bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of the 2023 Duke-International Society of Cardiovascular Infectious Diseases Diagnostic Criteria for Infective Endocarditis in Relation to the Modified Duke Criteria and to Clinical Management—Reanalysis of Retrospective Bacteremia Cohorts
Authors: Lindberg Helena , Berge Andreas , Jovanovic-Stjernqvist Martin , Hagstrand Aldman Malin , Krus David , Öberg Jonas , Kahn Fredrik , Bläckberg Anna , Sunnerhagen Torgny , Rasmussen Magnus 
Published: February 2024

Abstract

Background
Revised diagnostic criteria for infective endocarditis (IE), the 2023 Duke-ISCVID criteria, were recently presented and need validation. Here, we compare the 2000 modified Duke criteria for IE with Duke-ISCVID among patients with bacteremia and relate the diagnostic classification to IE treatment.

Methods
We reanalyzed patient cohorts with Staphylococcus aureus, Staphylococcus lugdunensis, non–β-hemolytic streptococci, Streptococcus-like bacteria, Streptococcus dysgalactiae, Enterococcus faecalis, and HACEK (Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella) bacteremia. Episodes were classified as definite, possible, or rejected IE with the modified Duke and Duke-ISCVID criteria. Reclassification included the microbiology criteria, positron emission tomography–computed tomography, and cardiac implanted electronic devices. To calculate sensitivity, patients treated for IE were considered as having IE.

Results
In 4050 episodes of bacteremia, the modified Duke criteria assigned 307 episodes (7.6%) as definite IE, 1190 (29%) as possible IE, and 2553 (63%) as rejected IE. Using the Duke-ISCVID criteria, 13 episodes (0.3%) were reclassified from possible to definite IE, and 475 episodes (12%) were reclassified from rejected to possible IE. With the modified Duke criteria, 79 episodes that were treated as IE were classified as possible IE, and 11 of these episodes were reclassified to definite IE with Duke-ISCVID. Applying the decision to treat for IE as a reference standard, the sensitivity of the Duke-ISCVID criteria was 80%. None of the 475 episodes reclassified to possible IE were treated as IE.

Conclusions
The Duke-ISCVID criteria reclassified a small proportion of episodes to definite IE at the expense of more episodes of possible IE. Future criteria should minimize the possible IE group while keeping or improving sensitivity.
First-break prediction in 3-D land seismic data using the dynamic time warping algorithm
Authors: Souza W E , Cerqueira A G , Porsani M J 
Published: February 2024

SUMMARY
This paper presents a new methodology to assist geophysicists in determining the first-break event in a 3-D seismic data set using the well-known technique called dynamic time warping algorithm (DTW), which is usually used to find the optimal alignment between two time-series. We used the optimal path from the cost matrix to identify the first break in the seismogram using a few picks (seeds) made by an interpreter as a reference to perform this task. Furthermore, the data were pre-conditioned by the topographic and linear moveout to improve the method’s accuracy. To demonstrate the technique’s robustness, first, we applied the methodology in a synthetic seismic data. After demonstrating the efficiency of the algorithm, we applied the aforementioned methodology in the Polo-Miranga 3-D seismic cube located in the Recôncavo sedimentary basin, Bahia-Brazil, and in the seismic data acquired from the Blackfoot field in Alberta, Canada. The high-quality results showed consistency in determining the first break in all ranges of offsets, demonstrating an alternative way to accelerate this seismic processing step. Furthermore, we compared the results obtained by the proposed methodology with an algorithm based on comparing the short-time averages with long-time averages. Finally, we performed the static correction calculation to ensure that the time distortion resulting from the terrain and the low-velocity layer was mitigated in shoot gathers and in the stacked section.
Analysis of the Infectious Diseases Fellowship Program Directors Postmatch 2023 Survey
Authors: Andrews Hayden S , Chirch Lisa M , Luther Vera P , Shnekendorf Rachel , Nolan Nathanial S , Paras Molly L 
Published: February 2024

