bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of an expanded, in-house library and an optimized preparation method for the identification of fungal isolates using MALDI-TOF mass spectrometry
Authors: Zvezdanova Margarita Estreya , de Aledo Manuel González , López-Mirones José Israel , Ortega Jesús , Canut Andrés , Castro Carmen , Gomez Carmen , Hernáez Silvia , Oviaño Marina , Ercibengoa María , Alkorta Miriam , Muñoz Patricia , Rodriguez-Temporal David , Rodríguez-Sánchez Belén 
Published: April 2023

Abstract
The goal of this study was to validate an optimized sample preparation method for filamentous fungal isolates coupled with the use of an in-house library for the identification of moulds using Matrix Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) in a multicenter context. For that purpose, three Spanish microbiology laboratories participated in the identification of 97 fungal isolates using MALDI-TOF MS coupled with the Filamentous Fungi library 3.0 (Bruker Daltonics) and an in-house library containing 314 unique fungal references. The isolates analyzed belonged to 25 species from the genus Aspergillus, Fusarium, Scedosporium/Lomentospora, the Mucorales order and the Dermatophytes group. MALDI-TOF MS identification was carried out from hyphae resuspended in water and ethanol. After a high-speed centrifugation step, the supernatant was discarded and the pellet submitted to a standard protein extraction step. The protein extract was analyzed with the MBT Smart MALDI Biotyper system (Bruker Daltonics). The rate of accurate, species-level identification obtained ranged between 84.5% and 94.8% and the score values were 1.8 for 72.2–94.9% of the cases. Two laboratories failed to identify only one isolate of Syncephalastrum sp. and Trichophyton rubrum, respectively and three isolates could not be identified in the third center (F. proliferatum, n = 1; T.interdigitale, n = 2). In conclusion, the availability of an effective sample preparation method and an extended database allowed high rates of correct identification of fungal species using MALDI-TOF MS. Some species, such as Trichophyton spp. are still difficult to identify. Although further improvements are still required, the developed methodology allowed the reliable identification of most fungal species.
The eROSITA Final Equatorial-Depth Survey (eFEDS) – Splashback radius of X-ray galaxy clusters using galaxies from HSC survey
Authors: Rana Divya , More Surhud , Miyatake Hironao , Grandis Sebastian , Klein Matthias , Bulbul Esra , Chiu I-Non , Miyazaki Satoshi , Bahcall Neta 
Published: April 2023

ABSTRACT
We present the splashback radius measurements around the SRG/eROSITA eFEDS X-ray selected galaxy clusters by cross-correlating them with HSC S19A photometric galaxies. The X-ray selection is expected to be less affected by systematics related to projection that affects optical cluster finder algorithms. We use a nearly volume-limited sample of 109 galaxy clusters selected in 0.5–2.0 keV band having luminosity $L_X \gt 10^{43.5}\, {\rm erg \, s}^{-1}\, h^{-2}$ within the redshift z &lt; 0.75 and obtain measurements of the projected cross-correlation with a signal to noise of 17.43. We model our measurements to infer a 3D profile and find that the steepest slope is sharper than −3 and associate the location with the splashback radius. We infer the value of the 3D splashback radius $r_{\rm sp} = 1.45^{+0.30}_{-0.26}\, h^{-1}\, {\rm Mpc}$ . We also measure the weak-lensing signal of the galaxy clusters and obtain halo mass $\log [M_{\rm 200m}/ h^{-1}\, {\rm M_\odot }] = 14.52 \pm 0.06$ using the HSC-S16A shape catalogue data at the median redshift z = 0.46 of our cluster sample. We compare our rsp values with the spherical overdensity boundary $r_{\rm 200m} = 1.75 \pm 0.08\, h^{-1} \, {\rm Mpc}$ based on the halo mass, which is consistent within 1.2σ with the ΛCDM predictions. Our constraints on the splashback radius, although broad, are the best measurements thus far obtained for an X-ray selected galaxy cluster sample.
Measurement of the evolving galaxy luminosity and mass function using clustering-based redshift inference
Authors: Karademir Geray S , Taylor Edward N , Blake Chris , Cluver Michelle E , Jarrett Thomas H , Triani Dian P 
Published: April 2023

