bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Testing Guidance for Coccidioidomycosis, Histoplasmosis, and Blastomycosis in Patients With Community-Acquired Pneumonia for Primary and Urgent Care Providers
Authors: Smith Dallas J , Free Rebecca J , Thompson George R , Baddley John W , Pappas Peter G , Benedict Kaitlin , Gold Jeremy A W ,   Endemic Mycoses Diagnostic Algorithm Subject Matter Expert Group, Andes David , Bradsher Robert W , Ebell Mark H , Spec Andrej , Bahr Nathan C , Kauffman Carol A , Mott Timothy , Saccente Michael , Blair Janis E , Galgiani John , Johnson Royce H , Rutherford Richard , Tushla Lisa A , Chiller Tom , Jackson Brendan R , Toda Mitsuru 
Published: October 2023

Abstract
Coccidioidomycosis, histoplasmosis, and blastomycosis are underrecognized and frequently misdiagnosed fungal infections that can clinically resemble bacterial and viral community-acquired pneumonia. This guidance is intended to help outpatient clinicians test for these fungal diseases in patients with community-acquired pneumonia to reduce misdiagnoses, unnecessary antibacterial use, and poor outcomes.
Effect of music therapy intervention on anxiety and pain during percutaneous renal biopsy: a randomized controlled trial
Authors: Giordano Filippo , Mitrotti Adele , Losurdo Antonia , Esposito Flavia , Granata Antonio , Pesino Alessandra , Rossini Michele , Natale Patrizia , Dileo Vincenzo , Fiorentino Marco , Gesualdo Loreto 
Published: October 2023

ABSTRACT

Background
Percutaneous renal biopsy (PRB) may subject patients to emotional distress and pain before and during the biopsy. The aim of this study was to evaluate the effects of complementary/non-pharmacological interventions such as music therapy (MT) on anxiety, pain and satisfaction in renal patients undergoing PRB.

Methods
A prospective, single-centre, single-blind, randomized controlled two-arm trial was conducted. Patients ≥18 years of age, hospitalized at the Nephrology, Dialysis and Transplantation Unit (Bari, Italy) and scheduled for PRB were screened. Participants were assigned to standard treatment (CG) or to the music therapy (MT) intervention group. Participants in the MT group received standard care and an MT intervention by a certified music therapist qualified in guided imagery and music. The CG patients received the standard of care. MT and CG patients were subjected to identical measurements (pre/post) of the parameters in the State Trait Anxiety Inventory Y1 (STAI-Y1), visual analogue scale for pain (VAS-P) and satisfaction (VAS-S) and heart rate variability.

Results
A statistically significant difference in the anxiety scores after PRB between MT and CG patients (STAI-Y1 35.4 ± 6.2 versus 42.9 ± 9.0) was observed. MT also had strong and significant effects on VAS-P compared with CG (5.0 ± 1.4 versus 6.3 ± 1.3, respectively; P &lt; .001) and VAS-S (7.8 ± 1.0 versus 6.0 ± 0.9, respectively; P &lt; .001). Decreased activity of the sympathetic nervous system and increased activity of the parasympathetic nervous system was observed after PRB in the MT group.

Conclusion
Our study supports the use of MT to mitigate the psychological anxiety, pain and sympathetic activation associated with PRB.
Chromosome-level assembly and annotation of the Xyrichtys novacula (Linnaeus, 1758) genome
Authors: Cruz Fernando , Gómez-Garrido Jèssica , Gut Marta , Alioto Tyler S , Pons Joan , Alós Josep , Barcelo-Serra Margarida 
Published: October 2023

Abstract
The pearly razorfish (Xyrichtys novacula), commonly known as raor in the Balearic Islands, is a wrasse within the family Labridae. This fish species has particular biological and socio-cultural characteristics making it an ideal model organism in the fields of behavioural ecology, molecular ecology and conservation biology. In this study, we present the first annotated chromosome-level assembly for this species. Sequencing involved a combination of long reads with Oxford Nanopore Technologies, Illumina paired-end short reads (2 × 151 bp), Hi-C and RNA-seq from different tissues. The nuclear genome assembly has a scaffold N50 of 34.33 Mb, a total assembly span of 775.53 Mb and 99.63% of the sequence assembled into 24 superscaffolds, consistent with its known karyotype. Quality metrics revealed a consensus accuracy (QV) of 42.92 and gene completeness &gt; 98%. The genome annotation resulted in 26,690 protein-coding genes and 12,737 non-coding transcripts. The coding regions encoded 39,613 unique protein products, 93% of them with assigned function. Overall, the publication of the X. novacula’s reference genome will broaden the scope and impact of genomic research conducted on this iconic and colourful species.
Echo Chambers: Social Learning under Unobserved Heterogeneity
Authors: Williams Cole 
Published: October 2023