Abstract
The 2023 United States infectious diseases (ID) fellowship match resulted in a large percentage of programs with unfilled positions. A survey was sent to ID program directors nationwide to better understand their perceptions on the match. Program directors perceived geography, a small applicant pool, and low specialty pay as contributing factors to the match results. Developing specialized fellowship tracks, increasing funding for the ID trainee pipeline, and national advocacy for higher compensation were identified as areas to focus on to increase the applicant pool. Areas of controversy, such as decreasing the number or size of fellowship programs, require further discussion.
Impact of Micafungin on Candida auris β-glucan Masking and Neutrophil Interactions
Authors: Horton Mark V , Eix Emily F , Johnson Chad J , Dean Megan E B , Andes Brody D , Wartman Kayla M , Nett Jeniel E 
Published: February 2024

Abstract
Invasive fungal pathogen Candida auris has become a public health threat causing outbreaks of high mortality infections. Drug resistance often limits treatment options. For Candida albicans, subinhibitory concentrations of echinocandins unmask immunostimulatory β-glucan, augmenting immunity. Here we analyze the impact of echinocandin treatment of C. auris on β-glucan exposure and human neutrophil interactions. We show subinhibitory concentrations lead to minimal glucan unmasking and only subtle influences on neutrophil functions for the isolates belonging to circulating clades. The data suggest that echinocandin treatment will not largely alter phagocytic responses. Glucan masking pathways appear to differ between C. auris and C. albicans.
Uropathogenic Escherichia coli Subverts Host Autophagic Defenses by Stalling Preautophagosomal Structures to Escape Lysosome Exocytosis
Authors: Li Xueping , Jiang Lingyan , Zhang Si , Zhou Jiarui , Liu Le , Jin Chen , Sun Hongmin , Wang Qian , Liu Yutao , Pang Yu 
Published: February 2024

Abstract
Urinary tract infections are primarily caused by uropathogenic Escherichia coli (UPEC). UPEC infects bladder epithelial cells (BECs) via fusiform vesicles and escapes into the cytosol by disrupting fusiform vesicle membrane using outer membrane phospholipase PldA, and establishes biofilm-like intracellular bacterial communities (IBCs) for protection from host immune clearance. Cytosolic UPEC is captured by autophagy to form autophagosomes, then transported to lysosomes, triggering the spontaneous exocytosis of lysosomes. The mechanism by which UPEC evades autophagy to recognize and form IBCs remains unclear. Here, we demonstrate that by inhibiting autophagic flux, UPEC PldA reduces the lysosome exocytosis of BECs. By reducing intracellular phosphatidylinositol 3-phosphate levels, UPEC PldA increases the accumulation of NDP52 granules and decreases the targeting of NDP52 to autophagy, hence stalling preautophagosome structures. Thus, our results uncover a critical role for PldA to inhibit autophagic flux, favoring UPEC escapes from lysosome exocytosis, thereby contributing to acute urinary tract infection.
Risk of Cardiovascular Events After Influenza: A Population-Based Self-Controlled Case Series Study, Spain, 2011–2018
Authors: Muñoz-Quiles Cintia , López-Lacort Mónica , Urchueguía Arantxa , Díez-Domingo Javier , Orrico-Sánchez Alejandro 
Published: February 2024

Abstract
This study explores the relationship between influenza infection, both clinically diagnosed in primary care and laboratory confirmed in hospital, and atherothrombotic events (acute myocardial infarction and ischemic stroke) in Spain. A population-based self-controlled case series design was used with individual-level data from electronic registries (n = 2 230 015). The risk of atherothrombotic events in subjects ≥50 years old increased more than 2-fold during the 14 days after the mildest influenza cases in patients with fewer risk factors and more than 4-fold after severe cases in the most vulnerable patients, remaining in them more than 2-fold for 2 months. The transient increase of the association, its gradient after influenza infection, and the demonstration by 4 different sensitivity analyses provide further evidence supporting causality. This work reinforces the official recommendations for influenza prevention in at-risk groups and should also increase the awareness of even milder influenza infection and its possible complications in the general population.
Mortality Rates of the Spanish Flu and Coronavirus Disease 2019 in the Netherlands: A Historical Comparison
Authors: Harteloh Peter , van Mechelen Rob 
Published: February 2024

