bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comprehensive, predictive mortality score for patients with bloodstream infections (PROBAC): a prospective, multicentre cohort study
Authors: De la Rosa-Riestra Sandra , López-Hernández Inmaculada , Pérez-Rodríguez María Teresa , Sousa Adrián , Goikoetxea Agirre Josune , Reguera Iglesias José María , León Eva , Armiñanzas Castillo Carlos , Sánchez Gómez Leticia , Fernández-Natal Isabel , Fernández-Suárez Jonathan , Boix-Palop Lucía , Cuquet Pedragosa Jordi , Jover-Sáenz Alfredo , Sánchez Calvo Juan Manuel , Martín-Aspas Andrés , Natera-Kindelán Clara , del Arco Jiménez Alfonso , Bahamonde Carrasco Alberto , Smithson Amat Alejandro , Vinuesa García David , Martínez Pérez-Crespo Pedro María , López-Cortés Luis Eduardo , Rodríguez-Baño Jesús ,   PROBAC/GEIRAS-SEIMC/SAMICEI, Retamar-Gentil Pilar , Ferrer José Bravo , Reche Isabel , Gea-Lázaro Isabel , Pérez-Camacho Inés , Porto Antonio Sánchez , García Marcos Guzmán , Carral Berta Becerril , de Lucas Esperanza Merino 
Published: June 2024

Abstract

Objectives
Bloodstream infections (BSI) are an important cause of mortality, although they show heterogeneity depending on patients and aetiological factors. Comprehensive and specific mortality scores for BSI are scarce. The objective of this study was to develop a mortality predictive score in BSI based on a multicentre prospective cohort.

Methods
A prospective cohort including consecutive adults with bacteraemia recruited between October 2016 and March 2017 in 26 Spanish hospitals was randomly divided into a derivation cohort (DC) and a validation cohort (VC). The outcome was all-cause 30-day mortality. Predictors were assessed the day of blood culture growth. A logistic regression model and score were developed in the DC for mortality predictors; the model was applied to the VC.

Results
Overall, 4102 patients formed the DC and 2009 the VC. Mortality was 11.8% in the DC and 12.34% in the CV; the patients and aetiological features were similar for both cohorts. The mortality predictors selected in the final multivariate model in the DC were age, cancer, liver cirrhosis, fatal McCabe underlying condition, polymicrobial bacteraemia, high-risk aetiologies, high-risk source of infection, recent use of broad-spectrum antibiotics, stupor or coma, mean blood pressure &lt;70 mmHg and PaO2/FiO2 ≤ 300 or equivalent. Mortality in the DC was &lt;2% for ≤2 points, 6%–14% for 3–7 points, 26%–45% for 8–12 points and ≥60% for ≥13 points. The predictive score had areas under the receiving operating curves of 0.81 (95% CI 0.79–0.83) in the DC and 0.80 (0.78–0.83) in the VC.

Conclusions
A 30 day mortality predictive score in BSI with good discrimination ability was developed and internally validated.
Chromosomal and plasmid localization of ileS2 in high-level mupirocin-resistant Staphylococcus pseudintermedius and Staphylococcus aureus isolated from canine and feline origins
Authors: Chanchaithong Pattrarat , Chueahiran Surawit , Pinpimai Komkiew , Sroithongkham Parinya , Leelapsawas Chavin , Indra Rusmin , Yindee Jitrapa , Chuanchuen Rungtip 
Published: June 2024

Abstract

Objectives
To characterize the mobile genetic elements and genetic localization of ileS2 in high-level mupirocin-resistant (Hi-MupR) methicillin-resistant Staphylococcus pseudintermedius (MRSP) and MRSA isolates recovered from canine and feline clinical samples.

Methods
The identification of bacterial species and presence of mecA and ileS2 genes in MRSP and MRSA isolates were performed using MALDI-TOF MS and PCR, respectively. Antimicrobial resistance (AMR) phenotypes were determined by broth microdilution assays. The genome characteristics, ileS2-containing elements and staphylococcal cassette chromosome mec (SCCmec) were illustrated using complete circular genomes obtained from hybrid assembly of Illumina short-reads and Oxford Nanopore Technologies long-reads. These were analysed through phylogenetic and bioinformatics approaches.

