bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic Epidemiology of Fluoroquinolone-Resistant Strains of Shigella sonnei and Shigella flexneri in the Iberian Peninsula From 2015 to 2022
Authors: Jacqueline Camille , Minetti Corrado , Monzon Fernandez Sara , Silveira Leonor , Cuesta De La Plaza Isabel , Pista Ângela , Herrera-Leon Silvia 
Published: November 2024

Abstract
Fluoroquinolone resistance in Shigella is among the serious antimicrobial resistance threats. We investigated the genomic epidemiology of fluoroquinolone-resistant (FQR) strains of S sonnei and S flexneri from 2015 to 2022 in Spain and Portugal. We determined the antimicrobial resistance profiles of 416 isolates (S flexneri and S sonnei), and FQR isolates were subjected to whole genome sequencing. The percentage of FQR isolates gradually increased to reach 38% and 80% of S flexneri and S sonnei isolates, respectively, in 2022. S sonnei isolates from men were significantly more likely to be FQR (relative risk, 4.9; 95% CI, 2.7–9.0). Genomic analysis revealed 2 major genetic clusters of FQR S sonnei from the CipR.MSM5 lineage, previously associated with extreme antimicrobial resistance and transmission in men having sex with men. This study contributes to a better understanding of FQR shigellosis transmission and highlights the added value of enhanced surveillance for these pathogens.
Characterization of NWM-1, a novel subclass B3 metallo-β-lactamase found in a clinical isolate of Pseudomonas aeruginosa
Authors: Höfken Lisa-Marie , Schauer Jennifer , Eisfeld Jessica , Dziobaka Jan , Gatermann Sören G , Pfennigwerth Niels 
Published: November 2024

Abstract

Objectives
To investigate the carbapenem resistance mechanism of a carbapenem-resistant clinical Pseudomonas aeruginosa isolate.

Methods
A clinical isolate of P. aeruginosa was sent to the German National Reference Centre for multidrug-resistant Gram-negative bacteria for carbapenemase detection. Phenotypic tests for carbapenemase detection and an EDTA-combined disc test were positive, therefore PCR-screenings were done for the most prevalent metallo-β-lactamase (MBL) encoding genes. As no MBL gene could be found, whole-genome sequencing was performed. For characterization, heterologous expression in a E. coli strain with subsequent MIC testing and purification of the new MBL to determine enzyme kinetics with in vitro hydrolysis assays was performed.

Results
WGS revealed the putative gene for a B3 MBL located on the chromosome between several disrupted IS elements with 67% identity to EVM-1, which was named NWM-1. MIC studies and enzyme kinetics confirmed MBL activity. No activity against ceftazidime was observed.

Conclusions
The identification of NWM-1 shows the importance of WGS to identify yet unknown carbapenemases and underlines the diversity of subclass B3 β-lactamases. It also shows that although several carbapenemase variants have already been identified and characterized, there are always new variants to be found in clinical isolates.
Maximum a posteriori Ly α estimator (MAPLE): band power and covariance estimation of the 3D Ly α forest power spectrum
Authors: Horowitz Benjamin , de Belsunce Roger , Lukić Zarija 
Published: November 2024

ABSTRACT
We present a novel maximum a posteriori estimator to jointly estimate band powers and the covariance of the three-dimensional power spectrum (P3D) of Ly $\alpha$ forest flux fluctuations, called MAPLE. Our Wiener-filter based algorithm reconstructs a window-deconvolved P3D in the presence of complex survey geometries typical for Ly $\alpha$ surveys that are sparsely sampled transverse to and densely sampled along the line of sight. We demonstrate our method on idealized Gaussian random fields with two selection functions: (i) a sparse sampling of 30 background sources per square degree designed to emulate the current Dark Energy Spectroscopic Instrument; (ii) a dense sampling of 900 background sources per square degree emulating the upcoming Prime Focus Spectrograph Galaxy Evolution Survey. Our proof-of-principle shows promise, especially since the algorithm can be extended to marginalize jointly over nuisance parameters and contaminants, i.e. offsets introduced by continuum fitting. Our code is implemented in JAX and is publicly available on GitHub.
Chemodynamic evolution of Sun-like stars in nearby moving groups
Authors: Lehmann Christian , Murphy Michael T , Liu Fan , Flynn Chris 
Published: November 2024