ABSTRACT
We develop a framework for using clustering-based redshift inference (cluster-$z$ ) to measure the evolving galaxy luminosity function (GLF) and galaxy stellar mass function (GSMF) using Wide-field Infrared Survey Explorer W1 (3.4 μm) mid-infrared photometry and positions. We use multiple reference sets from the Galaxy And Mass Assembly survey, Sloan Digital Sky Survey and Baryon Oscillation Spectroscopic Survey. Combining the resulting cluster-$z$ s allows us to enlarge the study area, and by accounting for the specific properties of each reference set, making best use of each reference set to produce the best overall result. Thus we are able to measure the GLF and GSMF over ∼7500 deg2 of the Northern Galactic Cap up to $z$ &lt; 0.6. Our method can easily be adapted for new studies with fainter magnitudes, which pose difficulties for the derivation of photo-$z$ s. With better statistics in future surveys this technique is a strong candidate for studies with new emerging data from, e.g. the Vera C Rubin Observatory, the Euclid mission or the Nancy Grace Roman Space Telescope.
Accurate mass–radius ratios for Hyades white dwarfs
Authors: Pasquini L , Pala A F , Salaris M , Ludwig H-G , Leão I , Weiss A , de Medeiros J R 
Published: April 2023

ABSTRACT
We use the ESPRESSO spectrograph at the Very Large Telescope to measure velocity shifts and gravitational redshifts of eight bona fide Hyades white dwarfs, with an accuracy better than 1.5 per cent. By comparing the gravitational redshift measurements of the mass-to-radius ratio with the same ratios derived by fitting the Gaia photometry with theoretical models, we find an agreement to better than one per cent. It is possible to reproduce the observed white dwarf cooling sequence and the trend of the mass-to-radius ratios as a function of colour using isochrones with ages between 725 and 800 Myr, tuned for the Hyades. One star, EGGR 29, consistently stands out in all diagrams, indicating that it is possibly the remnant of a blue straggler. We also computed mass-to-radius ratios from published gravities and masses, determined from spectroscopy. The comparison between photometric and spectroscopic stellar parameters reveals that spectroscopic effective temperature and gravity are systematically larger than the photometric values. Spectroscopic mass-to-radius ratios disagree with those measured from gravitational redshift, indicating the presence of systematics affecting the white dwarf parameters derived from the spectroscopic analysis.
A model of EUV emission from clusters of galaxies
Authors: Lieu Richard , Shi Chun-Hui 
Published: April 2023

ABSTRACT
With tantalizing evidence of the recent e-Rosita mission, re-discovering very soft X-rays and Extreme-Ultraviolet (EUV) radiation from a cluster of galaxies or its environment, the question of the origin of cluster EUV excess is revisited in this work. It will be shown that the gas temperature, density, and frozen-in magnetic field of the intracluster medium, collectively support the emission and propagation of coherent C̆erenkov radiation, which is low frequency and large amplitude radiation capable of accelerating charged particles to relativistic speeds. Owing to the spectrum of C̆erenkov radiation, most of the incipient relativistic electrons undergo inverse-Compton scattering with the cosmic microwave background. It turns out the scattered radiation has observable ramifications only in the EUV band, of photon energy 70–100 eV, having a luminosity ≈1044 ergs s−1. This luminosity is on par with the EUV excess level detected from Abell 1795 and the Coma cluster. It should be stressed, as caveat emptor, that although the main subject is the putative large amplitude coherent C̆erenkov modes which are highly non-linear, the results presented were derived using a quasi-linear approach to highlight the observable features of the phenomenon, namely, the EUV emission.
Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers
Authors: McGuffin Liam J , Edmunds Nicholas S , Genc Ahmet G , Alharbi Shuaa M A , Salehe Bajuna R , Adiyaman Recep 
Published: April 2023