AbstractPeople are often more influenced by opinions similar to their own and even seek information from those with whom they expect to most agree—behaviours often attributed to irrational biases. In this paper, I argue that these behaviours can be understood within the context of rational social learning by accounting for the presence of unobserved heterogeneity in preferences or priors. Individuals display local learning by placing greater weight on opinions that are closer to their own. When individuals choose whom to learn from, local learning leads to the development of echo chambers.
Evolutionarily labile dispersal behavior and discontinuous habitats enhance population differentiation in island versus continentally distributed swallows
Authors: Broyles Grant G , Myers Brian M , Friedman Nicholas R , Gawin Dency F , Mohd-Taib Farah S , Sahlan Penigran G M , Seneviratne Sampath S , de Silva N Chamalka G , Lekamlage Thilini T M , Hund Amanda K , Scordato Elizabeth S C 
Published: October 2023

Abstract
The causes of population divergence in vagile groups remain a paradox in evolutionary biology: dispersive species should be able to colonize new areas, a prerequisite for allopatric speciation, but dispersal also facilitates gene flow, which erodes population differentiation. Strong dispersal ability has been suggested to enhance divergence in patchy habitats and inhibit divergence in continuous landscapes, but empirical support for this hypothesis is lacking. Here we compared patterns of population divergence in a dispersive clade of swallows distributed across both patchy and continuous habitats. The Pacific Swallow (Hirundo tahitica) has an insular distribution throughout Southeast Asia and the Pacific, while its sister species, the Welcome Swallow (H. neoxena), has a continental distribution in Australia. We used whole-genome data to demonstrate strong genetic structure and limited introgression among insular populations, but not among continental populations. Demographic models show that historic changes in habitat connectivity have contributed to population structure within the clade. Swallows appear to exhibit evolutionarily labile dispersal behavior in which they reduce dispersal propensity after island colonization despite retaining strong flight ability. Our data support the hypothesis that fragmented habitats enhance population differentiation in vagile groups, and suggest that labile dispersal behavior is a key mechanism underlying this pattern.
A novel synthetic inhibitor of polyamine utilization in Streptomyces coelicolor
Authors: Krysenko Sergii , Lopez Maria , Meyners Christian , Purder Patrick L , Zinser Alina , Hausch Felix , Wohlleben Wolfgang 
Published: October 2023

Abstract
In this work, we present the first inhibitor of GlnA2Sc, a gamma-glutamylpolyamine synthetase, which allows Streptomyces coelicolor to detoxify high concentrations of polyamines and to utilize them as a carbon or nitrogen source. GlnA2 belongs to the class of glutamine synthetase-like (GS-like) enzymes that catalyze the glutamylation of different nitrogen-containing compounds. Whereas a number of inhibitors for GS are known, none of them are known to inhibit GlnA2. In this work, PPU268, an inhibitor for GlnA2 is presented that is structurally derived from the prototypic GS inhibitor—methionine sulfoximine (MSO). It combines two features: the binding mechanism of MSO and the amine substrate specificity of GlnA2Sc. This inhibitor is a novel compound to block the polyamine utilization in bacteria resulting in the inability to detoxify polyamines. This may offer a possibility to develop novel therapeutic strategies to combat actinobacterial human pathogens that encounter polyamines in the course of the infection processes.
Beyond Inflammaging: The Impact of Immune System Aging on Age-Related Muscle Decline, Results From the InCHIANTI Study
Authors: Pellegrino Raffaello , Paganelli Roberto , Di Iorio Angelo , Bandinelli Stefania , Moretti Antimo , Iolascon Giovanni , Sparvieri Eleonora , Tarantino Domiziano , Tanaka Toshiko , Ferrucci Luigi 
Published: October 2023