ABSTRACT
Sun-like stars are well represented in the solar neighbourhood but are currently underutilized, with many studies of chemical and kinematic evolution focusing on red giants (which can be observed further away) or turn-off stars (which have well-measured ages). Recent surveys (e.g. GALAH) provide spectra for large numbers of nearby Sun-like stars, which provides an opportunity to apply our newly developed method for measuring metallicities, temperatures, and surface gravities – the ${\small EPIC}$ algorithm – which yields improved ages via isochrone fitting. We test this on moving groups, by applying it to the large GALAH DR3 sample. This defines a sample of $72\,288$ solar analogue targets for which the stellar parameter measurements are most precise and reliable. These stars are used to estimate, and test the accuracy and precision of, age measurements derived with the samd isochrone fitting algorithm. Using these ages, we recover the age–metallicity relationships for nearby ($\lesssim 1 \,{\rm kpc}$) moving groups, traced by solar analogues, and analyse them with respect to the stellar kinematics. In particular, we found that the age–metallicity relationships of all moving groups follow a particular trend of young ($\textrm {age}\lt 6 \,{\rm Gyr}$) stars having constant metallicity and older ($\textrm {age} \ge 6 \,{\rm Gyr}$) stars decreasing in metallicity with increasing age. The Hercules stream carries the highest fraction of metal-rich young stars ($\sim 0.1 \,{\rm dex}$) in our sample, which is consistent with a migrating population of stars from the inner Galaxy, and we discuss the possible causes of this migration in the context of our results.
Logistic regression to boost exoplanet detection performances
Authors: Cambazard Hadrien , Catusse Nicolas , Chomez Antoine , Lagrange Anne-Marie 
Published: November 2024

ABSTRACT
Direct imaging of exoplanets requires to separate the background noise from the exoplanet signals. Statistical methods have been recently proposed to avoid subtracting any signal of interest as opposed to initial self-subtracting methods based on angular differential imaging (ADI). However, unless conservative thresholds are chosen to claim for a detection, such approaches tend to produce a list of candidates that include many false positives. Choosing high, conservative, thresholds leads to miss the faintest planets. We extend a statistical framework with a logistic regression to filter the list of candidates. Features with physical/optical meaning (in two wavelengths) are used, leading to a very fast and pragmatic approach. The overall method requires a simple edge detection (image processing) and clustering algorithm to work with sub-images. To estimate its efficiency, we apply our approach to targets observed with the European Southern Observatory/SPHERE (Spectro-Polarimetric High-contrast Exoplanet REsearch) high contrast imager, that were previously used as tests for blind surveys. Experimental results with injected signals show that either the number of false detections is considerably reduced or faint exoplanets that would otherwise not be detected can be sometimes found. Typically, on the blind tests performed, we are now able to detect around 50 per cent more of the injected planets with a signal-to-noise ratio below 5, and with a very low number of additional candidates.
Exploring the convective core of the high-amplitude δ Scuti star TIC 120857354 with asteroseismology
Authors: Chen Xinghao , Zhang Xiaobin , Li Yan 
Published: November 2024

ABSTRACT
Based on 2-min cadence TESS data, 20 confident independent frequencies were identified for the star TIC 120857354. The Kolmogorov–Smirnov test reveals a rotational splitting of 2.40 $\mu$Hz and a uniform frequency spacing of 74.6 $\mu$Hz. Subsequently, five sets of rotational splittings were discerned, including a quintuplet and four pairs of doublets, aligning with the characteristics of p-mode rotational splitting. Based on the sets of rotational splittings and the uniform frequency spacing, we finally identified four radial modes, six dipole modes, and 10 quadrupole modes. Furthermore, we found that the frequency separations within the $\ell$ = 2 sequences show a decreasing trend towards lower order modes, analogous to the $\ell$ = 0 sequences. A grid of theoretical models were computed to match the identified frequencies, revealing that TIC 120857354 is a main-sequence star with M = 1.54 $\pm$ 0.04 $\mathrm{M}_{\odot }$, Z = 0.015 $\pm$ 0.003, $T_{\rm eff}$ = 7441 $\pm$ 370 K, $\log g$ = 4.27 $\pm$ 0.01, R = 1.52 $\pm$ 0.01 $\mathrm{R}_{\odot }$, L = 6.33 $\pm$ 1.53 $\mathrm{L}_{\odot }$, age = 0.53 $\pm$ 0.07 Gyr, and $X_\mathrm{ c}/X_0$ = 0.84 $\pm$ 0.05. In-depth analyses suggest that $\ell$ = 2 may be p-dominated mixed modes with pronounced g-mode characteristics, enabling us to probe deeper into interiors of the star and determine the relative size of the convective core to be $R_\mathrm{ c}/R$ = 0.092 $\pm$ 0.002.
The JCMT BISTRO Survey: the magnetized evolution of star-forming cores in the Ophiuchus molecular cloud interpreted using histograms of relative orientation
Authors: Perry James P , Pattle Kate , Johnstone Doug , Kwon Woojin , Bourke Tyler L , Chung Eun Jung , Coudé Simon , Doi Yasuo , Fanciullo Lapo , Hwang Jihye , Khan Zacariyya A , Kwon Jungmi , Lai Shih-Ping , Le Gouellec Valentin J M , Lee Chang Won , Ohashi Nagayoshi , Sadavoy Sarah , Savini Giorgio , Sharma Ekta , Tamura Motohide 
Published: November 2024

