancer following neoadjuvant therapy: international interobserver study (ISGPP-1)
Authors: Janssen Boris V , van Roessel Stijn , van Dieren Susan , de Boer Onno , Adsay Volkan , Basturk Olca , Brosens Lodewijk , Campbell Fiona , Chatterjee Deyali , Chou Angela , Doglioni Claudio , Esposito Irene , Feakins Roger , Fuchs Talia L , Fukushima Noriyoshi , Gill Anthony J , Hong Seung-Mo , Hruban Ralph H , Kaplan Jeffrey , Krasinkas Alyssa , Luchini Claudio , Shi Chanjuan , Singhi Aatur , Thompson Elizabeth , Velthuysen Marie-Louise F , Besselink Marc G , Verheij Joanne , Wang Huamin , Verbeke Caroline , Fariña Arantza ,   for the International Study Group of Pancreatic Pathologists (ISGPP)
Published: November 2022

Abstract

Background
Most tumour response scoring systems for resected pancreatic cancer after neoadjuvant therapy score tumour regression. However, whether treatment-induced changes, including tumour regression, can be identified reliably on haematoxylin and eosin-stained slides remains unclear. Moreover, no large study of the interobserver agreement of current tumour response scoring systems for pancreatic cancer exists. This study aimed to investigate whether gastrointestinal/pancreatic pathologists can reliably identify treatment effect on tumour by histology, and to determine the interobserver agreement for current tumour response scoring systems.

Methods
Overall, 23 gastrointestinal/pancreatic pathologists reviewed digital haematoxylin and eosin-stained slides of pancreatic cancer or treated tumour bed. The accuracy in identifying the treatment effect was investigated in 60 patients (30 treatment-naive, 30 after neoadjuvant therapy (NAT)). The interobserver agreement for the College of American Pathologists (CAP) and MD Anderson Cancer Center (MDACC) tumour response scoring systems was assessed in 50 patients using intraclass correlation coefficients (ICCs). An ICC value below 0.50 indicated poor reliability, 0.50 or more and less than 0.75 indicated moderate reliability, 0.75 or more and below 0.90 indicated good reliability, and above 0.90 indicated excellent reliability.

Results
The sensitivity and specificity for identifying NAT effect were 76.2 and 49.0 per cent respectively. After NAT in 50 patients, ICC values for both tumour response scoring systems were moderate: 0.66 for CAP and 0.71 for MDACC.

Conclusion
Identification of the effect of NAT in resected pancreatic cancer proved unreliable, and interobserver agreement for the current tumour response scoring systems was suboptimal. These findings support the recently published International Study Group of Pancreatic Pathologists recommendations to score residual tumour burden rather than tumour regression after NAT.
Incidence, Clinical Characteristics, and Impact of Absent Echocardiographic Signs in Patients With Infective Endocarditis After Transcatheter Aortic Valve Implantation
Authors: Mangner Norman , Panagides Vassili , del Val David , Abdel-Wahab Mohamed , Crusius Lisa , Durand Eric , Ihlemann Nikolaj , Urena Marina , Pellegrini Costanza , Giannini Francesco , Gasior Tomasz , Wojakowski Wojtek , Landt Martin , Auffret Vincent , Sinning Jan-Malte , Cheema Asim N , Nombela-Franco Luis , Chamandi Chekrallah , Campelo-Parada Francisco , Munoz-Garcia Erika , Herrmann Howard C , Testa Luca , Kim Won-Keun , Eltchaninoff Helene , Søndergaard Lars , Himbert Dominique , Husser Oliver , Latib Azeem , Le Breton Hervé , Servoz Clement , Gervais Philippe , Côté Mélanie , Thiele Holger , Holzhey David , Linke Axel , Rodés-Cabau Josep 
Published: November 2022

