bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population Pharmacokinetic Modeling of Cefepime, Meropenem, and Piperacillin-Tazobactam in Patients With Cystic Fibrosis
Authors: Rolsma Stephanie L , Sokolow Andrew , Patel Pratish C , Sokolow Katherine , Jimenez-Truque Natalia , Fissell William H , Ryan Vivian , Kirkpatrick Carl M , Nation Roger L , Gu Kenan , Teresi Mary , Fishbane Nicholas , Kontos Marissa , An Guohua , Winokur Patricia , Landersdorfer Cornelia B , Creech C Buddy 
Published: September 2024

Abstract

Background
Patients with cystic fibrosis (CF) experience recurrent bacterial pulmonary exacerbations. Management of these infections is increasingly challenging due to decreased antimicrobial susceptibility to β-lactam antibiotics. The pharmacokinetics (PK) of these agents are inadequately characterized in patients with CF.

Methods
This study enrolled 155 pediatric and adult participants with CF who were receiving the following β-lactam antibiotics: cefepime (n = 82), meropenem (n = 42), or piperacillin-tazobactam (n = 31). Opportunistic blood samples were obtained during hospitalization. Population PK analysis was conducted via nonlinear mixed effects modeling. Clinical and demographic characteristics were evaluated as potential covariates. Monte Carlo simulations were performed to evaluate the probability of target attainment (PTA) for different dosing regimens.

Results
Estimated creatinine clearance and total or lean body weight affected the PK of cefepime and meropenem. No covariates were identified for piperacillin and tazobactam. In the cefepime group, a 3-hour infusion achieved a higher PTA than a 0.5-hour infusion for all participants. Estimated breakpoints—the respective minimum inhibitory concentration up to which ≥90% of patients are predicted to reach a PK/pharmacodynamic target—were 2- to 4-fold higher in pediatric participants receiving a 3- vs 0.5-hour infusion. In the meropenem group, increased creatinine clearance led to reduced PTA. In the piperacillin-tazobactam group, total daily dose and mode of administration were principal drivers of PTA.

Conclusions
Standard dosing regimens fail to achieve specific minimum inhibitory concentration targets in patients with CF. Therefore, clinicians should incorporate local antibiograms and PK models to determine optimal dosing. Further PK optimization to account for interindividual differences could be achieved by real-time β-lactam therapeutic drug monitoring.
Using integrative taxonomy to delimit species in the plant bug genus Pseudoloxops (Hemiptera: Miridae) in French Polynesia
Authors: Balukjian Brad , Van Dam Matthew H 
Published: September 2024

Abstract
We use integrative taxonomy to elucidate species boundaries of the plant bug genus Pseudoloxops (Kirkaldy 1905) in the Austral and Society archipelagos of French Polynesia. We operationalize the unified species concept by treating each individual as a potential species and then establish initial groupings (putative species) following statistically highly-supported reciprocal monophyly of individuals in a phylogenetic analysis of CO1, 16S, and 28S gene fragments. We then test our species hypotheses against additional lines of evidence from geometric morphometrics, genetic distance, discrete genitalic morphology, plant association, and geographic distribution partitions. Twenty species endemic to French Polynesia are recognized as follows: Pseudoloxops aama Balukjian & Van Dam, sp. nov., Pseudoloxops anaana Balukjian & Van Dam, sp. nov., Pseudoloxops baileyi Balukjian & Van Dam, sp. nov., Pseudoloxops chastaoliancai Balukjian & Van Dam, sp. nov., Pseudoloxops harrisonfordi Balukjian & Van Dam, sp. nov., Pseudoloxops kamalaharrisae Balukjian & Van Dam, sp. nov., Pseudoloxops oboyskii Balukjian & Van Dam, sp. nov., Pseudoloxops papepihaa Balukjian & Van Dam, sp. nov., Pseudoloxops puarata Balukjian & Van Dam, sp. nov., Pseudoloxops raimana Balukjian & Van Dam, sp. nov., Pseudoloxops ravataputuarai Balukjian & Van Dam, sp. nov., Pseudoloxops simberloffi Balukjian & Van Dam, sp. nov., Pseudoloxops tairoto Balukjian & Van Dam, sp. nov., Pseudoloxops temehanirahi Balukjian & Van Dam, sp. nov., Pseudoloxops tiapai Balukjian & Van Dam, sp. nov., Pseudoloxops toparaamahana Balukjian & Van Dam, sp. nov., Pseudoloxops tupapaau Balukjian & Van Dam, sp. nov. New synonyms are proposed for Pseudoloxops flavus (Knight, 1937) [=Pseudoloxops rubrocuneatus (Knight, 1937)] and Pseudoloxops adamsoni (Knight, 1937) [= Pseudoloxops nigribasicornis (Knight, 1937) and = Pseudoloxops tahiticus (Knight, 1937)]. Pseudoloxops rubroclavus (Knight, 1937) is redescribed.
The 129 strain-derived passenger mutations in ACKR1-deficient mice alter the expression of PYHIN and Fc-gamma receptor genes
Authors: Möller-Ramon Zoe , Aslani Maria , Sobczak Nikola , Hristov Michael , Weber Christian , Rot Antal , Duchêne Johan 
Published: September 2024