ABSTRACT
The relationship between B-field orientation and density structure in molecular clouds is often assessed using the histogram of relative orientations (HRO). We perform a plane-of-the-sky geometrical analysis of projected B-fields, by interpreting HROs in dense, spheroidal, pre-stellar, and protostellar cores. We use James Clerk Maxwell Telescope POL-2 850 $\mu$m polarization maps and Herschel column density maps to study dense cores in the Ophiuchus molecular cloud complex. We construct two-dimensional core models, assuming Plummer column density profiles and modelling both linear and hourglass B-fields. We find that high-aspect ratio ellipsoidal cores produce strong HRO signals, as measured using the shape parameter $\xi$. Cores with linear fields oriented $&lt;\!\! 45 ^{\circ }$ from their minor axis produce constant HROs with $-1 \lt \xi \lt 0$, indicating that fields are preferentially parallel to column density gradients. Fields parallel to the core minor axis produce the most negative value of $\xi$. For low-aspect ratio cores, $\xi \approx 0$ for linear fields. Hourglass fields produce a minimum in $\xi$ at intermediate densities in all cases, converging to the minor-axis-parallel linear field value at high and low column densities. We create HROs for six dense cores in Ophiuchus. $\rho$ Oph A and IRAS 16293 have high aspect ratios and preferentially negative HROs, consistent with moderately strong field behaviour. $\rho$ Oph C, L1689A, and L1689B have low aspect ratios, and $\xi \approx 0$. $\rho$ Oph B is too complex to be modelled using a simple spheroidal field geometry. We see no signature of hourglass fields, agreeing with previous findings that dense cores generally exhibit linear fields on these size scales.
10257- GEN-15 CURRENT STATUS AND UTILITY OF CANCER GENE PANEL TESTING
Authors: Ohba Shigeo , SUDO Tamotsu , Sugihara Eiji , Takimoto Tetsuya , Mase Tatsunori , Tanaka Shiho , Matsumura Kazuyasu , Fujiwara Eiji , Kojima Daijiro , Kumon Masanobu , Yamada Seiji , Joko Masahiro , Nakae Shunsuke , Nishiyama Yuya , Muto Jun , Adachi Kazuhide , Inoue Tatsushi , Kawada Kenji , Abe Masato , Saya Hideyuki , Hirose Yuichi 
Published: November 2024

Abstract
In recent years, cancer gene panel testing has been covered by insurance, and its utility has been reported. At our institution, in addition to the insurance-covered cancer gene panel test, we have conducted the PleSSision-Rapid test, which can measure 156 genes, on various tumors as part of clinical research. The insurance-covered panel test was conducted in 37 cases, 86% of which were gliomas. Gene abnormalities leading to therapeutic drugs were identified in 5 cases (TMB high: 3 cases, NTRK2 fusion gene: 1 case, FGFR1: 1 case). On the other hand, in the clinical research panel testing, analysis was performed on 142 cases, including 54 cases of glioma, 49 cases of meningioma, and 16 cases of metastatic brain tumors. The clinical research panel test serves three main purposes: (1) diagnostic assistance, (2) screening before insurance-covered panel testing, and (3) research based on genetic analysis. For diagnostic assistance, it is possible to evaluate genes such as IDH1/2, TP53, ATRX, TERT promoter, and CDKN2A. In screening, in 11 cases where both tests were performed, mutations such as TMB high and FGFR1, identified in the insurance-covered panel, could also be detected. In research, frequent mutations in glioblastoma, including TERT promoter, KDM6, RB1, PTEN, as well as copy number variations in PTEN, CDKN2A, RB1, CHK2, and SMO, were confirmed. In oligodendroglioma, mutations in ERBB4 and KDM6A, in addition to IDH1 and TERT promoter, were observed. In meningiomas, a higher frequency of NF2 and KDM6A mutations was observed in Grade 2/3 compared to Grade 1, as well as a significantly higher frequency of copy number abnormalities in genes related to DNA repair, histone modification, and chromatin remodeling. Based on these findings, we are working on the development of new therapies.
10112- ET-10 EVALUATING PBC-IP AS A NOVEL BORON CARRIER IN BNCT
Authors: Kawabata Shinji , Nakamura Hiroyuki , Tsujino Kohei , Eza Kenichiro , Kazuki Rina , Fujikawa Yoshiki , Kashiwagi Hideki , Nonoguchi Naosuke , Furuse Motomasa , Takami Toshihiro , Wanibuchi Masahiko 
Published: November 2024