Results
A total of 18 MRSP clinical isolates and four MRSA clinical isolates exhibited the Hi-MupR phenotype and carried multiple AMR genes, including mecA and ileS2 genes. MRSP ST182-SCCmec V (n = 6) and ST282-ΨSCCmec57395-t10 (n = 4) contained the ileS2 transposable unit associated with IS257 on the chromosome. Three MRSA ST398-SCCmec V-t034/t4652 isolates carried ∼42 kb pSK41-like ileS2 plasmids, whereas similar ileS2 plasmids lacking tra genes were found in MRSP ST282-ΨSCCmec57395-t72/t21 isolates. Furthermore, a new group of ileS2 plasmids, carried by MRSP ST45-ΨSCCmec57395, ST433-ΨSCCmecKW21-t05 and ST2165-SCCmec IV-t06, and by one MRSA ST398-SCCmec V-t034 strain, shared the plasmid backbone with the cfr/fexA-carrying plasmid pM084526_1 in MRSA ST398.

Conclusions
This study provides the first evidence of ileS2 integration into the S. pseudintermedius chromosome, which is a rare occurrence in staphylococcal species, and plasmids played a pivotal role in dissemination of ileS2 in both staphylococcal species.
Impact of an antimicrobial stewardship programme on antibiotic utilization and resistance burden in patients with acute leukaemia: an 11-year longitudinal cohort study using interrupted time-series analysis
Authors: Lee Raeseok , Nho Dukhee , Cho Sung-Yeon , Park Silvia , Cho Byung-Sik , Kim Hee-Je , Yoon Jae-Ho , Lee Seok , Kim Yoo-Jin , Lee Dong-Gun 
Published: June 2024

Abstract

Background
Antimicrobial resistance (AMR), driven by inappropriate and overuse of antibiotics, poses a significant threat, especially to patients with acute leukaemia.

Objectives
To evaluate the impact of antimicrobial stewardship programmes (ASPs) on antibiotic use and analyse temporal changes in bloodstream infections (BSI) caused by AMR organisms.

Methods
We performed a retrospective, interventional, longitudinal cohort study spanning an 11-year period. ASPs included optimizing antibiotic use, enhancing tracking and reporting systems and delineating leadership and accountability. A segmented regression model of interrupted time series was used to evaluate the trend of antibiotic consumption and BSI with AMR organisms after the interventions.

Results
A total of 3296 BSI episodes with 454 419 days of therapy (DOT) from 7754 patients were obtained. ASPs were significantly associated with an immediate reduction [−70.03 DOT/1000 patient-days (PD), P = 0.036] and a decreasing trend (−11.65 DOT/1000 PD per quarter, P &lt; 0.001) in overall antibiotic use. The increasing incidence of BSI with AMR before ASP intervention was notably curbed and revealed a decreasing trend (slope change: −0.06 BSI/1000 PD per quarter, P = 0.002). The decreasing trend was more significant for Enterobacterales: ciprofloxacin-resistant and ESBL-producing isolates showed a slope change of −0.06 BSI/1000 PD and −0.08 BSI/1000 PD per quarter, respectively (all P &lt; 0.05). However, Pseudomonas aeruginosa BSI increased.

Conclusions
Multidimensional ASPs effectively reduced both the immediate and trends in overall antibiotic usage even in patients with acute leukaemia. Additionally, there was a notable decrease in the incidence of BSI caused by AMR organisms, particularly among Enterobacterales.
FAS(APO), DAMP, and AKT Phosphoproteins Expression Predict the Development of Nosocomial Infection After Pediatric Burn Injury
Authors: Penatzer Julia , Steele Lisa , Breuer Julie , Fabia Renata , Hall Mark , Thakkar Rajan K 
Published: June 2024

Abstract
Pediatric burn injuries are a leading cause of morbidity with infections being the most common acute complication. Thermal injuries elicit a heightened cytokine response while suppressing immune function; however, the mechanisms leading to this dysfunction are still unknown. Our aim was to identify extracellular proteins and circulating phosphoprotein expression in the plasma after burn injury to predict the development of nosocomial infection (NI). Plasma was collected within 72 hours after injury from 64 pediatric burn subjects; of these, 18 went on to develop an NI. Extracellular damage-associated molecular proteins, FAS(APO), and protein kinase b (AKT) signaling phosphoproteins were analyzed. Subjects who went on to develop an NI had elevated high-mobility group box 1, heat shock protein 90 (HSP90), and FAS expression than those who did not develop an NI after injury (NoNI). Concurrently, phosphorylated (p-)AKT and mammalian target of rapamycin (p-mTOR) were elevated in those subjects who went on to develop an NI. Quadratic discriminant analysis revealed distinct differential profiles between NI and NoNI burn subjects using HSP90, FAS, and p-mTOR. The area under the receiver-operator characteristic curves displayed significant ability to distinguish between these 2 burn subject cohorts. These findings provide insight into predicting the signaling proteins involved in the development of NI in pediatric burn patients. Further, these proteins show promise as a diagnostic tool for pediatric burn patients at risk of developing infection while additional investigation may lead to potential therapeutics to prevent NI.
AI-powered fire engineering design and smoke flow analysis for complex-shaped buildings
Authors: Zeng Yanfu , Zheng Zhe , Zhang Tianhang , Huang Xinyan , Lu Xinzheng 
Published: June 2024