Abstract
Most genetically modified mice have been produced using 129 strain-derived embryonic stem cells. Despite ample backcrosses with other strains, these may retain characteristics for 129 passenger mutations, leading to confounding phenotypes unrelated to targeted genes. Here we show that widely used Ackr1−/−129ES mice have approximately 6 Mb of the 129-derived genome retained adjacently to the Ackr1 locus on chromosome 1, including several characteristic polymorphisms. These most notably affect the expression of PYHIN and Fc-gamma receptor genes in myeloid cells, resulting in the overproduction of IL-1β by activated macrophages and the loss of Fc-gamma receptors on myeloid progenitor cells. Therefore, caution is warranted when interpreting Ackr1−/−129ES mouse phenotypes as being solely due to the ACKR1 deficiency. Our findings call for a careful reevaluation of data from previous studies using Ackr1−/−129ES mice and underscore the limitations and pitfalls inherent to mouse models produced using traditional genetic engineering techniques involving 129 embryonic stem cells.
Limited proteolysis of neutrophil granule proteins by the bacterial protease RgpB depletes neutrophil antimicrobial capacity
Authors: Cooper Kelley N , Wielento Aleksandra , Morris Savannah C , Terekhova Marina , Rodriguez-Hernandez Carlos J , Potempa Barbara , Carey Katherine A , Artyomov Maxim N , Potempa Jan , Bagaitkar Juhi 
Published: September 2024

Abstract
Neutrophils are highly abundant in the gingival tissues where they play an essential role in immune homeostasis by preventing microbial invasion. Here, we show that the oral periodontal pathogen Porphyromonas gingivalis utilizes its cysteine proteases (gingipains) to disengage phagosomal antimicrobial capacity. Arginine gingipains are a subfamily of trypsin-like proteases produced by P. gingivalis that cleave several host proteins at arginine residues. We find that RgpB-mediated proteolysis of host proteins is not limited to the extracellular or plasma membrane-associated host proteins, but also results in the degradation of several intracellular proteins. Using 2D-difference gel electrophoresis coupled with mass spectrometry, we identified several cytoskeletal and cytoplasmic proteins, including metabolic enzymes and antimicrobial proteins such as neutrophil elastase, myeloperoxidase, and proteinase 3 within neutrophil granules that were cleaved by RgpB. Strikingly, despite the breakdown of multiple proteins, RgpB-treated neutrophils did not undergo apoptosis but increased integrin expression and underwent broad transcriptional changes consistent with proinflammatory programming. However, despite their primed status and augmented inflammatory capacity, RgpB-treated neutrophils were conducive to intracellular bacterial survival due to the reduced activity of granule proteins and oxidative burst. Thus, our data show a previously unknown role for P. gingivalis proteases in the attenuation of neutrophil microbicidal capacity via proteolysis of intracellular proteins.
Characterization of colistin-resistant carbapenemase producing Klebsiella pneumoniae in a river receiving wastewater treatment plant effluent
Authors: Swain Pragyan Paramita , Sahoo Saubhagini , Behera Birasen , Behera Dibyajyoti Uttameswar , Subudhi Enketeswara , Sahoo Rajesh Kumar 
Published: September 2024