Abstract
The coronavirus disease 2019 (COVID-19) pandemic has been called the deadliest disease event in history. In this study, we compared the cause-specific mortality rate of the Spanish flu (1918–1920) with that of COVID-19 (2020–2022) in the Netherlands. During the periods of exposure, about 50 000 people died of COVID-19 and 32 000 people of the Spanish flu. In absolute numbers, COVID-19 seems to be deadlier than Spanish flu. However, the crude mortality rates for COVID-19 and Spanish flu were 287 and 486 per 100 000 inhabitants, respectively. Comparing age-standardized mortality rates, there would have been 28 COVID-19– and 194 Spanish flu–related deaths in 1918–1920, or 214 Spanish flu– and 98 COVID-19–related deaths in 2020–2022 per 100 000 inhabitants per year. Thus, taking the population differences into account, the Spanish flu would have been deadlier than COVID-19.
Molecular Interactions Leading to Advancements in the Techniques for COVID-19 Detection: A Review
Authors: Kashif Mohammad , Acharya Swati , Khalil Adila 
Published: February 2024

Abstract
Since 2019 the world has been in a combat with the highly contagious disease COVID-19 which is caused by the rapid transmission of the SARS-CoV-2 virus (severe acute respiratory syndrome coronavirus 2). Detection of this disease in an early stage helps to control its spread and management. To combat this epidemic with one-time effective medication, improved quick analytical procedures must be developed and validated. The requirement for accurate and precise analytical methods for the diagnosis of the virus and antibodies in infected patients has been a matter of concern. The global impact of this virus has motivated scientists and researchers to investigate and develop various analytical diagnostic techniques. This review includes the study of standard methods which are reliable and accredited for the analytical recognition of the said virus. For early detection of SARS-CoV-2 RNA, RT-PCR (Real-time reverse transcriptase-polymerase chain reaction) is an accurate method among other methods and, thus, considered as the “gold standard” technique. Here, we outline the most extensively used analytical methods for diagnosing COVID-19, along with a brief description of each technique and its analytical aspects/perspective.
Genetic mapping reveals new loci and alleles for flowering time and plant height using the double round-robin population of barley
Authors: Cosenza Francesco , Shrestha Asis , Van Inghelandt Delphine , Casale Federico A , Wu Po-Ya , Weisweiler Marius , Li Jinquan , Wespel Franziska , Stich Benjamin 
Published: February 2024

Abstract
Flowering time and plant height are two critical determinants of yield potential in barley (Hordeum vulgare). Despite their role in plant physiological regulation, a complete overview of the genetic complexity of flowering time and plant height regulation in barley is still lacking. Using a double round-robin population originated from the crossings of 23 diverse parental inbred lines, we aimed to determine the variance components in the regulation of flowering time and plant height in barley as well as to identify new genetic variants by single and multi-population QTL analyses and allele mining. Despite similar genotypic variance, we observed higher environmental variance components for plant height than flowering time. Furthermore, we detected new QTLs for flowering time and plant height. Finally, we identified a new functional allelic variant of the main regulatory gene Ppd-H1. Our results show that the genetic architecture of flowering time and plant height might be more complex than reported earlier and that a number of undetected, small effect, or low-frequency genetic variants underlie the control of these two traits.
The role of the co-chaperone HOP in plant homeostasis during development and stress
Authors: Castellano M Mar , Muñoz Alfonso , Okeke Isabel C , Novo-Uzal Esther , Toribio René , Mangano Silvina 
Published: February 2024

Abstract
Proteins need to acquire their native structure in order to become fully functional. In specific cases, the active conformation is obtained spontaneously; nevertheless, many proteins need the assistance of chaperones and co-chaperones to be properly folded. These proteins help to maintain protein homeostasis under control conditions and under different stresses. HOP (HSP70–HSP90 organizing protein) is a highly conserved family of co-chaperones that assist HSP70 and HSP90 in the folding of specific proteins. In the last few years, findings in mammals and yeast have revealed novel functions of HOP and re-defined the role of HOP in protein folding. Here, we provide an overview of the most important aspects of HOP regulation and function in other eukaryotes and analyse whether these aspects are conserved in plants. In addition, we highlight the HOP clients described in plants and the role of HOP in plant development and stress response.
Quasar outflow deceleration or acceleration: predictions and a search
Authors: Hall P B , Weiss E , Brandt W N , Mulholland C J 
Published: February 2024

