bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pleomorphic sarcoma secondary to proximal femoral epiphysiolysis with bone infarction over 4 years after cementless total hip replacement in a dog
Authors: Barnhart Matthew D. , Pool Roy , Liska William D. 
Published: August 2024

AbstractObjectiveTo report a capital physeal fracture as the result of a bone infarction with subsequent neoplastic transformation 4 years following total hip replacement.Study designCase report.AnimalsFive‐year‐old female spayed golden retriever.MethodsThe dog was initially presented for evaluation of a 2 week history of spontaneous right hind‐limb lameness. Pelvic radiographs demonstrated a displaced capital epiphysis and proximal femur changes consistent with a bone infarction. A cementless total hip replacement was performed, and limb function returned to normal until 51 months after surgery. A radiolucency adjacent to the femoral stem at the greater trochanter, partial calcar resorption, and stable implants were present on pelvic radiographs acquired 52 months after surgery. Surgical exploration of the surgical site for tissue collection for histopathology and bacteria culture was performed 58 months following surgery. No bacterial growth occurred and histologic findings were nonspecific. A right hind‐limb amputation was performed 61 months after total hip replacement due to the dog's progression to a non‐weight‐bearing lameness, Additional tissue samples were taken from the femur for histopathologic examination.ResultsHistopathologic examination was consistent with a pleomorphic sarcoma. No metallic or polyethylene particulate debris was present. Nine months after surgery there was evidence of regional and distant spread of the neoplasia.ConclusionIn similar cases, submitting the femoral head for histopathologic examination should be considered at the time of the hip replacement surgery. If bone infarction is diagnosed as a causative agent, given the possibility of malignant transformation, long‐term serial radiographic monitoring should be given serious consideration.
Evaluation of Data-Driven Classifiers for an Ignition Forecast of Large Gas Turbines
Authors: Lang Florian , Savtschenko Maximilian , Yadav Vikas , Ghani Abdulla 
Published: August 2024

Abstract
Prediction of successful ignition is a challenging task that requires knowledge of the local thermochemical state in highly turbulent flow conditions. For typical industrial gas turbine (GTs) conditions operated on active service, these pieces of information are not directly available despite the high impact of ignition on technological and economic performance. The success of ignition mainly depends on the experiences made with the specific GT during long-term operation. Hence, there is a need for reliable prediction models for successful ignition that take the current conditions of the engine into account. We demonstrate the performance of supervised machine learning (ML) models to predict both successful and failed ignitions of GTs based on “real world” fleet data from the SGTx-8000H frame. This study compares the classification ability of seven widely used algorithms, for which we initially select 22 engineering-relevant parameters based on sensor data. We employ correlation and elimination techniques to reduce the parameter space drastically so that with only two input parameters we achieve a high (87%) prediction accuracy. Finally, we highlight the generalizability of the best performing ML model by application to unseen data of a different GT and report, for another case, on a recommissioned GT that is assisted by the ML model and consistently ignites the engine over an extended period of time.
Deoxyshikonin: a promising lead drug grass against drug resistance or sensitivity to
Helicobacter pylori
in an acidic environment
Authors: Xu Jia-yin , Dong Hui-hua , Liao Li-juan , Yang Shi-xian , Wang Lu-yao , Chen Hao , Luo Peipei , Huang Liang , Guan Ai-xing , Huang Yan-Qiang 
Published: August 2024

ABSTRACT

Helicobacter pylori
(
H. pylori
) is closely associated with the diseases such as gastric sinusitis, peptic ulcers, and gastric adenocarcinoma. Its drug resistance is very severe, and new antibiotics are urgently needed. Nine comfrey compounds were screened by antimicrobial susceptibility testing, among which deoxyshikonin had the best inhibitory effect, with a minimum inhibitory concentration (MIC) of 0.5–1 µg/mL. In addition, deoxyshikonin also has a good antibacterial effect in an acidic environment, it is highly safe, and
H. pylori
does not readily develop drug resistance. Through
in vivo
experiments, it was proven that deoxyshikonin (7 mg/kg) had a beneficial therapeutic effect on acute gastritis in mice infected with the multidrug-resistant
H. pylori
BS001 strain. After treatment with desoxyshikonin, colonization of
H. pylori
in the gastric mucosa of mice was significantly reduced, gastric mucosal damage was repaired, inflammatory factors were reduced, and the treatment effect was better than that of standard triple therapy. Therefore, deoxyshikonin is a promising lead drug to solve the difficulty of drug resistance in
H. pylori
, and its antibacterial mechanism may be to destroy the biofilm and cause an oxidation reaction.
An approach to analyze spatiotemporal patterns of gene expression at single-cell resolution in
Candida albicans
-infected mouse tongues
Authors: Lindemann-Perez Elena , Rodríguez Diana L. , Pérez J. Christian 
Published: August 2024

ABSTRACT

Microbial gene expression measurements derived from infected organs are invaluable to understand pathogenesis. However, current methods are limited to “bulk” analyses that neglect microbial cell heterogeneity and the lesion's spatial architecture. Here, we report the use of hybridization chain reaction RNA fluorescence
in situ
hybridization (HCR RNA-FISH) to visualize and quantify
Candida albicans
transcripts at single-cell resolution in tongues of infected mice. The method is compatible with fixed-frozen and formalin-fixed paraffin-embedded tissues. We document cell-to-cell variation and intriguing spatiotemporal expression patterns for
C. albicans
mRNAs that encode products implicated in oral candidiasis. The approach provides a spatial dimension to gene expression analyses of host-
Candida
interactions.