Abstract
Genes conferring antibiotic resistance phenotype, particularly to last resort antibiotics, pose a significant concern globally. Wastewater treatment plant (WWTP) effluent substantially contributes to antibiotic resistance in receiving rivers, threatening human health. Globally, colistin- and carbapenem-resistant Klebsiella pneumoniae infections cause high morbidity and mortality. We investigated colistin-resistant carbapenemase-producing K. pneumoniae (Co-CRKP) isolates in Kathajodi river receiving WWTP effluent, their resistance genes, and pathogenic potential. Four isolates (Co-CRKP-7, Co-CRKP-8, Co-CRKP-10, and Co-CRKP-15) exhibited extensively drug-resistant (XDR) phenotype, harbouring blaTEM-1, blaCTX-M-15, blaNDM-5, and blaOXA-48 genes. Colistin resistance was attributed to mutations in the pmrA and pmrB genes. Virulence genes (fimH, mrkD, entB, iucA, iutA, and irp1), capsular serotypes (K1, K2) and biofilm formation in the isolates explicated their pathogenicity. Furthermore, Inc plasmid replicons (Y, FrepB, P, K/B, L/M, N, FIA, A/C, and FIB) indicated the dissemination potential of the resistance genes in Co-CRKP isolates. The multi-locus sequence typing showed that Co-CRKP-7 and Co-CRKP-8 belonged to ST42, while Co-CRKP-10 and Co-CRKP-15 were ST16 and ST231, respectively. These high-risk clones carrying multidrug resistance and virulence genes, implicated in numerous outbreaks, have spread worldwide. Our findings emphasize the necessity for effective treatment of hospital wastes to restrict the spread of clinical isolates into aquatic environments.
Improving the medium composition for the production of the natural blue-violet pigment violacein by a new Janthinobacterium sp. isolate
Authors: Ishimoto Caroline Kie , Lima Junior Rodolfo Dantas , Scaramussa Simone Aparecida de Lima , Fill Taicia Pacheco , Oliveira Valéria Maia , Bicas Juliano Lemos 
Published: September 2024

Abstract
The interest in natural compounds has increased primarily due to their beneficial health and environmental aspects. However, natural sources of some compounds, such as bluish pigments, are limited, requiring the development of efficient processes to meet commercial demands. This study isolated a blue-violet bacterium from spoiled cooked rice and identified it as a potential new species of Janthinobacterium through 16S rDNA analysis. Ultra-high performance liquid chromatography–tandem mass spectrometry analyses confirmed that the blue-violet pigment violacein was responsible for the bluish color. In laboratory conditions, different carbon and nitrogen sources were evaluated in submerged culture media to enhance pigment production. Glycerol did not result in significant pigment production by this strain, as expected from previous reports. Instead, a culture medium composed of yeast extract and fructose yielded higher pigment production, reaching about 113.68 ± 16.68 mg l−1 after 120 h. This result provides crucial insights for future studies aiming for sustainable and commercially viable violacein production. Based on a bioeconomy concept, this approach has the potential to supply natural and economic bluish pigments for various industrial sectors, including pharmaceutical, cosmetic, and food.
The Alphabet Soup of Microscopy: An Introduction to Advanced Imaging Techniques. Part II: What the FLIP, FLAP, FRAP, FRET, and FLIM is Going On?
Authors: Worden Austin N 
Published: September 2024

Abstract
The use of fluorescence in imaging has been a pivotal factor in advancing our scientific understanding. As microscopy continues to evolve, the terminology used to describe these techniques becomes increasingly complex, often resulting in a bewildering array of acronyms that resemble alphabet soup. Among the most prominent acronyms are those associated with advanced fluorescence microscopy techniques: Fluorescence Loss in Photobleaching (FLIP), Fluorescence Localization after Photobleaching (FLAP), Fluorescence Recovery after Photobleaching (FRAP), Förster Resonance Energy Transfer (FRET), and Fluorescence Lifetime Imaging Microscopy (FLIM). Each of these methods provides invaluable insights into molecular dynamics and interactions within living cells and tissues. This article, Part 2 of the Alphabet Soup of Microscopy series, aims to clarify these widely used fluorescence microscopy techniques and to illuminate their contributions to our understanding of cellular processes.
The DESI Early Data Release white dwarf catalogue
Authors: Manser Christopher J , Izquierdo Paula , Gänsicke Boris T , Swan Andrew , Koester Detlev , Robert Akshay , Xu Siyi , Inight Keith , Amroota Ben , Fusillo N P Gentile , Koposov Sergey E , Kim Bokyoung , Dey Arjun , Prieto Carlos Allende , Aguilar J , Ahlen S , Blum R , Brooks D , Claybaugh T , Cooper A P , Dawson K , de la Macorra A , Doel P , Forero-Romero J E , Gaztañaga E , Gontcho S Gontcho A , Honscheid K , Kisner T , Kremin A , Lambert A , Landriau M , Le Guillou L , Levi Michael E , Li T S , Meisner A , Miquel R , Moustakas J , Nie J , Palanque-Delabrouille N , Percival W J , Poppett C , Prada F , Rezaie M , Rossi G , Sanchez E , Schlafly E F , Schlegel D , Schubnell M , Seo H , Silber J , Tarlé G , Weaver B A , Zhou Z , Zou H 
Published: September 2024