AbstractBackgroundEchocardiography is the primary imaging modality for diagnosis of infective endocarditis (IE) in prosthetic valve endocarditis (PVE) including IE after transcatheter aortic valve implantation (TAVI). This study aimed to evaluate the characteristics and clinical outcomes of patients with absent compared with evident echocardiographic signs of TAVI-IE.MethodsPatients with definite TAVI-IE derived from the Infectious Endocarditis after TAVI International Registry were investigated comparing those with absent and evident echocardiographic signs of IE defined as vegetation, abscess, pseudo-aneurysm, intracardiac fistula, or valvular perforation or aneurysm.ResultsAmong 578 patients, 87 (15.1%) and 491 (84.9%) had absent (IE-neg) and evident (IE-pos) echocardiographic signs of IE, respectively. IE-neg were more often treated via a transfemoral access with a self-expanding device and had higher rates of peri-interventional complications (eg, stroke, major vascular complications) during the TAVI procedure (P &lt; .05 for all). IE-neg had higher rates of IE caused by Staphylococcus aureus (33.7% vs 23.2%; P = .038) and enterococci (37.2% vs 23.8%; P = .009) but lower rates of coagulase-negative staphylococci (4.7% vs 20.0%, P = .001). IE-neg was associated with the same dismal prognosis for in-hospital mortality in a multivariate binary regression analysis (odds ratio: 1.51; 95% confidence interval [CI]: .55–4.12) as well as a for 1-year mortality in Cox regression analysis (hazard ratio: 1.10; 95% CI: .67–1.80).ConclusionsEven with negative echocardiographic imaging, patients who have undergone TAVI and presenting with positive blood cultures and symptoms of infection are a high-risk patient group having a reasonable suspicion of IE and the need for an early treatment initiation.
Anti-Bolshevism and the periodical press in interwar Britain: the case of the Saturday Review, 1933–6
Authors: Vessey David 
Published: November 2022

Abstract
Using the example of the Saturday Review under the ownership of Lady Houston, this article explores how anti-Bolshevism was constituted in interwar Britain, and how the paper embodied the immoderate views of the radical Right, acting as a de facto promotional hub for a multifarious network of disaffected Conservatives. It shows how the Review integrated conspiratorial anti-Bolshevism into editorial argument and ostensible news provision, and how this found an attentive readership for a short-lived period. The article further demonstrates the utility of the periodical press for broadening historians’ engagement with overarching trends in politics and society during the interwar period.
Sitafloxacin pharmacokinetics/pharmacodynamics against multidrug-resistant bacteria in a dynamic urinary tract infection in vitro model
Authors: Guo Siwei , Li Xin , Li You , Tong Huan , Wei Minji , Yan Bingqian , Tian Miaomei , Xu Bing , Shao Jing 
Published: November 2022

Abstract

Objectives
Sitafloxacin is one of the newer generation fluoroquinolones with highly active against multidrug-resistant (MDR) bacteria. Our objectives were to identify the sitafloxacin pharmacokinetic/pharmacodynamic (PK/PD) index and breakpoints against MDR isolate in the urinary tract infection model.

Methods
Forty-eight MDR isolates underwent sitafloxacin and levofloxacin microdilution susceptibility testing. A 24 h in vitro model was established that simulated the healthy subjects urodynamics of sitafloxacin fumarate injection. Ten MDR isolates (four carbapenem-resistant Escherichia coli, three carbapenem-resistant P. aeruginosa and three vancomycin-resistant E. faecium) were selected. The drug efficacy was quantified by the change in log colony counts within 24 h. A sigmoid Emax model was fitted to the killing effect data. Monte Carlo simulations were performed to assess target attainment for the sitafloxacin fumarate doses of 100 and 200 mg q24h.

Results
Analysis indicated that the MICs of sitafloxacin were all significantly lower than that of levofloxacin (P &lt; 0.01). The UAUC0–24h/MIC targets required to achieve stasis, 1-log10 killing and 2-log10 killing were 63.60, 79.49 and 99.45 (carbapenem-resistant E. coli), 60.85, 90.31 and 128.95 (carbapenem-resistant P. aeruginosa), 65.91, 77.81 and 103.11 (vancomycin-resistant E. faecium). Monte Carlo simulation showed the infusion of sitafloxacin fumarate 100 mg q24h was able to achieve 90% probability of target attainment against bacteria with MIC of 8 mg/L for the common complicated urinary tract infections.

