bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of
Clostridioides difficile
nucleic acid amplification test (NAAT) results using fresh and frozen stool specimens and rectal swabs
Authors: Dumm Rebekah E. , Burnham Carey-Ann D. , Hink Tiffany , Reske Kimberly A. , Struttmann Emily , Iqbal Zainab Hassan , Cass Candice , Kwon Jennie H. , Olsen Margaret A. , Dubberke Erik R. 
Published: December 2023

ABSTRACT

Nucleic acid amplification tests (NAATs) are frequently used in
Clostridioides difficile
research and diagnostic testing, but the effect of freezing specimens on
C. difficile
NAAT performance is not well characterized. We compared
C. difficile
NAAT results between fresh and frozen fecal (
n
= 354) and rectal swab specimens (eSwab) (
n
= 132) using the Xpert system. Specimens were collected prospectively from 384 hospitalized patients admitted to the hematopoietic cell transplant and acute leukemia wards at a tertiary care hospital. Categorical concordance of NAAT results (agreement of positive/positive or negative/negative) was excellent between fresh and frozen conditions for fecal specimens (Kappa = 0.92) and very good for rectal swabs (Kappa = 0.78). Cycle threshold value correlation was similarly consistent between fresh and frozen conditions for swabs and stool specimens (Spearman’s correlation = 0.88). These results support the use of frozen fecal and rectal swab specimens to provide accurate results for research purposes when
C. difficile
NAAT testing on fresh specimens is not available or feasible.

IMPORTANCE

Nucleic acid amplification tests (NAATs) are frequently used in
Clostridioides difficile
research and diagnostic testing, but the effect of freezing specimens on
C. difficile
NAAT performance is not well characterized. This study evaluated the concordance of NAAT results between fresh and frozen specimens (fecal and rectal swabs) and found it to be very good to excellent. The results indicate that frozen fecal and rectal swab specimens may be used for
C. difficile
NAAT testing in research when fresh specimens are not available.
Changes in lipid composition of host-derived extracellular vesicles following
Salmonella
infection
Authors: Emerson Lisa E. , Mosby Chanel A. , Enslow Samantha , Hui Winnie W. , Jones Melissa K. , Ferraro Mariola J. 
Published: December 2023

ABSTRACT

Extracellular vesicles are small membrane-bound structures secreted by host cells that are involved in a variety of functions and the transmission of cargo. Vesicular cargo contains a variety of biomolecules, including lipids. Limited research has focused on the cargo content of extracellular vesicles during infections, particularly the alterations in lipid cargo that occur following bacterial infections. Our study investigates the lipid composition of extracellular vesicles generated by RAW 264.7 macrophages before and after infection with
Salmonella enterica
serovar Typhimurium at 24 and 48 hours post-infection. Our results reveal that both time and infection conditions significantly alter specific lipids in host-derived small extracellular vesicles. The altered lipids primarily comprise glycerophospholipids, sphingolipids, and prenol lipids. Our findings have important implications for understanding molecular mechanisms underlying the trafficking of lipids to extracellular compartments during infection.

IMPORTANCE

This study delves into the previously unexplored territory of extracellular vesicle (EV) cargo and composition, specifically focusing on lipid composition changes in EVs following
Salmonella
infection. EVs play crucial roles in intercellular communication, carrying a variety of biomolecules. Investigating how these EV cargo lipids change post-infection with
Salmonella
is significant for understanding the molecular mechanisms underlying lipid trafficking during infection. Given the impact of lipid composition on EV function, this research uncovers distinct differences in the lipid profiles of EVs at different time points post-infection and between infected and uninfected macrophages. This study identified lipids that are differentially abundant in EVs produced by the host during infection, offering novel insights into the dynamics of lipid profiles in EVs during cellular processes and infections. This work advances our understanding of host-pathogen interactions, specifically lipid-mediated EV functions during infection.
Metabolic and transcriptional activities underlie stationary-phase
Pseudomonas aeruginosa
sensitivity to Levofloxacin
Authors: Hare Patricia J. , Gonzalez Juliet R. , Quelle Ryan M. , Wu Yi I. , Mok Wendy W. K. 
Published: December 2023