Abstract
This study aims to expand the application scope of boron neutron capture therapy (BNCT) for BPA-insensitive cancers. To apply BNCT in the treatment of brain tumors, convection-enhanced delivery (CED) is used as the drug administration method. CED is expected to enhance therapeutic efficacy by delivering drugs directly to tumor tissues. Therefore, the development of BNCT necessitates planning non-clinical trials from both pharmaceutical and medical device perspectives, including tests on standards, quality, and safety for clinical trial implementation. Previous investigations have demonstrated the high efficacy of BNCT using PBC-IP, a novel boron carrier targeting folate receptors, in a rat brain tumor model administered via CED. The group receiving PBC-IP CED irradiation alone showed 50% long-term survival (over 90 days), significantly outperforming the BNCT using intravenously administered boronophenylalanine (BPA) (MST: 37.0 days) used in clinical settings. Furthermore, studies on catheter insertion positions and neutron irradiation timing indicated that maintaining efficacy when administering drugs to the tumor margin and during the treatment window post-drug administration is feasible.Non-clinical trials, unlike routine basic investigations, are conducted following prior consultations with regulatory authorities, a process unfamiliar to many clinicians. Specific tests include general toxicity studies using rats and dogs. The results of these studies inform clinical trial planning and are essential for submission during regulatory consultations for clinical trial approval. As part of clinical trial preparation, drug efficacy evaluations and catheter performance data are considered to explore the clinical positioning of this drug in the treatment of malignant gliomas. Based on these findings, clinical trial implementation plans are formulated, aiming for the submission of a clinical trial application. This report examines the roadmap of drug development and current challenges in new drug development based on the current state of academic drug discovery.
10015- STMO-1 EXPRESSION OF ANESTHETIC FADE IN INTRAOPERATIVE MEP MONITORING DURING BRAIN TUMOR SURGERY
Authors: Tanaka Satoshi , Tomio Ryosuke , Ichimasu Norio , Akimoto Jiro 
Published: November 2024

Abstract
We retrospectively examined whether anesthetic fade (AF) occurred in brain tumor surgery with direct motor field stimulation motor evoked potential (dMEP) and transcranial stimulation MEP (tcMEP), and whether it could have been avoided by compound muscle action potential (CMAP) after peripheral nerve stimulation normalization, and examined the causes of AF. In 108 muscles in 40 patients where tcMEP was performed and 24 muscles in 24 cases where dMEP was performed, and whether AF could be avoided by CMAP normalization was examined. In 108 muscles where tcMEP was performed, the relative amplitude of surgery with an operative time of 190 minutes or more was 1.07±0.88, which was significantly lower than the relative amplitude of surgery with an operative time of less than 190 minutes (1.67±2.69) (P=0.0447, Student’s t-test). The relative amplitude values under CMAP normalization were also 1.29±1.62 over 190 minutes and 1.24±1.48 under 190 minutes, indicating no significant difference (P = 0.4430).The relative amplitude of surgery with an operative time of 360 minutes or more was 0.56±0.26 in the 24 muscles where dMEP was performed, and a significant difference was observed between the relative amplitude of surgery with an operative time of less than 360 minutes (1.43±0.75) (P = 0.0045). The relative amplitude values under CMAP normalization were 0.57±0.25 over 360 minutes and 1.48±0.72 under 360 minutes, which was also significant (P = 0.0038). AF was also more intense in dMEP and could not be avoided by CMAP normalization. Although there were few cases and it required consideration of direct invasion of the pyramidal tract in brain tumor surgery, it is suggested that a decrease in the transmissibility of neuromuscular junctions is considered to be a cause of AF that and a decrease in excitability of motor field pyramidal cells may be more active at 6 hours or more.
10179- STMO-11 ESTABLISHMENT OF INTRA-OPERATIVE RAPID GENOTYPING SYSTEM AS A NOVEL MODALITY FOR ADULT-TYPE DIFFUSE GLIOMA REMOVAL
Authors: Nakamura Akihiro , Ohka Fumiharu , Maeda Sachi , Deguchi Shoichi , Shiba Yoshiki , Yamaguchi Junya , Shimizu Hiroki , Takido Yuhei , Yamamoto Ryo , Ito Shohei , Saito Ryuta 
Published: November 2024