ABSTRACT
Quasar winds can shock and sweep up ambient interstellar medium (ISM) gas, contributing to galactic quenching. We combine and extend past models of energy-conserving shock bubbles around quasars, investigate model implications from an observational standpoint, and test model predictions using new high-resolution spectroscopic observations of the broad absorption-line quasar SDSS J030000.56+004828.0 (J0300). Even with constant energy input from the wind, a bubble’s expansion decelerates over time as more ISM gas is swept up. Our new observations enable a direct search for this deceleration. We obtain the tightest reported 3σ limit on the average rest-frame deceleration (or acceleration) of a quasar outflow: |a| &lt; 0.1 km s−1 yr−1 (&lt;3 × 10−4 cm s−2) in the relatively low-velocity Ca ii outflow of J0300 over 9.65 rest-frame years. We can satisfy these limits with certain parameter choices in our model, but the large velocity range of the Ca ii absorption in J0300 rules out the hypothesis that such gas shares the velocity of the swept-up ISM gas in a self-similar shock bubble. We investigate the possibility of ram-pressure acceleration of preexisting ISM clouds and conclude that the velocity range seen in Ca ii in J0300 is potentially consistent with such an explanation. The Ca ii-absorbing gas clouds in J0300 have been inferred to have high densities by Choi et al., in which case they can only have been accelerated to their current speeds if they were originally at least an order of magnitude less dense than they are today.
Observations of interstellar scattering of six pulsars using Polish LOFAR station PL611
Authors: Filothodoros Alexandros , Lewandowski Wojciech , Kijak Jarosław , Śmierciak Bartosz , Chyży Krzysztof , Błaszkiewicz Leszek , Krankowski Andrzej 
Published: February 2024

ABSTRACT
We present the preliminary results of 4 yr of observations of the scattering of pulsar radiation in the interstellar medium using the Low Frequency Array (LOFAR) PL611 station located in Lazy near Krakow. In this work we show the initial results for six pulsars from our observing campaign. We used the HBA antennas of the station, with a central frequency of 154 MHz and a 72 MHz bandwidth and we were able to detect the frequency-dependent change in the pulse profiles. Splitting the bandwidth into a number of separate sub-bands we obtained independent scatter time estimates, which allowed for the estimation of the scattering frequency scaling slope for each individual observation. Our project has been accumulating data for more than 4 yr and as a result we are in a position to study the time variability of the scattering parameters over this period. We detected significant changes in the scatter time and its frequency scaling for at least two of pulsars. The average values of the frequency scaling index for the six pulsars selected for this work are below the range of values predicted by the simple thin screen model of interstellar scattering. This is in accordance with previous results shown for both higher dispersion measure pulsars observed in the past, as well as the more recent LOFAR observations and other projects similar in the observing frequency. We also discuss the advantages of using individual LOFAR stations (or similar instruments) for this kind of research.
Multiplex gene editing reveals cucumber MILDEW RESISTANCE LOCUS O family roles in powdery mildew resistance
Authors: Ma Mingru , Yang Li , Hu Zhenzhu , Mo Changjuan , Geng Shouyu , Zhao Xin , He Qiuyu , Xiao Li , Lu Liurong , Wang Dan , Li Shanggui , Kong Qiusheng , Li Dawei , Bie Zhilong 
Published: February 2024