ABSTRACT
The Early Data Release (EDR) of the Dark Energy Spectroscopic Instrument (DESI) comprises spectroscopy obtained from 2020 December 14 to 2021 June 10. White dwarfs were targeted by DESI both as calibration sources and as science targets and were selected based on Gaia photometry and astrometry. Here, we present the DESI EDR white dwarf catalogue, which includes 2706 spectroscopically confirmed white dwarfs of which approximately 60 per cent have been spectroscopically observed for the first time, as well as 66 white dwarf binary systems. We provide spectral classifications for all white dwarfs, and discuss their distribution within the Gaia Hertzsprung–Russell diagram. We provide atmospheric parameters derived from spectroscopic and photometric fits for white dwarfs with pure hydrogen or helium photospheres, a mixture of those two, and white dwarfs displaying carbon features in their spectra. We also discuss the less abundant systems in the sample, such as those with magnetic fields, and cataclysmic variables. The DESI EDR white dwarf sample is significantly less biased than the sample observed by the Sloan Digital Sky Survey, which is skewed to bluer and therefore hotter white dwarfs, making DESI more complete and suitable for performing statistical studies of white dwarfs.
The gravitational lensing imprints of DES Y3 superstructures on the CMB: a matched filtering approach
Authors: Demirbozan U , Nadathur S , Ferrero I , Fosalba P , Kovács A , Miquel R , Davies C T , Pandey S , Adamow M , Bechtol K , Drlica-Wagner A , Gruendl R A , Hartley W G , Pieres A , Ross A J , Rykoff E S , Sheldon E , Yanny B , Abbott T M C , Aguena M , Allam S , Alves O , Bacon D , Bertin E , Bocquet S , Brooks D , Rosell A Carnero , Carretero J , Cawthon R , da Costa L N , Pereira M E S , De Vicente J , Desai S , Doel P , Everett S , Flaugher B , Friedel D , Frieman J , Gatti M , Gaztanaga E , Giannini G , Gutierrez G , Hinton S R , Hollowood D L , James D J , Jeffrey N , Kuehn K , Lahav O , Lee S , Marshall J L , Mena-Fernández J , Mohr J J , Myles J , Ogando R L C , Malagón A A Plazas , Roodman A , Sanchez E , Sevilla-Noarbe I , Smith M , Soares-Santos M , Suchyta E , Swanson M E C , Tarle G , Weaverdyck N , Weller J , Wiseman P 
Published: September 2024

ABSTRACT
Low-density cosmic voids gravitationally lens the cosmic microwave background (CMB), leaving a negative imprint on the CMB convergence $\kappa$. This effect provides insight into the distribution of matter within voids, and can also be used to study the growth of structure. We measure this lensing imprint by cross-correlating the Planck CMB lensing convergence map with voids identified in the Dark Energy Survey Year 3 (DES Y3) data set, covering approximately 4200 deg$^2$ of the sky. We use two distinct void-finding algorithms: a 2D void-finder that operates on the projected galaxy density field in thin redshift shells, and a new code, Voxel, which operates on the full 3D map of galaxy positions. We employ an optimal matched filtering method for cross-correlation, using the Marenostrum Institut de Ciències de l’Espai N-body simulation both to establish the template for the matched filter and to calibrate detection significances. Using the DES Y3 photometric luminous red galaxy sample, we measure $A_\kappa$, the amplitude of the observed lensing signal relative to the simulation template, obtaining $A_\kappa = 1.03 \pm 0.22$ ($4.6\sigma$ significance) for Voxel and $A_\kappa = 1.02 \pm 0.17$ ($5.9\sigma$ significance) for 2D voids, both consistent with Lambda cold dark matter expectations. We additionally invert the 2D void-finding process to identify superclusters in the projected density field, for which we measure $A_\kappa = 0.87 \pm 0.15$ ($5.9\sigma$ significance). The leading source of noise in our measurements is Planck noise, implying that data from the Atacama Cosmology Telescope, South Pole Telescope and CMB-S4 will increase sensitivity and allow for more precise measurements.
Contribution of astrophysical events to the chemical evolution of a dwarf irregular galaxy
Authors: Fukagawa Nao , Prantzos Nikos 
Published: September 2024