Abstract
Aging is characterized by chronic low-level inflammation and is associated with geriatric syndromes such as sarcopenia and frailty. Our aim was to evaluate the longitudinal variation of muscle area, muscle quality, and muscle strength, relative to the variation of leukocyte-derived markers, and to assess the presence of a pathway of associations among derived leukocyte ratios, and the components of muscle health. The InCHIANTI is a longitudinal cohort study of aging that began in 1998 with follow-up visits every 3 years. Out of the 1 453 participants enrolled at baseline, this study includes 1 179 participants with complete data. Muscle strength was assessed by hand grip strength test, whereas muscle density and fat area were considered as indirect markers of muscle quality, derived from peripheral quantitative computed tomography of the calf. Muscle area was associated with neutrophil-to-lymphocyte ratio (NL-ratio), age, gender, comorbidities, and body mass index (BMI). Muscle density variation over time was inversely associated with age, comorbidities, and BMI, while being positively associated with monocyte-to-lymphocyte ratio (ML-ratio) and male gender. Fat area was inversely associated with age, interleukine-6 (IL-6), male gender, and NL-ratio, while being positively associated with ML-ratio, comorbidities, and BMI. Handgrip strength decreased with age, IL-6 levels, comorbidities, and NL-ratio, but increased with ML-ratio, being male, and having a higher BMI. In a path-analysis model, ML-ratio positively correlates with muscle mass, density, and strength, while NL-ratio only correlates inversely with muscle mass and density. NL-ratio and ML-ratio are associated with aging and may be implicated in age-related mechanisms that affect body composition and muscle strength. These ratios may represent a link between aging of the immune system and decline of muscle health with aging. However, further studies are needed to identify their usefulness for early detection of sarcopenia, myosteatosis, and frailty in the older adult.
Imaging upper mantle anisotropy with traveltime and splitting intensity observations from teleseismic shear waves: insights from tomographic reconstructions of subduction simulations
Authors: VanderBeek Brandon P , Bue Rosalia Lo , Rappisi Francesco , Faccenda Manuele 
Published: October 2023

SUMMARYTeleseismic traveltime tomography remains one of the most popular methods for obtaining images of Earth’s upper mantle. However, despite extensive evidence for an elastically anisotropic mantle, the isotropic assumption remains commonplace in such imaging studies. This can result in significant model artefacts which in turn may yield misguided inferences regarding mantle dynamics. The nature of anisotropy-induced apparent velocity anomalies has been well-documented in P-wave imaging and various strategies have been proposed to constrain both isotropic and anisotropic heterogeneity from these data. In contrast, few studies have explored the consequences for shear wave tomography and no practical framework for the anisotropic inversion of S-wave delays exists. Here, we propose a new method for constraining arbitrarily oriented hexagonal anisotropy using both traveltime and splitting intensity observations from direct S phases. Our approach accounts for polarization and finite-frequency effects and allows for isotropic starting models. The imaging method is validated through the tomographic analysis of a realistic synthetic dataset produced from waveform simulations through a geodynamic model of subduction. Results illustrate that neglecting anisotropy produces distortions in slab geometry and the appearance of sub- and supraslab low-velocity zones. Anisotropic inversions remove these artefacts while also constraining geodynamically relevant fabric properties including dip.
Towards the usage of quarry blasts as an active seismic source for subsurface characterization and imaging
Authors: Li Peiyao , Nakata Nori , Kolawole Folarin , Carpenter Brett M , Qiu Hongrui 
Published: October 2023

SUMMARY
Active or man-made seismic sources are often used to delineate subsurface geological structures via seismic imaging techniques. Although conventional controlled seismic sources have provided high-resolution subsurface images, the high cost of data acquisition necessitates improved use of cheaper alternative seismic sources for subsurface imaging, such as traffic noise, quarry blasts and earthquakes. Here, we explore the potential use of quarry blasts as an active seismic source for subsurface imaging. The goal of our study is to demonstrate the utility of quarry blasts as seismic sources for investigating subsurface structure with a field experiment in Mill Creek, southern Oklahoma. We deployed a 7455-m-long receiver line of 72 receivers (105 m spacing) extending away from a quarry, with a recording time of 28 d. We analyse similarities between blasts, wave types, origin time and excitation location of quarry blasts, which is important information for using such signal as an active source. Given a relative homogeneous geological condition in the study area, we could not observe clear reflected waves. However, the use of P- and S-wave velocities led to the delineation of a major basement damage zone in the study area, which further demonstrates the viability of quarry blasts as a useful seismic source for subsurface geological imaging.
The intersection of HIF-1α, O-GlcNAc, and skeletal muscle loss in chronic obstructive pulmonary disease
Authors: Sekar Jinendiran , Attaway Amy H 
Published: October 2023