Conclusions
Sitafloxacin fumarate injection is an alternative therapeutic agent for the treatment of UTIs caused by MDR isolates.
Multicentre validation of a modified EUCAST MIC testing method and development of associated epidemiologic cut-off (ECOFF) values for rezafungin
Authors: Arendrup Maiken Cavling , Arikan-Akdagli Sevtap , Castanheira Mariana , Guinea Jesus , Locke Jeffrey B , Meletiadis Joseph , Zaragoza Oscar 
Published: November 2022

Abstract

Objectives
Rezafungin EUCAST MIC testing has been associated with notable inter-laboratory variation, which prevented ECOFF setting for C. albicans. We assessed in vitro susceptibility and reproducibility for a modified EUCAST methodology and established associated wild-type upper limits (WT-ULs).

Methods
MICs against 150 clinical Candida isolates (six species), molecularly characterized fks mutants (n = 13), and QC strains (n = 6) were determined at six laboratories according to E.Def 7.3 but using Tween 20 supplemented medium. WT-ULs were determined using the derivatization method, the ECOFFinder programme and visual inspection. Consensus WT-ULs were determined.

Results
The laboratory- and species-specific MIC distributions were Gaussian with &gt;99.5% MICs within four 2-fold dilutions except for C. parapsilosis (92.8%). The following consensus WT-UL were determined: C. albicans 0.008 mg/L; C. dubliniensis and C. glabrata 0.016 mg/L; C. krusei and C. tropicalis 0.03 mg/L; and C. parapsilosis 4 mg/L. Adopting these WT-UL, six clinical isolates were non-wild-type, five of which harboured Fks alterations. For 11/13 mutants, all 670 MICs were categorized as non-wild-type whereas MICs for C. glabrata Fks2 D666Y and C. tropicalis Fks1 R656R/G overlapped with the corresponding wild-type distributions. Repeat testing of six reference strains yielded 98.3%–100% of MICs within three 2-fold dilutions except for C. albicans CNM-CL-F8555 (96%) and C. parapsilosis ATCC 22019 (93.3%).

Conclusions
The modified EUCAST method significantly improved inter-laboratory variation, identified wild-type populations and allowed perfect separation of wild-type and fks mutants except for two isolates harbouring weak mutations. These consensus WT-UL have been accepted as ECOFFs and will be used for rezafungin breakpoint setting.
Protection of intellectual property rights during the Mobile World Congress
Authors: Monedero Montiano Monteagudo , García Pérez Javier 
Published: November 2022

Abstract
The Barcelona Mobile World Congress is one of the world’s largest events for the technology industry worldwide. This showcasing of creativity and innovation is also a prime opportunity for legal intellectual property violations to be committed with regard to copyright, trade marks, patents, designs, unfair competition law and advertising laws. In order to guarantee a fast, balanced and effective system of interim protection, the assemblies of commercial court judges of Barcelona and Alicante jointly adopt every year an on-call rapid response protocol. This unique protocol has proven to be a clear example of success in the protection of intellectual property rights on international exhibitions.
Detection of cesium in the atmosphere of the hot He-rich white dwarf HD 149499B
Authors: Chayer P , Mendoza C , Meléndez M , Deprince J , Dupuis J 
Published: November 2022

ABSTRACT
We report the first detection of cesium (Z = 55) in the atmosphere of a white dwarf. Around a dozen absorption lines of Cs iv, Cs v, and Cs vi have been identified in the Far Ultraviolet Spectroscopic Explorer spectrum of the He-rich white dwarf HD 149499B (Teff = 49 500 K, log g = 7.97). The lines have equivalent widths ranging from 2.3 to 26.9 mÅ. We performed a spectral synthesis analysis to determine the cesium content in the atmosphere. Non-local thermodynamic equilibrium atmosphere models were computed by considering cesium explicitly in the calculations. For this purpose we calculated oscillator strengths for the bound–bound transitions of Cs iv–Cs vi with both autostructure (multiconfiguration Breit–Pauli) and grasp2k (multiconfiguration Dirac–Fock) atomic structure codes as neither measured nor theoretical values are reported in the literature. We determined a cesium abundance of log N(Cs)/N(He) = −5.45 ± 0.35, which can also be expressed in terms of the mass fraction log XCs = −3.95 ± 0.35.
Modelling the magnetic structure of a large-scale horse-shoe-like filament in a decaying and diffuse active region
Authors: Kang Kaifeng , Guo Yang , Roussev Ilia I , Keppens Rony , Lin Jun 
Published: November 2022