Abstract
The IntFOLD server based at the University of Reading has been a leading method over the past decade in providing free access to accurate prediction of protein structures and functions. In a post-AlphaFold2 world, accurate models of tertiary structures are widely available for even more protein targets, so there has been a refocus in the prediction community towards the accurate modelling of protein-ligand interactions as well as modelling quaternary structure assemblies. In this paper, we describe the latest improvements to IntFOLD, which maintains its competitive structure prediction performance by including the latest deep learning methods while also integrating accurate model quality estimates and 3D models of protein-ligand interactions. Furthermore, we also introduce our two new server methods: MultiFOLD for accurately modelling both tertiary and quaternary structures, with performance which has been independently verified to outperform the standard AlphaFold2 methods, and ModFOLDdock, which provides world-leading quality estimates for quaternary structure models. The IntFOLD7, MultiFOLD and ModFOLDdock servers are available at: https://www.reading.ac.uk/bioinf/.
PASSer: fast and accurate prediction of protein allosteric sites
Authors: Tian Hao , Xiao Sian , Jiang Xi , Tao Peng 
Published: April 2023

AbstractAllostery refers to the biological process by which an effector modulator binds to a protein at a site distant from the active site, known as allosteric site. Identifying allosteric sites is essential for discovering allosteric process and is considered a critical factor in allosteric drug development. To facilitate related research, we developed PASSer (Protein Allosteric Sites Server) at https://passer.smu.edu, a web application for fast and accurate allosteric site prediction and visualization. The website hosts three trained and published machine learning models: (i) an ensemble learning model with extreme gradient boosting and graph convolutional neural network, (ii) an automated machine learning model with AutoGluon and (iii) a learning-to-rank model with LambdaMART. PASSer accepts protein entries directly from the Protein Data Bank (PDB) or user-uploaded PDB files, and can conduct predictions within seconds. The results are presented in an interactive window that displays protein and pockets’ structures, as well as a table that summarizes predictions of the top three pockets with the highest probabilities/scores. To date, PASSer has been visited over 49 000 times in over 70 countries and has executed over 6 200 jobs.
Phase II Trial of MEDI0457 and Durvalumab for Patients With Recurrent/Metastatic Human Papillomavirus-Associated Cancers
Authors: Morris Van K , Jazaeri Amir , Westin Shannon N , Pettaway Curtis , George Solly , Huey Ryan W , Grinsfelder Michaela , Shafer Aaron , Johnson Benny , Vining David , Guo Ming , Fellman Bryan , Frumovitz Michael 
Published: April 2023

Abstract

Background
Human papillomavirus (HPV) types 16/18 drive oncogenesis for most patients with cervical, anal, and penile cancers. MEDI0457, a therapeutic DNA vaccine containing plasmids for E6 and E7 HPV-16/18 viral oncogenes and IL-12 adjuvant, is safe and provokes an immune response against E6/E7. We tested MEDI0457 with the anti-PD-L1 antibody durvalumab for patients with HPV-associated cancers.

Methods
Patients with recurrent/metastatic, treatment-refractory HPV-16/18 cervical cancer, or rare HPV-associated (anal and penile) cancers were eligible. Prior immune checkpoint inhibition was not permitted. Patients received MEDI0457 7 mg intramuscularly (weeks 1, 3, 7, 12, and every 8 weeks thereafter) and durvalumab 1500 mg intravenously every 4 weeks. The primary endpoint was overall response (RECIST 1.1). In this Simon two-stage phase 2 trial (Ho: p &lt; 0.15; Ha: p ≥ 0.35), ≥2 responses were needed in both cervical and non-cervical cohorts during the first stage for the trial to proceed to stage 2 with an additional 25 patients (34 total) enrolled.

Results
Twenty-one patients (12 cervical, 7 anal, and 2 penile) were evaluable for toxicity and 19 for response Overall response rate was 21% (95% CI, 6%-46%) among evaluable patients. Disease control rate was 37% (95% CI, 16%-62%). Median duration of response among responders was 21.8 months (95% CI, 9.7%-not estimable). Median progression-free survival was 4.6 months (95% CI, 2.8%-7.2%). Median overall survival was 17.7 months (95% CI, 7.6%-not estimable). Grades 3-4 treatment-related adverse events occurred in 6 (23%) participants.