Abstract
Powdery mildew (PM) is one of the most widespread and prevalent diseases that affects a wide range of crops. In cucumber (Cucumis sativus L.), previous forward genetic studies have identified MILDEW RESISTANCE LOCUS O 8 (CsMLO8) as necessary but alone insufficient for cucumber PM resistance (PMR) and suggested the involvement of other members of the CsMLO family. However, the function of other CsMLO family members in cucumber remains largely unknown. Here, we developed a highly efficient multiplex gene editing system in cucumber to generate a series of Csmlo mutants from all the 13 family members. Systematic analysis of these mutants revealed growth effects of these CsMLO family members on development and PMR. Importantly, we obtained the Csmlo1/8/11 triple mutant with complete resistance to PM. Transcriptome and proteome analysis of PM-resistant Csmlo mutants suggested that the kinesin-like calmodulin-binding protein (KCBP)-interacting Ca2+-binding protein (CsKIC), calmodulin-like protein 28 (CsCML28), and Ca2+-dependent protein kinase 11 (CsCPK11)-mediated calcium signaling pathway is involved in PMR. CsMLO8 interacted directly with CsKIC, and the simultaneous silencing of both genes resulted in a phenotype that resembled the silencing of CsKIC alone. Silencing CsCML28 and CsCPK11 increased susceptibility to PM, whereas overexpressing CsCPK11 through genetic transformation enhanced cucumber's PMR, demonstrating their positive regulatory roles in PMR. Given the importance of PMR for cucurbit crops, this research provides unprecedented insights into the function of the proteins encoded by the CsMLO gene family as well as the plant defense response to PM pathogen.
Gene inversion led to the emergence of brackish archaeal heterotrophs in the aftermath of the Cryogenian Snowball Earth
Authors: Fan Lu , Xu Bu , Chen Songze , Liu Yang , Li Fuyan , Xie Wei , Prabhu Apoorva , Zou Dayu , Wan Ru , Li Hongliang , Liu Haodong , Liu Yuhang , Kao Shuh-Ji , Chen Jianfang , Zhu Yuanqing , Rinke Christian , Li Meng , Zhu Maoyan , Zhang Chuanlun 
Published: February 2024

Abstract
Land–ocean interactions greatly impact the evolution of coastal life on earth. However, the ancient geological forces and genetic mechanisms that shaped evolutionary adaptations and allowed microorganisms to inhabit coastal brackish waters remain largely unexplored. In this study, we infer the evolutionary trajectory of the ubiquitous heterotrophic archaea Poseidoniales (Marine Group II archaea) presently occurring across global aquatic habitats. Our results show that their brackish subgroups had a single origination, dated to over 600 million years ago, through the inversion of the magnesium transport gene corA that conferred osmotic-stress tolerance. The subsequent loss and gain of corA were followed by genome-wide adjustment, characterized by a general two-step mode of selection in microbial speciation. The coastal family of Poseidoniales showed a rapid increase in the evolutionary rate during and in the aftermath of the Cryogenian Snowball Earth (∼700 million years ago), possibly in response to the enhanced phosphorus supply and the rise of algae. Our study highlights the close interplay between genetic changes and ecosystem evolution that boosted microbial diversification in the Neoproterozoic continental margins, where the Cambrian explosion of animals soon followed.
Marangoni spreading on liquid substrates in new media art
Authors: Chan San To , Fried Eliot 
Published: February 2024

Abstract
With the advent of new media art, artists have harnessed fluid dynamics to create captivating visual narratives. A striking technique known as dendritic painting employs mixtures of ink and isopropanol atop paint, yielding intricate tree-like patterns. To unravel the intricacies of that technique, we examine the spread of ink/alcohol droplets over liquid substrates with diverse rheological properties. On Newtonian substrates, the droplet size evolution exhibits two power laws, suggesting an underlying interplay between viscous and Marangoni forces. The leading edge of the droplet spreads as a precursor film with an exponent of 3/8, while its main body spreads with an exponent of 1/4. For a weakly shear-thinning acrylic resin substrate, the same power laws persist, but dendritic structures emerge, and the texture of the precursor film roughens. The observed roughness and growth exponents (3/4 and 3/5) suggest a connection to the quenched Kardar–Parisi–Zhang universality class, hinting at the existence of quenched disorder in the liquid substrate. Mixing the resin with acrylic paint renders it more viscous and shear-thinning, refining the dendrite edges and further roughening the precursor film. At larger paint concentrations, the substrate becomes a power-law fluid. The roughness and growth exponents then approach 1/2 and 3/4, respectively, deviating from known universality classes. The ensuing structures have a fractal dimension of 1.68, characteristic of diffusion-limited aggregation. These findings underscore how the nonlinear rheological properties of the liquid substrate, coupled with the Laplacian nature of Marangoni spreading, can overshadow the local kinetic roughening of the droplet interface.