ABSTRACTA large-scale, horse-shoe-like filament was investigated and the magnetic field around it was reconstructed. This is an intermediate filament (IF) that appeared on the solar disc for the first time at 02:00 ut on 2015 November 7, and took 8 d to move to the central median on the solar disc. The active region AR 12452 around which the filament occurred was diffuse so that the magnetic field nearby was weak, the average field strength is 106 G. Therefore, the existing approaches to extrapolating the coronal magnetic field and to constructing the filament configuration in the region with strong background field do not work well here. On the basis of the regularized Biot–Savart laws method, we successfully constructed a data-constrained, non-linear force-free field configuration for this IF observed on 2015 November 14. The overall IF configuration obtained in this way matches well the morphology suggested by a 304 Å image taken by the Atmospheric Imaging Assembly on board Solar Dynamics Observatory. Magnetic dips in the configuration were coincident in space with the H α features of the filament, which is lower in altitude than the features seen in 304 Å. This suggests that the cold plasma fills the lower part of the filament, and hot plasma is situated in the higher region. A quasi-separatrix layer wraps the filament, and both the magnetic field and the electric current are stronger near the inner edge of the filament.
Differences between the globular cluster systems of the Virgo and Fornax galaxy clusters
Authors: Dabringhausen Jörg , Fellhauer Michael , Mieske Steffen 
Published: November 2022

ABSTRACT
It is well-known that Globular cluster systems are different among galaxies. Here, we test to which degree these differences remain on the scale of galaxy clusters by comparing the globular clusters (GCs) in optical surveys of the Virgo galaxy cluster (ACSVCS) and the ACS Fornax galaxy cluster (ACSFCS) in Kolmogorov–Smirnoff Tests. Both surveys were obtained with the Advanced Camera for Surveys (ACS) on board the Hubble Space Telescope, and contain thousands of GCs in dozens of galaxies each. Also, well over 100 point sources in the Chandra X-ray Observatory source catalogue were attributed to the GCs in both optical catalogues, and interpreted as low-mass X-ray binaries (LMXBs). Thus, the optical and X-ray data are as uniform as possible. Our main findings are as follows: (1) The spread in luminosities and half-light radii is larger in the ACSVCS than in the ACSFCS. (2) The ratio between the half-light radii for the F475W-passband and the F850LP-passband is on average smaller in the ACSVCS. (3) The distribution of the LMXBs with the luminosity of the GCs is different between both surveys. These findings are significant. The first finding could be a consequence of a wider spread in the distances of the GCs in the ACSVCS, but the others must have internal reasons in the GCs. Thus, the GC systems are also different on a galaxy cluster scale.
The non-thermal secondary CMB anisotropies from a cosmic distribution of radio galaxy lobes
Authors: Acharya Sandeep Kumar , Majumdar Subhabrata , Nath Biman B 
Published: November 2022