Abstract
This paper aims to automatize the performance-based design of fire engineering and the fire risk assessment of buildings with large open spaces and complex shapes. We first establish a database of high-quality fire simulations for diverse building shapes with heights up to 60 m and complex atriums with volumes up to 22 400 m³. Then, artificial intelligence (AI) models are trained to predict the soot visibility slices for new fire cases in buildings of different atrium shapes, symmetricities, and volumes. Two deep learning models were demonstrated: the pix2pix generative adversarial network (GAN) and image-prompt diffusion model. Compared with high-fidelity computational fluid dynamics fire modeling, the available safe egress time predicted by both models shows a high accuracy of 92% for random atrium shapes that are not distinct from the training cases, proving their performance in actual design practices. The diffusion model reproduces more flow details of the smoke visibility profiles than GAN, but it takes a longer computational time to render the fire scene. This work demonstrates the potential of leveraging AI technologies in building fire safety design, offering significant cost and time reductions and optimal solution identification.
Franseen needle in endobronchial ultrasound-guided transbronchial needle aspiration: a phase II prospective study
Authors: Shikano Kohei , Ikari Jun , Nakajima Takahiro , Ota Masayuki , Shiko Yuki , Naito Akira , Abe Mitsuhiro , Kawasaki Takeshi , Ikeda Jun-Ichiro , Ozawa Yoshihito , Suzuki Takuji 
Published: June 2024

Abstract

Background
Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) has been used to diagnose and stage lung cancer. Acquire™ Pulmonary and Expect™ Pulmonary dedicated EBUS-TBNA needles were introduced as the Franseen and Lancet needles, respectively. It is still unclear whether the Franseen or Lancet needles yield a higher quality specimen especially focusing on next-generation sequencing-based molecular testing.

Methods
A single-center, prospective study performed at the Chiba University Hospital randomly assigned patients to two groups: Group A, wherein the first and second EBUS-TBNA were performed using Lancet and Franseen needles, respectively, and Group B, wherein the first and second EBUS-TBNA were performed using Franseen and Lancet needles, respectively. Each specimen was compared and analyzed pathologically. The primary outcome was the histological tissue area except blood clot and the cellularity of each sample. We also examined the success rate of molecular testing.

Results
Twelve patients who underwent EBUS-TBNA between November 2022 and February 2023 were enrolled in this study. The tissue area of the specimens obtained by the Franseen and Lancet needles was 13.3 ± 6.4 mm2 and 10.6 ± 6.3 mm2, respectively (P = .355). The tumor cellularity in the specimens obtained using the Franseen and Lancet needles was 54.0 ± 30.3 and 46.2 ± 36.3%, respectively (P = .608). The success rate of molecular testing using the single-pass sample by Franseen needle was 85.7 and 57.1% by Lancet needle. No serious complications were reported.

Conclusions
The Franseen needle tended to show a greater amount of specimen with higher tumor cellularity than the Lancet needle which may contribute higher success rate of molecular testing. Further studies must be conducted to validate the results of this study.

Key findings
What is known and what is new?
What is the implication, and what should change now?
The Original Presidency: A Conception of Administrative Control
Authors: Wurman Ilan 
Published: June 2024