Conclusions
The combination of MEDI0457 and durvalumab demonstrated acceptable safety and tolerability in patients with advanced HPV-16/18 cancers. The low ORR among patients with cervical cancer led to study discontinuation despite a clinically meaningful disease control rate.
Development of a Multivariate Prognostic Model for Lenvatinib Treatment in Hepatocellular Carcinoma
Authors: Li Xiaomi , Ding Xiaoyan , Liu Mei , Wang Jingyan , Li Wei , Chen Jinglong 
Published: April 2023

Abstract

Background
Lenvatinib is a first-line agent for advanced hepatocellular carcinoma (HCC), but individual responses to treatment are highly heterogeneous. The aim of this study was to investigate the clinical parameters that influence the efficacy of Lenvatinib and to develop a prognostic model.

Methods
We retrospectively enrolled 333 Lenvatinib-treated patients with HCC with a median age of 57 years. Two hundred nd sixty-three of these patients had BCLC (2022) stage C. The median overall survival (mOS) time within the cohort was 12.1 months, and the median progression-free survival (mPFS) time was 4.7 months. Univariate Cox regression, best subset regression, and Lasso regression were used to screen primary variables for possible contribution to OS, multivariate Cox analysis was used to fit selected models, and the final model was selected using the maximum area under the curve (AUC) and minimum AIC. Receiver operating curves (ROC), calibration curves, and decision curve analysis were plotted to assess model performance, and 5-fold cross-validation was performed for internal validation. X-tile software was used to select the best cutoff points and to divide the study cohort into 3 different risk groups.

Results
Seven variables were included in the final model: BCLC stage, prior transarterial chemoembolization and immunotherapy history, tumor number, prognostic nutritional index, log (alpha-fetoprotein), and log (platelet-to-lymphocyte ratio). We named this final model the “multivariate prognostic model for Lenvatinib” (MPML), and a nomogram was constructed to predict the probability of survival at 6, 9, and 12 months. The MPML had good discrimination, calibration, and applicability. Cross-validation showed mean AUC values of 0.7779, 0.7738, and 0.7871 at 6, 9, and 12 months, respectively. According to nomogram points, mOS time was 21.57, 8.70, and 5.37 months in the low, medium, and high-risk groups, respectively (P &lt; .001), and these differences were also observed in the PFS survival curve (P &lt; .001).

Conclusions
The MPML stratified patients according to baseline clinical characteristics had a strong performance in predicting Lenvatinib efficacy and has the potential for use as an auxiliary clinical tool for individualized decision-making.
Perioperative Chemotherapy Could Not Improve the Prognosis of Gastric Cancer Patients With Mismatch Repair Deficiency: A Multicenter, Real-World Study
Authors: Zhao Lulu , Fu Yongliang , Niu Penghui , Zhang Fan , Jiao Fuzhi , Zhou Xiadong , Wu Zhenkun , Wang Wanqing , Luan Xiaoyi , Han Xue , He Mingyan , Guan Quanlin , Li Yumin , Zhao Dongbing , Gao Jidong , Chen Yingtai 
Published: April 2023

Abstract

Introduction
To date, the role of deficient mismatch repair (dMMR) remains to be proven in gastric cancer, and it is difficult to judge its value in clinical application. Our study aimed to investigate how MMR status affected the prognosis in patients with gastrectomy, as well as the efficacy of neoadjuvant chemotherapy and adjuvant chemotherapy in patients with dMMR with gastric cancer.

Materials and Methods
Patients with gastric cancer with certain pathologic diagnosis of dMMR or proficient MMR (pMMR) using immunohistochemistry from 4 high-volume hospitals in China were included. Propensity score matching was used to match patients with dMMR or pMMR in 1:2 ratios. Overall survival (OS) and progression-free survival (PFS) curves were plotted using the Kaplan-Meier method and compared statistically using the log-rank test. Univariate and multivariate Cox proportional hazards models based on hazard ratios (HRs) and 95% confidence intervals (CIs) were used to determine the risk factors for survival.