ABSTRACT
Current and upcoming high angular resolution and multifrequency experiments are well poised to explore the rich landscape of secondary cosmic microwave background (CMB) anisotropies. In this context, we compute, for the first time, the power spectrum of CMB fluctuations from a cosmological distribution of evolving lobes of giant radio galaxies. We also explicitly take into account the non-thermal electron distribution, which has important implications for the inference of the CMB angular power spectrum. We calculate the mean global non-thermal y-distortion, 〈y〉NT. For observationally reasonable distribution of the jet luminosities in the range of 1045–1047 erg s−1, we find 〈y〉NT to be less than 10−5, and hence not violating the cosmic background explorer limit as previously claimed. Using the unique spectral dependence of the non-thermal Sunyaev–Zeldovich (SZ), we show that a detection of 〈y〉NT can be within reach at the level of ≳5σ from a future Primordial Inflation Explorer (PIXIE)-like experiment provided we understand the foregrounds precisely. The total non-thermal SZ power spectrum, $C^{\mathrm{ NT}}_\ell$, from the radio lobes peaks at ℓ ∼ 3000 with an amplitude $\sim 1{{\ \rm per\ cent}}$ of thermal SZ power spectrum from galaxy clusters. A detection of the $C^{\mathrm{ NT}}_\ell$, with a PIXIE-like sensitivity experiment, can lead to ∼5σ constraint on the mass dependence of the jet luminosity with the constraint becoming at least ten times better for the proposed more ambitious CMB-HD survey. This will further lead to the tightest constraint on the central black hole mass-to-host halo mass scaling relations.
LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations
Authors: Li Zhao , Liu Lin , Feng Changrui , Qin Yuxin , Xiao Jingfa , Zhang Zhang , Ma Lina 
Published: November 2022

Abstract
LncBook, a comprehensive resource of human long non-coding RNAs (lncRNAs), has been used in a wide range of lncRNA studies across various biological contexts. Here, we present LncBook 2.0 (https://ngdc.cncb.ac.cn/lncbook), with significant updates and enhancements as follows: (i) incorporation of 119 722 new transcripts, 9632 new genes, and gene structure update of 21 305 lncRNAs; (ii) characterization of conservation features of human lncRNA genes across 40 vertebrates; (iii) integration of lncRNA-encoded small proteins; (iv) enrichment of expression and DNA methylation profiles with more biological contexts and (v) identification of lncRNA–protein interactions and improved prediction of lncRNA-miRNA interactions. Collectively, LncBook 2.0 accommodates a high-quality collection of 95 243 lncRNA genes and 323 950 transcripts and incorporates their abundant annotations at different omics levels, thereby enabling users to decipher functional significance of lncRNAs in different biological contexts.
Design and population of the VALOR-CKD study: a multicenter, randomized, double-blind, placebo-controlled trial evaluating the efficacy and safety of veverimer in slowing progression of chronic kidney disease in patients with metabolic acidosis
Authors: Mathur Vandana S , Bushinsky David A , Inker Lesley , Klaerner Gerrit , Li Elizabeth , Parsell Dawn , Perkovic Vlado , Stasiv Yuri , Walker Michael , Wesson Donald E , Wheeler David C , Tangri Navdeep 
Published: November 2022

ABSTRACT

Background
Whether treating metabolic acidosis slows progression of chronic kidney disease (CKD) has not been established. Veverimer is a novel hydrochloric acid binder that removes acid from the gastrointestinal tract leading to an increase in serum bicarbonate; it is being developed to treat metabolic acidosis with the goal of slowing progression of CKD.

Methods
The VALOR-CKD trial is an international, randomized, multicenter, double-blind, placebo-controlled study designed to evaluate the effect of once-daily veverimer on kidney disease progression in patients with metabolic acidosis and CKD. Eligibility criteria include a serum bicarbonate in the range of 12–20 mmol/L and an estimated glomerular filtration rate (eGFR) of 20–40 mL/min/1.73 m2. The primary outcome is kidney disease progression defined as the development of end-stage kidney disease, a sustained decline in eGFR of &gt;40% from baseline or death due to kidney failure. Key secondary endpoints include effects on physical function.

Results
Between December 2018 and December 2021, 1480 participants were randomized. The mean age at baseline was 65.1 years and 42% of the patients were female. The mean baseline eGFR was 29.1 mL/min/1.73 m2 and mean serum bicarbonate was 17.5 mmol/L. The median urine albumin-to-creatinine ratio at screening was 201 mg/g and the median 5-year predicted risk of kidney failure was 32%. Diabetes and hypertension were present in 56% and 98% of participants, respectively.

Conclusions
VALOR-CKD has recruited a large population of people with metabolic acidosis at high risk for CKD progression to determine the effects of veverimer on the risk of progressive loss of kidney function.