ABSTRACT

The ubiquitous opportunistic pathogen
Pseudomonas aeruginosa
is highly adaptive and refractory to several different classes of antibiotics. However, we found in this study that stationary-phase
P. aeruginosa
cultures exhibit greater sensitivity to the fluoroquinolone Levofloxacin (Levo) than other bactericidal antibiotics, including an aminoglycoside (Tobramycin) and β-lactam (Aztreonam). To understand the basis of this sensitivity, we conducted time-lapse fluorescence microscopy experiments of cells during Levo treatment. We discovered that stationary-phase
P. aeruginosa
cells die rapidly during treatment and undergo heterogeneous morphological changes, including explosive lysis, filamentation, and gradual loss of membrane integrity as evidenced by propidium iodide uptake. These morphologies are reminiscent of how the model organism
Escherichia coli
appears when recovering from fluoroquinolone treatment, a period when activation of the DNA damage-induced SOS response is crucial. Accordingly, we monitored the morphologies and survival of
P. aeruginosa
Δ
recA
mutants and found that the SOS response is not involved in
P. aeruginosa
Levo sensitivity like it is for
E. coli
. We hypothesized that Levo sensitivity may be due to
P. aeruginosa
maintaining active metabolism in stationary phase. We determined that stationary-phase
P. aeruginosa
cells transcribe, maintain reductase activity, and accumulate reactive metabolic species which contribute to Levo-mediated death. By elucidating how
P. aeruginosa
cells sustain metabolic activity during the stationary phase, we can design strategies to sensitize these persistent subpopulations to Levo and maintain the efficacy of this clinically important fluoroquinolone antibiotic.

IMPORTANCE

The bacterial pathogen
Pseudomonas aeruginosa
is responsible for a variety of chronic human infections. Even in the absence of identifiable resistance mutations, this pathogen can tolerate lethal antibiotic doses through phenotypic strategies like biofilm formation and metabolic quiescence. In this study, we determined that
P. aeruginosa
maintains greater metabolic activity in the stationary phase compared to the model organism,
Escherichia coli
, which has traditionally been used to study fluoroquinolone antibiotic tolerance. We demonstrate that hallmarks of
E. coli
fluoroquinolone tolerance are not conserved in
P. aeruginosa
, including the timing of cell death and necessity of the SOS DNA damage response for survival. The heightened sensitivity of stationary-phase
P. aeruginosa
to fluoroquinolones is attributed to maintained transcriptional and reductase activity. Our data suggest that perturbations that suppress transcription and respiration in
P. aeruginosa
may actually protect the pathogen against this important class of antibiotics.
U-Th-Pb dating, trace elements, and Sr-Nd isotopes of monazite and allanite as recorders for multi-stage rare earth element mineralization and remobilization in carbonatite dike systems
Authors: Zhang Hao-Xiang , Jiang Shao-Yong , Liu Si-Qi , Yuan Feng , Chen Wei , Su Hui-Min 
Published: December 2023