ABSTRACT
We study the contribution of various astrophysical events asymptotic giant branch (AGB stars, core collapse and thermonuclear supernovae, neutron star mergers, and collapsars) to the abundances of elements both up to and heavier than the iron peak in a Local Group dwarf irregular galaxy, Wolf–Lundmark–Melotte (WLM). Its star formation history has been recently determined by observations with the JWST, and we use it to estimate the occurrence of the astrophysical sources. The rates of the gas accretion and the outflow are roughly determined based on the stellar metallicity distribution, the oxygen abundance of H ii regions, and the gas fraction. As discussed in the literature, the difference in time-scales on which the astrophysical events release the nucleosynthesis products is seen in the occurrence of the events and the evolution of abundance ratios. WLM has an extended star formation history and massive stars are recently and currently formed. Thus, the contribution of rotating massive stars through the weak s-process appears in the abundance ratios of light trans-iron elements to iron at later time of the evolution.
Detailed analysis of local climate at the CTAO-North site on La Palma from 20 yr of MAGIC weather station data
Authors: Gaug Markus , Longo Alessandro , Bianchi Stefano , Font Lluís , Almirante Sofia , Kornmayer Harald , Doro Michele , Hahn Alexander , Blanch Oscar , Plastino Wolfango , Dorner Daniela 
Published: September 2024

ABSTRACT
The Observatorio del Roque de los Muchachos will host the northern site of the Cherenkov Telescope Array Observatory (CTAO), in an area about 200 m below the mountain rim, where the optical telescopes are located. The site currently hosts the MAGIC (Major Atmospheric Gamma-ray Imaging Cherenkov) telescopes, which have gathered a unique series of 20 yr of weather data. We use advanced profile-likelihood methods to determine seasonal cycles, the occurrence of weather extremes, weather downtime, and long-term trends correctly taking into account data gaps. The fractality of the weather data is investigated by means of multifractal detrended fluctuation analysis. The data are published according to the Findable, Accessible, Interoperable, and Reusable (FAIR) principles. We find that the behaviour of wind and relative humidity show significant differences compared to the mountain rim. We observe an increase in temperature of $0.55\pm 0.07\mathrm{(stat.)}\pm 0.07\mathrm{(syst.)}$$^{\circ }$C decade−1, the diurnal temperature range of $0.13\pm 0.04\mathrm{(stat.)}\pm 0.02\mathrm{(syst.)}$$^{\circ }$C decade−1 (accompanied by an increase of seasonal oscillation amplitude of $\Delta C_m=0.29\pm 0.10\mathrm{(stat.)}\pm 0.04\mathrm{(syst.)}$$^{\circ }$C decade−1), and relative humidity of $4.0\pm 0.4\mathrm{(stat.)}\pm 1.1\mathrm{(syst.)}$ per cent decade−1, and a decrease in trade wind speeds of $0.85\pm 0.12\mathrm{(stat.)}\pm 0.07\mathrm{(syst.)}$ (km h−1) decade−1. The occurrence of extreme weather, such as tropical storms and long rains, remains constant over time. We find a significant correlation of temperature with the North Atlantic Oscillation Index and multifractal behaviour of the data. The site shows a weather-related downtime of 18.5 per cent–20.5 per cent, depending on the wind gust limits employed. No hints are found of a degradation of weather downtime under the assumption of a linear evolution of environmental parameters over time.
Simulated analogues II: a new methodology for non-parametric matching of models to observations
Authors: Al-Belmpeisi Rami , Tuhtan Vito , Christensen Mikkel Bregning , Kuruwita Rajika , Haugbølle Troels 
Published: September 2024

ABSTRACT
Star formation is a multiscale problem, and only global simulations that account for the connection from the molecular cloud-scale gas flow to the accreting protostar can reflect the observed complexity of protostellar systems. Star-forming regions are characterized by supersonic turbulence, and as a result, it is not possible to simultaneously design models that account for the larger environment and in detail reproduce observed stellar systems. Instead, the stellar inventories can be matched statistically, and the best matches found that approximate specific observations. Observationally, a combination of single-dish telescopes and interferometers are now able to resolve the nearest protostellar objects on all scales from the protostellar core to the inner $10\, \mathrm{au}$. We present a new non-parametric methodology which uses high-resolution simulations and post-processing methods to match simulations and observations using deep learning. Our goal is to perform a down-selection from large data sets of synthetic images to a ranked list of best-matching candidates with respect to the observation. This is particularly useful for binary and multiple stellar systems that form in turbulent environments. The objective is to accelerate the rate at which we can do such comparisons, remove biases from hand-picking matches, and contribute to identifying the underlying physical processes that drive the creation and evolution of observed protostellar systems.