Abstract
Sarcopenia, defined as the loss of muscle mass and strength, is a major cause of morbidity and mortality in COPD (chronic obstructive pulmonary disease) patients. However, the molecular mechanisms that cause sarcopenia remain to be determined. In this review, we will highlight the unique molecular and metabolic perturbations that occur in the skeletal muscle of COPD patients in response to hypoxia, and emphasize important areas of future research. In particular, the mechanisms related to the glycolytic shift that occurs in skeletal muscle in response to hypoxia may occur via a hypoxia-inducible factor 1-alpha (HIF-1α)-mediated mechanism. Upregulated glycolysis in skeletal muscle promotes a unique post-translational glycosylation of proteins known as O-GlcNAcylation, which further shifts metabolism toward glycolysis. Molecular changes in the skeletal muscle of COPD patients are associated with fiber-type shifting from Type I (oxidative) muscle fibers to Type II (glycolytic) muscle fibers. The metabolic shift toward glycolysis caused by HIF-1α and O-GlcNAc modified proteins suggests a potential cause for sarcopenia in COPD, which is an emerging area of future research.
Intratracheal recurrence of thymoma 7 years after complete resection
Authors: Fukuyama Kaoru , Funakoshi Yasunobu 
Published: October 2023

Abstract
A 66-year-old woman with a massive anterior mediastinal tumour was diagnosed with type B2 thymoma. After 2 courses of chemotherapy, extended thymectomy and partial resection of the lung and large vessels were performed, and the tumour was completely resected. The patient received no postoperative therapy. Seven years after the surgery, follow-up chest computed tomography showed a papillary soft tissue tumour in the trachea almost obstructing the airway. Intratracheal tumour resection was performed under rigid bronchoscopy, and the pathological diagnosis of intratracheal recurrence of thymoma was made. The patient received postoperative radiotherapy and has remained alive without disease progression 9 months after the second operation.
The Clinical and Economic Burden of Antibiotic Use in Pediatric Patients With Varicella Infection: A Retrospective Cohort Analysis of Real-World Data in England
Authors: Kujawski Stephanie A , Banks Victoria , Casey Caroline S , Drysdale Simon B , Patel Amisha , Massey Olivia , Holbrook Tim , Pawaskar Manjiri 
Published: October 2023

Abstract

Background
Varicella is a highly infectious disease, particularly affecting children, that can lead to complications requiring antibiotics or hospitalization. Antibiotic use for varicella management is poorly documented. This study assessed antibiotic use for varicella and its complications in a pediatric population in England.

Methods
Data were drawn from medical records in the Clinical Practice Research Datalink and Hospital Episode Statistics data sets. The study included patients &lt;18 years old with varicella diagnosed during 2014–2018 and 3-month follow-up available. We determined varicella-related complications, medication use, healthcare resource utilization, and costs from diagnosis until 3 months after diagnosis.

Results
We identified 114 578 children with a primary varicella diagnosis. Of these, 7.7% (n = 8814) had a varicella-related complication, the most common being ear, nose, and throat related (37.1% [n = 3271]). In all, 25.9% (n = 29 706 of 114 578) were prescribed antibiotics. A higher proportion of patients with complications than without complications were prescribed antibiotics (64.3% [n = 5668 of 8814] vs 22.7% [n = 24 038 of 105 764]). Mean annualized varicella-related costs were £2 231 481 for the study cohort. Overall, antibiotic prescriptions cost approximately £262 007.

Conclusions
This study highlights high antibiotic use and healthcare resource utilization associated with varicella management, particularly in patients with complications. A national varicella vaccination program in England may reduce varicella burden and related complications, medication use, and costs.
Growth of alfalfa in the presence of metabolites from a dark septate endophyte strain Alternaria sp. 17463 cultured with a nonionic surfactant and emulsifier
Authors: Tan Hai , Bi Yinli , Zhang Shishuang , Wang Shuhui 
Published: October 2023

Abstract

Aim
Dark septate endophytes (DSE) were widely used in the agriculture and ecological restoration. The objective of this work was to assess the effect of culture media nonionic surfactant and emulsifier on the biomass and metabolites of DSE strain Alternaria sp. 17463.