Abstract
Carbonatite hosts the most important rare earth resources in the world, but the precise timing, ore-forming history, and mechanism of rare earth mineralization in carbonatite systems are still in debate. Here, we report a rare corona texture of monazite-allanite-fluorapatite from the Huangjiagou carbonatite in the Lesser Qinling of central China, and demonstrate that the U-Th-Pb dating, trace elements, and Sr-Nd isotopes of these minerals in the corona are useful tools to unravel multiple-stage events for rare earth element (REE) mineralization and mobilization. The first mineralization event took place at ca. 219 Ma as revealed by the monazite U-Pb age, the same as regional carbonatite forming ages, but the Th-Pb age has been disturbed, which shows a negative correlation with Th contents. The second mineralization event occurred at ca. 128 Ma, as revealed by in situ U-Pb dating of allanite, coeval with the intrusions of neighboring I-type granite. The initial Sr-Nd isotope ratios of allanite show a downtrend from the center to the rim of monazite-allanite-apatite coronas to approach the ratios of neighboring granite, indicating an increasing effect by the metasomatism of magmatic-hydrothermal fluids during the growth of these REE-mineral coronas. Therefore, a two-episode REE mineralization was recognized with the replacement of ca. 219 Ma monazite by ca. 128 Ma allanite-apatite coronas on the function of magmatic-hydrothermal fluid metasomatism, and this process accompanies the disturbance of Th/Pb geochronology in monazite. Allanite as the product of monazite dissolution can represent the later-stage REE mineralization tracing the REE reworking processes under the hydrothermal conditions in carbonatite systems. Our study highlights the implication of monazite-allanite-fluorapatite coronas on the REE remobilization and mineralization in carbonatite systems.
Differentiation and convection in a magma chamber: Novel insights on the origin of mafic microgranular enclaves in the Tongkeng pluton, Xiaojiang area, SE China
Authors: Zhang Ruo-Xi , Yang Shui-Yuan , Jiang Shao-Yong , Fu Bin , Cui Ji-Qiang 
Published: December 2023

Abstract
Mafic microgranular enclaves (MMEs), commonly found in granitoid intrusions, can provide unique perspectives on the nature of magma sources and evolution, physicochemical properties of magmas, and geotectonic dynamic evolution. However, their origin and generation remain under debate. In this paper, the Cretaceous Tongkeng pluton with MME occurrence located in the Xiaojiang area of Zhejiang Province, SE China, was examined. Zircon U-Pb dating indicates that the gabbroic diorite, MMEs, and their host quartz diorite all crystallized at 107–106 Ma. All samples from the Tongkeng pluton show a comparable range of initial 87Sr/86Sr values (0.70746–0.70841), εNd(t) values (−4.9 to −2.9), and zircon εHf(t) values (−7.3 to −2.9) with the peak value of −6 to −4. In addition, Pb isotope compositions are fairly consistent. Petrology, geochemical and isotopic compositions, and geochemical modeling suggest that the gabbroic diorite, MMEs, and their host rock were cognate and their primary magma was derived from the mixing between a mantle-derived magma and a crustal magma. The “magma differentiation and convection” model, proposed in this paper to improve our understanding of the origin of the MMEs and their host rock, suggests that the gabbroic and quartz dioritic magmas were formed by cognate magma differentiation, and the MME magma is a portion of the gabbroic dioritic magma that is incorporated into and mingled with the quartz dioritic magma. Misjudgment in the origin and generation of MMEs leads to an erroneous understanding of mantle properties, the genesis of granitoids, and therefore, many other geological processes. Hence, caution is needed when considering the relationship between the host granitoid and its associated MMEs with similar chemical and isotopic compositions, particularly for those exposed in areas where mafic rocks are absent (or undiscovered).
The role of melatonin in preventing amiodarone-induced rat liver damage
Authors: Petrović Dejan , Ilić Marina Deljanin , Simonović Dejan , Stojanović Milovan , Stanković Milica , Stanišić Slaviša , Stojanović Sanja , Arsić Nebojša , Sokolović Dušan T. 
Published: December 2023

Long-term exposure to amiodarone, an antiarrhythmic drug, can induce different organ damage, including liver. Cell damage included by amiodarone is a consequence of mitochondrial damage, reactive oxygen species production, and cell energy depletion leading to programmed cell death. In the present study, hepatoprotective potential of neurohormone melatonin (50 mg/kg/day) was evaluated in a chronic experimental model of liver damage induced by a 4-week application of amiodarone (70 mg/kg/day). The obtained results indicate that amiodarone induces an increase in xanthine oxidase activity, as well as the content of the lipid and protein oxidatively modified products and p53 levels. Microscopic analysis further corroborated the biochemical findings revealing hepatocyte degeneration, apoptosis, and occasional necrosis, with the activation of Kupffer cells. Coadministration of melatonin and amiodaron prevented an increase in certain damage associated parameters, due to its multiple targets. In conclusion, the application of melatonin together with amiodarone prevented an increase in tissue oxidative damage parameters and moderately prevented liver cell apoptosis, indicating that the damage of hepatocytes provoked by amiodarone supersedes the protective properties of melatonin in a given dose.
A Prospective Study of Graft Repositioning over Flap Technique for Reconstruction of Fingertip Amputation
Authors: KALADAGI Nitin , MANAS Raj Kumar 
Published: December 2023