Results
In total, data from 6176 patients with gastric cancer were ultimately analyzed, and loss of expression of one or more MMR proteins was observed in 293 patients (293/6176, 4.74%). Compared to patients with pMMR, patients with dMMR are more likely to be older (≥66, 45.70% vs. 27.94%, P &lt; .001), distal location (83.51% vs. 64.19%, P &lt; .001), intestinal type (42.21% vs. 34.46%, P &lt; .001), and in the earlier pTNM stage (pTNM I, 32.79% vs. 29.09%, P = .009). Patients with gastric cancer with dMMR showed better OS than those with pMMR before PSM (P = .002); however, this survival advantage was not observed for patients with dMMR after PSM (P = .467). As for perioperative chemotherapy, results of multivariable Cox regression analysis showed that perioperative chemotherapy was not an independent prognostic factor for PFS and OS in patients with dMMR with gastric cancer (HR = 0.558, 95% CI, 0.270-1.152, P = .186 and HR = 0.912, 95% CI, 0.464-1.793, P = .822, respectively).

Conclusion
In conclusion, perioperative chemotherapy could not prolong the OS and PFS of patients with dMMR with gastric cancer.
Policing re-centralization or de-centralization? A study of state responses in England and Hong Kong during COVID-19
Authors: Chan Jason Kwun-hong , McCarthy Daniel , Ho Lawrence Ka-Ki 
Published: April 2023

Abstract
The persisting challenge of COVID-19 is urging states to respond with evolving strategies via policing systems. Policing systems are now mandated with new tasks beyond daily maintenance of law and order. First, states rely largely on empowering the public police officers as sovereign enforcers against COVID-19. Yet, the enforcement of COVID-19 displays considerable variation across nations, despite the existence of specific laws designed to curtail behaviour. This study seeks to analyse and explain the diverged pattern of policing during the pandemic via the experiences of Hong Kong and England. Different severity of quarantine, social distancing, and lockdown orders have been imposed in both Hong Kong and England since March 2020, but with different levels of engagement in pandemic policing. Our paper explains how and why England (de-centralized and comparatively light policing) and Hong Kong (aggressive, re-centralized policing response) have experienced such divergences in policing response.
Understanding Factors Associated with Burnout Symptoms amongst Investigators working on Rape and Serious Sexual Offence (RASSO) investigations in England and Wales
Authors: Sondhi Arun , Harding Richard , Maguire Linda , Williams Emma 
Published: April 2023

Abstract
Prolonged stress leading to job-related burnout is of increasing interest in policing. Police officers involved in rape and serious sexual offences (RASSO) investigations experience heightened scrutiny alongside increased forensic demands whilst providing an accountable, victim-orientated service. The objective of the study was to examine correlates associated with burnout symptoms [emotional exhaustion (EE), depersonalization and lack of personal accomplishment (PA)]. RASSO investigators (n = 538) completed a cross-sectional online survey across five police force areas in England and Wales. Measures were screened using the Least Absolute Shrinkage and Selection Operator method, and three regression models were run against the three outcome measures. Excessive job demands encompassing workload, work–life balance and team pressures from colleagues and managers were strongly related to EE and DP. Male officers reported elevated levels of depersonalization. The learning climate was associated with all three burnout measures. The findings suggest that creating an effective learning environment for RASSO investigations and establishing effective organizational health policies to enhance team cohesion can reduce burnout. Further work is required to understand male officers’ higher levels of depersonalization.
Regulating low wages: cross-national policy variation and outcomes
Authors: Pedersen Siri Hansen , Picot Georg 
Published: April 2023

Abstract
This article provides a comparative analysis of three central policies to regulate low wages: statutory minimum wages, state support for collective bargaining and topping up low wages with public transfers (in-work benefits). We map the variation of these policies across 33 OECD countries and analyze the incidence of low-wage employment they are associated with. We find three approaches to regulating low wages. In the first, ‘wage scale protection’, states put most emphasis on supporting collective bargaining. In the second, ‘bare minimum’, there is not much else than the statutory minimum wage. In the third, ‘state pay’, the statutory minimum wage is supplemented by sizeable public financial support for low earners. When analyzing policy outcomes, ‘wage scale protection’ is associated with least low-wage employment. For ‘bare minimum’, much depends on the level of the statutory minimum wage. Although ‘state pay’ props up workers’ disposable income, many workers receive low gross pay.