Methods and results
Changes in the composition of DSE metabolites following the addition of Tween 80 during liquid culture of a DSE fungus were analyzed and used in growth tests of alfalfa.
Shaking flask fermentation was carried out and the surfactant was fed to the fungus during the fermentation. The residual sugar content and pH declined significantly in the medium and the biomass of DSE increased by 7.27% over controls with no surfactant. Metabolomic analysis showed that adding the surfactant significantly increased the content of 63 metabolites (P &lt; 0.05). These include lipids and lipid-like molecules, organooxygen compounds, amino acids and organic acids, and flavonoids. Enrichment analysis of metabolic pathways indicates that surfactant addition promoted carbohydrate metabolism and amino acid synthesis. A plant hydroponic experiment indicated that these changes in metabolites altered the root structure of alfalfa seedlings. They also promoted significant increases in root length and root surface area, and increased alfalfa total biomass by 50.2%.

Conclusions
The addition of the surfactant promoted sugar utilization by the DSE fungus and increased the synthesis of lipids and amino acids, resulting in the ability of the fungal metabolites to change root structure and promote plant growth.
Induction of Skin Allograft Chimerism by Pharmacological Mobilization of Endogenous Bone Marrow-Derived Stem Cells
Authors: Ahmadi Ali R , Wesson Russell N , Huang Jinny , Harmon John , Burdick James F , Cameron Andrew M , Sun Zhaoli 
Published: October 2023

Abstract
Skin substitutes including allografts remain a standard therapeutic approach to promote healing of both acute and chronic large wounds. However, none have resulted in the regrowth of lost and damaged tissues and scarless wound healing. Here, we demonstrate skin allograft chimerism and repair through the mobilization of endogenous bone marrow-derived stem and immune cells in rats and swine. We show that pharmacological mobilization of bone marrow stem cells and immune cells into the circulation promotes host repopulation of skin allografts and restoration of the skin’s normal architecture without scarring and minimal contracture. When skin allografts from DA rats are transplanted into GFP transgenic Lewis recipients with a combination of AMD3100 and low-dose FK506 (AF) therapy, host-derived GFP-positive cells repopulate and/or regenerate cellular components of skin grafts including epidermis and hair follicles and the grafts become donor-host chimeric skin. Using AF combination therapy, burn wounds with skin allografts were healed by newly regenerated chimeric skin with epidermal appendages and pigmentation and without contracture in swine.
Effects of lysine deacetylase inhibitor treatment on LPS responses of alveolar-like macrophages
Authors: Russo Sara , Kwiatkowski Marcel , Wolters Justina C , Gerding Albert , Hermans Jos , Govorukhina Natalia , Bischoff Rainer , Melgert Barbro N 
Published: October 2023

Abstract
Macrophages are key immune cells that can adapt their metabolic phenotype in response to different stimuli. Lysine deacetylases are important enzymes regulating inflammatory gene expression and lysine deacetylase inhibitors have been shown to exert anti-inflammatory effects in models of chronic obstructive pulmonary disease. We hypothesized that these anti-inflammatory effects may be associated with metabolic changes in macrophages. To validate this hypothesis, we used an unbiased and a targeted proteomic approach to investigate metabolic enzymes, as well as liquid chromatography–mass spectrometry and gas chromatography–mass spectrometry, to quantify metabolites in combination with the measurement of functional parameters in primary murine alveolar-like macrophages after lipopolysaccharide-induced activation in the presence or absence of lysine deacetylase inhibition. We found that lysine deacetylase inhibition resulted in reduced production of inflammatory mediators such as tumor necrosis factor α and interleukin 1β. However, only minor changes in macrophage metabolism were observed, as only one of the lysine deacetylase inhibitors slightly increased mitochondrial respiration while no changes in metabolite levels were seen. However, lysine deacetylase inhibition specifically enhanced expression of proteins involved in ubiquitination, which may be a driver of the anti-inflammatory effects of lysine deacetylase inhibitors. Our data illustrate that a multiomics approach provides novel insights into how macrophages interact with cues from their environment. More detailed studies investigating ubiquitination as a potential driver of lysine deacetylase inhibition will help developing novel anti-inflammatory drugs for difficult-to-treat diseases such as chronic obstructive pulmonary disease.