Abstract
Genetic abnormalities such as IDH, TERT promoter, and CDKN2A play a critical role in diagnosing adult-type diffuse gliomas. Intraoperative genetic diagnosis offers a strategic advantage by informing surgical decisions based on accurate genetic information. Recent findings suggest that the presence or absence of these molecular abnormalities could differentiate tumor cells from normal brain tissue, potentially guiding intraoperative margin assessments where the boundary with normal tissue is unclear. This study explores a rapid intraoperative genetic diagnostic method using the GeneSoC system, which performs 50 cycles of quantitative PCR in approximately 15 minutes. We targeted IDH1 R132H, TERT promoter mutations, and CDKN2A homozygous deletions (HD) for analysis. Primers and probes were carefully designed, and PCR conditions were optimized to establish a reliable diagnostic method. DNA was extracted by boiling tumor specimens for 5 minutes, followed by genetic analysis using the GeneSoC system. The entire process, from specimen collection to result, took about 20 minutes. We analyzed 111 glioma specimens for IDH1 R132H and TERT promoter mutations, and 50 specimens for CDKN2A HD. The sensitivity and specificity of the GeneSoC system were 98% and 98% for IDH1 R132H, 100% and 100% for TERT promoter mutations, and 100% and 83% for CDKN2A HD, respectively. Our study successfully established a rapid intraoperative genetic diagnostic method using the compact and high-speed GeneSoC system. The genetic analysis aligned with MRI FLAIR imaging findings, confirming IDH mutations in high-signal regions but not in adjacent iso-signal regions. Although further case studies are needed, integrating genetic diagnosis with imaging could enhance intraoperative margin assessments, positioning this method as a promising new modality in brain tumor surgery.
10010- NI-1 QUANTITATIVE ANALYSIS OF RECURRENCE PATTERNS AND DIRECTIONALITY IN PRIMARY GLIOBLASTOMA USING LESION MAPS & TRACTOGRAPHY
Authors: Shimizu Takeshi , Satoh Hirotaka , Sanada Takahiro , Saitou Masato , Mitsui Nobuyuki , Hiroshima Satoru , Kinoshita Manabu 
Published: November 2024

Abstract

INTRODUCTION
Identifying the sites of recurrence in primary glioblastoma is crucial for developing aggressive initial treatments. This study focuses on glioblastoma originating in the frontal lobe, hypothesizing that “recurrence progression is related to nerve fiber trajectories.” We quantitatively examined recurrence patterns.

METHODS
We analyzed 30 cases of primary glioblastoma in the frontal lobe treated at our institution with confirmed recurrences. For each patient, primary and recurrent lesion localizations were delineated using contrast-enhanced MRI and transformed to standard brain coordinates. This visualized the localization of lesions and allowed quantitative analysis of distribution changes. Additionally, virtual fiber tracking using DTI data from healthy subjects was performed with the primary lesion as a seed, and the correlation between the direction of recurrence and nerve fibers was analyzed using Pearson’s correlation coefficient.

RESULTS
Primary lesions were distributed in the MNI space across the frontal lobe, white matter, insula, putamen, thalamus, parietal lobe, temporal lobe, occipital lobe, and cerebellum at frequencies of 65.8%, 12.5%, 5.7%, 4.8%, 3.6%, 4.9%, 2.7%, 0.0%, and 0.0%, respectively. Recurrent lesions were distributed at 59.9%, 9.7%, 5.7%, 5.8%, 1.0%, 12.1%, 4.0%, 1.4%, and 0.3%, respectively. The changes in lesion distribution were statistically significant (p&lt;0.001, Chi-square test), and post hoc Fisher’s test showed a tendency for increased occurrence in the parietal lobe (P=0.065). Recurrent lesion vectors significantly correlated with nerve fiber vectors (mean absolute correlation: 0.60, p&lt;0.00001).

CONCLUSION
Primary glioblastomas in the frontal lobe tend to progress towards the parietal lobe, influenced by nerve fiber trajectories. These findings suggest that considering the direction of lesion progression could be essential in developing initial treatment strategies for glioblastoma.