Abstract
The two predominant conceptions of executive power and supervision over the administrative state are inadequate. One maintains that all administrative discretion is the President’s, and that by virtue of the grant of executive power the President can both remove and control the discretion of all subordinate officers. That poses a possible textual problem: it seems to make the Opinions Clause superfluous. The other conception maintains that the President is, at best, a “persuader-in-chief,” with no constitutional right to control administrative discretion or to remove officers tasked with implementing statutory duties. Although this view makes sense of the Opinions Clause, there is no historical evidence for it. The proponents of these two schools of thought have thus been locked in a decades-long stalemate, with competing and irreconcilable paradigms of total control or no control. This Article recovers another, lost way of thinking about presidential power. According to this conception, Congress can insulate inferior officers from removal because they must follow orders. As for principal officers, the President can remove but not control them, at least not directly. There is no constitutional obligation on the part of principal officers to obey; the only inducement is the threat of removal. The Opinions Clause, far from being superfluous, then assures the President the power to acquire information to exercise intelligently the power to remove. In addition to this account’s textual and structural virtues, it appears to have been a relatively widely shared understanding of presidential power at the Founding, enough so to be within the range of plausible original meanings. This understanding of executive power may seem overly formalistic, but it is functionally more desirable than the two competing accounts that allow for total control or total balkanization.
Digitally filtered resonant arguments for deep learning classification of asteroids in secular resonances
Authors: Carruba V , Aljbaae S , Domingos R C , Caritá G , Alves A , Delfino E M D S 
Published: June 2024

ABSTRACT
Node secular resonances, or s-type secular resonances, occur when the precession frequencies of the node of an asteroid and some planets are in commensurability. They are important for changing the proper inclination of asteroids interacting with them. Traditionally, identifying the asteroid resonant status was mostly performed by visual inspection of plots of the time series of the asteroid resonant argument to check for oscillations around an equilibrium point. Recently, deep learning methods based on convolutional neural networks (CNNs) for the automatic classification of images have become more popular for these kinds of tasks, allowing for the classification of thousands of orbits in a few minutes. In this work, we study 11 s-type resonances in the asteroid main belt and in the Hungaria region and focus on the four most diffusive ones. Two secular resonances in the Hungaria region, the 2 · s − s4 − s6 and the s − 2 · s6 + s7 − g6 + g8 overlap, but this has negligible effects in terms of chaotic dynamics. Here, we obtained filtered images of the resonant arguments by filtering out all low-frequency signals with a Butterworth filter. A simple method based on amplitudes and periods of librations can perform a preliminary selection of asteroids in librating orbits. Our results show that CNN models applied to filtered images are much more effective in terms of metrics like accuracy, Precision, Recall, and F1-score than those that use images of osculating resonant arguments. Filtered resonant arguments should be preferentially used to identify asteroids interacting with secular resonances.
Detection of open cluster members inside and beyond tidal radius by machine learning methods based on Gaia DR3
Authors: Noormohammadi M , Khakian Ghomi M , Javadi A 
Published: June 2024

ABSTRACT
In our previous work, we introduced a method that combines two unsupervised algorithms: Density-based spatial clustering of applications with noise (DBSCAN) and Gaussian mixture model (GMM). We applied this method to 12 open clusters based on Gaia Early Data Release 3 (EDR3) data, demonstrating its effectiveness in identifying reliable cluster members within the tidal radius. However, for studying cluster morphology, we need a method capable of detecting members both inside and outside the tidal radius. By incorporating a supervised algorithm into our approach, we successfully identified members beyond the tidal radius. In our current work, we initially applied DBSCAN and GMM to identify reliable members of cluster stars. Subsequently, we trained the random forest algorithm using DBSCAN- and GMM-selected data. Leveraging the random forest, we can identify cluster members outside the tidal radius and observe cluster morphology across a wide field of view. Our method was then applied to 15 open clusters based on Gaia DR3, which exhibit a wide range of metallicity, distances, members, and ages. Additionally, we calculated the tidal radius for each of the 15 clusters using the King profile and detected stars both inside and outside this radius. Finally, we investigated mass segregation and luminosity distribution within the clusters. Overall, our approach significantly improved the estimation of the tidal radius and detection of mass segregation compared to the previous work. We found that in Collinder 463, low-mass stars do not segregate in comparison to high-mass and intermediate-mass stars. Additionally, we detected a peak of luminosity in the clusters, some of which were located far from the centre, beyond the tidal radius.
Mapping the structural landscape of the yeast Ty3 retrotransposon RNA genome
Authors: Andrzejewska-Romanowska Angelika , Gumna Julita , Tykwińska Ewa , Pachulska-Wieczorek Katarzyna 
Published: June 2024