Background: Replantation of digital tip amputations, especially Allen III and IV, is challenging for hand surgeons as it requires a high level of microsurgical expertise and fine instruments. The graft repositioning over flap (GRF) technique is a simple and reliable procedure that provides length, sensation and nail growth and GRF has become popular in the last few years. The aim of this study is to report the short-term outcomes of the GRF technique. Methods: This is a prospective study of all patients who underwent a GRF reconstruction for Allen III and IV digital amputations at our hospital over a 12-month period. In addition to demographic data and injury details, we collected outcomes data with regard to flap and nailbed graft survival, capillary refill time, nail growth, sensation (2-point discrimination), bone union and gain in length of digit compared to length at injury. Results: Twenty patients underwent GRF reconstruction of digital amputation. They included 18 men and 2 women with an average age of 29 years. The thumb was the most frequently injured digit (n = 7). Electric saws (n = 5) and industrial machines (n = 5) accounted for 50% of injuries. Twelve amputations were Allen IV. Five patients were lost to follow-up and outcomes data was available for 15 patients. There was loss of flap and nail bed in three patients. There was no growth of nail in three patients. The distal phalanx graft was lost in six patients and united in the remaining nine patients. Conclusions: The GRF technique is a simple and reliable option in patients in whom replantation is not possible. It restores length, provides sensation and nail growth in the reconstructed fingers. Level of Evidence: Level IV (Therapeutic)
Observed Relationships between Sea Surface Temperature, Vertical Wind Shear, Tropical Organized Deep Convection, and Radiative Effects
Authors: Hsiao Wei-Ting , Maloney Eric D. , Leitmann-Niimi Nicolas M. , Kummerow Christian D. 
Published: December 2023

Abstract
Organized deep convective activity has been routinely monitored by satellite precipitation radar from the Tropical Rainfall Measuring Mission (TRMM) and Global Precipitation Mission (GPM). Organized deep convective activity is found to increase not only with sea surface temperature (SST) above 27°C, but also with low-level wind shear. Precipitation shows a similar increasing relationship with both SST and low-level wind shear, except for the highest low-level wind shear. These observations suggest that the threshold for organized deep convection and precipitation in the tropics should consider not only SST, but also vertical wind shear. The longwave cloud radiative feedback, measured as the tropospheric longwave cloud radiative heating per amount of precipitation, is found to generally increase with stronger organized deep convective activity as SST and low-level wind shear increase. Organized deep convective activity, the longwave cloud radiative feedback, and cirrus ice cloud cover per amount of precipitation also appear to be controlled more strongly by SST than by the deviation of SST from its tropical mean. This study hints at the importance of non-thermodynamic factors such as vertical wind shear for impacting tropical convective structure, cloud properties, and associated radiative energy budget of the tropics.

Significance Statement
This study uses tropical satellite observations to demonstrate that vertical wind shear affects the relationship between sea surface temperature and tropical organized deep convection and precipitation. Shear also affects associated cloud properties and how clouds affect the flow of radiation in the atmosphere. Although how vertical wind shear affects convective organization has long been studied in the mesoscale community, the study attempts to apply mesoscale theory to explain the large-scale mean organization of tropical deep convection, cloud properties, and radiative feedbacks. The study also provides a quantitative observational baseline of how vertical wind shear modifies cloud radiative effects and convective organization, which can be compared to numerical simulations.
Providing a computationally derived, mechanically optimised target correction during preoperative planning can improve joint contact mechanics of hip dysplasia treated with periacetabular osteotomy
Authors: Aitken Holly D , Miller Aspen , Rivas Dominic JL , Tatum Marcus , Westermann Robert W , Willey Michael C , Goetz Jessica E 
Published: December 2023