Abstract
Long terminal repeat (LTR)-retrotransposons are significant contributors to the evolution and diversity of eukaryotic genomes. Their RNA genomes (gRNA) serve as a template for protein synthesis and reverse transcription to a DNA copy, which can integrate into the host genome. Here, we used the SHAPE-MaP strategy to explore Ty3 retrotransposon gRNA structure in yeast and under cell-free conditions. Our study reveals the structural dynamics of Ty3 gRNA and the well-folded core, formed independently of the cellular environment. Based on the detailed map of Ty3 gRNA structure, we characterized the structural context of cis-acting sequences involved in reverse transcription and frameshifting. We also identified a novel functional sequence as a potential initiator for Ty3 gRNA dimerization. Our data indicate that the dimer is maintained by direct interaction between short palindromic sequences at the 5′ ends of the two Ty3 gRNAs, resembling the model characteristic for other retroelements like HIV-1 and Ty1. This work points out a range of cell-dependent and -independent Ty3 gRNA structural changes that provide a solid background for studies on RNA structure-function relationships important for retroelement biology.
International regime uncertainty
Authors: Milner Helen V , Voeten Erik 
Published: June 2024

Abstract:
Questions about the future of US supremacy, the global spread of liberal democracy, and liberal international economic institutions create what we call ‘international regime uncertainty’: doubts about the fundamental principles, rules, norms, and decision-making procedures that govern areas of international affairs. This includes both probabilistic assessments of the risk that prevailing principles and institutions cease to function but also fundamental uncertainty over what alternative institutional arrangements and governing principles may emerge. Irrespective of actual systemic change, international regime uncertainty can affect transnational economic and political activities by increasing structural policy uncertainty and the probability of bargaining failures. The political uproar over energy transition policies that seemingly violate core principles of the international trade regime illustrates these points.
Cities on a Hill: American Religious Exceptionalism and White Christian Nationalism
Authors: Wilcox Clyde 
Published: June 2024

Abstract
Scholarly attention has shifted from a focus on white evangelicals and the Christian Right to the more pressing threat of white Christian nationalism. In The Everyday Crusade: Christian Nationalism in American Politics, Eric L. McDaniel, Irfan Nooruddin, and Allyson F. Shortle explore the antecedent ideology of American religious exceptionalism. They report that many elements of this ideology are present across the political spectrum, but the strongest believers are distinctive in many ways. American religious exceptionalism can be a basis for a variety of political mobilizations, but it has most recently been used primarily in an effort to deliver Christian nationalist votes to Republican candidates, including Donald Trump.
Syngeneic mesenchymal stem cells loaded with telomerase-dependent oncolytic adenoviruses enhance anti-metastatic efficacy
Authors: Yang Mei-Lin , Hu Che-Yuan , Lee Ya-Che , Chang Chao-Ching , Chen Yi-Cheng , Lee Pei-Ru , Su Bing-Hua , Chen Pi-Che , Shiau Ai-Li , Shieh Gia-Shing , Wu Chao-Liang , Wu Pensee 
Published: June 2024

Abstract
Oncolytic adenoviruses have emerged as a promising therapeutic approach for cancer therapy. However, systemic delivery of the viruses to metastatic tumors remains a major challenge. Mesenchymal stem cells (MSCs) possess tumor tropism property and can be used as cellular vehicles for delivering oncolytic adenoviruses to tumor sites. Since telomerase activity is found in ~90% of human carcinomas, but undetected in normal adult cells, the human telomerase reverse transcriptase gene (TERT) promoter can be exploited for regulating the replication of oncolytic adenoviruses. Here, we evaluated the antitumor effects of syngeneic murine MSCs loaded with the luciferase-expressing, telomerase-dependent oncolytic adenovirus Ad.GS2 (MSC-Ad.GS2) and Ad.GS2 alone on metastatic MBT-2 bladder tumors. MSCs supported a low degree of Ad.GS2 replication, which could be augmented by coculture with MBT-2 cells or tumor-conditioned medium (TCM), suggesting that viral replication is increased when MSC-Ad.GS2 migrates to tumor sites. MBT-2 cells and TCM enhanced viral replication in Ad.GS2-infected MSCs. SDF-1 is a stem cell homing factor. Our results suggest that the SDF-1/STAT3/TERT signaling axis in MSCs in response to the tumor microenvironment may contribute to the enhanced replication of Ad.GS2 carried by MSCs. Notably, we demonstrate the potent therapeutic efficacy of systemically delivered MSC-Ad.GS2 in pleural disseminated tumor and experimental metastasis models using intrapleural and tail vein injection of MBT-2 cells, respectively. Treatment with MSC-Ad.GS2 significantly reduced tumor growth and prolonged the survival of mice bearing metastatic bladder tumors. Since telomerase is expressed in a broad spectrum of cancers, this therapeutic strategy may be broadly applicable.