Aim: Preoperative identification of acetabular corrections that optimally improve joint stability and reduce elevated contact stresses could further reduce osteoarthritis progression in patients with hip dysplasia who are treated with periacetabular osteotomy (PAO). The purpose of this study was to investigate how providing patient-specific, mechanically optimal acetabular reorientations to the surgeon during preoperative planning affected the surgically achieved correction. Methods: Preoperative CT scans were used to create patient-specific hip models for 6 patients scheduled for PAO. A simulated acetabular fragment was extracted from the preoperative pelvis model and computationally rotated to simulate candidate acetabular reorientations. For each candidate, discrete element analysis was used to compute contact stresses during walking, which were summed over the gait cycle and scaled by patient age to obtain chronic contact stress-time exposure. The ideal patient-specific reorientation was identified using a cost function that balances minimising chronic stress exposures and achieving surgically acceptable acetabular coverage angles. The optimal reorientation angles and associated contact mechanics were provided to the surgeon preoperatively. After PAO was performed, a model of the surgically achieved correction was created from a postoperative CT scan. Radiographic coverage and contact mechanics were compared between preoperative, optimal, and surgically achieved orientations. Results: While surgically achieved reorientations were not significantly different from optimal reorientations in radiographically measured lateral ( p = 0.094) or anterior ( p = 0.063) coverage, surgically achieved reorientations had significantly ( p = 0.031) reduced total contact area compared to optimal reorientations. The difference in lateral coverage and peak chronic exposure between surgically achieved and optimal reorientations decreased with increasing surgeon experience using the models (R² = 0.758, R2 = 0.630, respectively). Conclusions: Providing hip surgeons with a patient-specific, computationally optimal reorientation during preoperative planning may improve contact mechanics after PAO, which may help reduce osteoarthritis progression in patients with hip dysplasia.
Provider perspectives on equity in use of mobile health autism screening tools
Authors: Zuckerman Katharine E , Rivas Vazquez Luis Andres , Morales Santos Yesenia , Fuchu Plyce , Broder-Fingert Sarabeth , Dolata Jill K , Bedrick Steven , Fernandez Jasmine , Fombonne Eric , Sanders Benjamin W 
Published: December 2023

Mobile health (mHealth) screening tools for autism are gaining in prevalence, and have benefits such as video content and direct resources linkage. However, it is unclear whether such tools will ameliorate autism inequities or will help only those already advantaged in autism care. To investigate this issue, we conducted semi-structured qualitative interviews with 18 primary care and Early Intervention/Early Childhood Special Education providers in six US states. Providers were given hypothetical scenarios in which a family presents to care with results from one of 9 mHealth autism screening tools. Providers discussed their clinical approach and assessed the tool’s fit with their patient/client population. Each transcript was audio-recorded, transcribed, and coded; a phenomenological approach was used to develop key themes. 4 themes and 18 subthemes emerged. These included Clinical and business factors (e.g. scope of practice concerns and clinical efficiency), Validity and trustworthiness (e.g. familiarity, data privacy/security), Family interaction quality (e.g. supporting family advocacy, provision of information, affecting family anxiety, and emotional support), and Accessibility (e.g. English proficiency/language issues, cultural inclusivity, and literacy/educational level). Providers suggested modifications to enhance equity, such as portraying diverse families, reducing the reading level of text, and making tools shorter to better fit clinical context. Lay Abstract Families may find information about autism online, and health care and education providers may use online tools to screen for autism. However, we do not know if online autism screening tools are easily used by families and providers. We interviewed primary care and educational providers, asking them to review results from online tools that screen for autism. Providers had concerns about how usable and accessible these tools are for diverse families and suggested changes to make tools easier to use.