IMPORTANCE

Candida albicans
is a fungal pathobiont inhabiting multiple mucosal surfaces of the human body. Immunosuppression, antibiotic-induced microbial dysbiosis, or implanted medical devices can impair mucosal integrity enabling
C. albicans
to overgrow and disseminate, causing either mucosal diseases such as oropharyngeal candidiasis or life-threatening systemic infections. Profiling fungal genes that are expressed in the infected mucosa or in any other infected organ is paramount to understand pathogenesis. Ideally, these transcript profiling measurements should reveal the expression of any gene at the single-cell level. The resolution typically achieved with current approaches, however, limits most gene expression measurements to cell population averages. The approach described in this report provides a means to dissect fungal gene expression in infected tissues at single-cell resolution.
Gut dysbiosis contributes to the development of Budd-Chiari syndrome through immune imbalance
Authors: Lu Qinwei , Zhu Rongtao , Zhou Lin , Zhang Ruifang , Li Zhen , Xu Peng , Wang Zhiwei , Wu Gang , Ren Jianzhuang , Jiao Dechao , Song Yan , Li Jian , Wang Weijie , Liang Ruopeng , Ma Xiuxian , Sun Yuling 
Published: August 2024

ABSTRACT

Budd-Chiari syndrome (B-CS) is a rare and lethal condition characterized by hepatic venous outflow tract blockage. Gut microbiota has been linked to numerous hepatic disorders, but its significance in B-CS pathogenesis is uncertain. First, we performed a case-control study (
N
case
= 140,
N
control
= 63) to compare the fecal microbiota of B-CS and healthy individuals by metagenomics sequencing. B-CS patients’ gut microbial composition and activity changed significantly, with a different metagenomic makeup, increased potentially pathogenic bacteria, including
Prevotella
, and disease-linked microbial function. Imbalanced cytokines in patients were demonstrated to be associated with gut dysbiosis, which led us to suspect that B-CS is associated with gut microbiota and immune dysregulation. Next, 16S ribosomal DNA sequencing on fecal microbiota transplantation (FMT) mice models examined the link between gut dysbiosis and B-CS. FMT models showed damaged liver tissues, posterior inferior vena cava, and increased
Prevotella
in the disturbed gut microbiota of FMT mice. Notably, B-CS-FMT impaired the morphological structure of colonic tissues and increased intestinal permeability. Furthermore, a significant increase of the same cytokines (IL-5, IL-6, IL-9, IL-10, IL-17A, IL-17F, and IL-13) and endotoxin levels in B-CS-FMT mice were observed. Our study suggested that gut microbial dysbiosis may cause B-CS through immunological dysregulation.

IMPORTANCE

This study revealed that gut microbial dysbiosis may cause Budd-Chiari syndrome (B-CS). Gut dysbiosis enhanced intestinal permeability, and toxic metabolites and imbalanced cytokines activated the immune system. Consequently, the escalation of causative factors led to their concentration in the portal vein, thereby compromising both the liver parenchyma and outflow tract. Therefore, we proposed that gut microbial dysbiosis induced immune imbalance by chronic systemic inflammation, which contributed to the B-CS development. Furthermore,
Prevotella
may mediate inflammation development and immune imbalance, showing potential in B-CS pathogenesis.
Comprehensive evaluation of primer pairs targeting the ammonia monooxygenase subunit A gene of complete ammonia-oxidizing
Nitrospira
Authors: Blom Pieter , Smith Garrett J. , van Kessel Maartje A. H. J. , Koch Hanna , Lücker Sebastian 
Published: August 2024

ABSTRACT

Since the discovery of complete ammonia oxidizers (comammox) within the genus
Nitrospira
, their distribution and abundance across habitats have been intensively studied to better understand their ecological significance. Many primers targeting their ammonia monooxygenase subunit A gene (
amoA
) have been designed to detect and quantify comammox bacteria and to describe their community structure. We identified 38 published primers, but only few had high coverage and specificity for all known comammox
Nitrospira
or one of the two described subclades. For each target group, we comprehensively evaluated selected primer pairs using
in silico
analyses, endpoint PCRs, qPCRs, and amplicon sequencing on samples from various environments. Endpoint PCRs and qPCRs showed that the most commonly used primer pairs (comaA-244F/659R, comaB-244F/659R, and Ntsp-amoA162F/359R) produced several bands, which likely inflated quantifications via qPCR. In contrast, the recently published primer combinations CA377F/C576R, CB377F/C576R, and CA-CB377F/C576R resulted mostly in a single band. Furthermore, amplicon sequencing demonstrated that these primer combinations also captured the highest richness of comammox
Nitrospira
. Taken together, our results indicate that few existing comammox
amoA
primer combinations have both high specificity and coverage and that the choice of these high-specificity and high-coverage primer pairs substantially impacts the accurate detection, quantification, and community description of comammox bacteria. We, therefore, recommend using the CA377F/C576R, CB377F/C576R, and CA-CB377F/C576R primer pairs.

IMPORTANCE
Bacteria that can fully convert ammonia via nitrite to nitrate, the complete ammonia oxidizers (comammox), were recently discovered and are found in many natural and engineered environments. PCR-based tools to study their abundance and diversity were rapidly developed, resulting in a plethora of primers available, many of which are widely used. The presence of comammox bacteria in an environment can, however, only be correctly determined if the used primers detect all members of this group while not detecting any other guilds. This study assesses the coverage and specificity of existing primers targeting comammox bacteria using both computational and standard molecular techniques, revealing large differences in their performance. The uniform usage of well-performing primers across studies could aid in generating comparable and generalizable data to better understand the importance of comammox bacteria in the environment.
Whole genome analysis of multidrug-resistant
Escherichia coli
isolate collected from drinking water in Armenia revealed the plasmid-borne
mcr-1.1-
mediated colistin resistance
Authors: Karpenko Anna , Shelenkov Andrey , Manzeniuk Igor , Kulikova Nina , Gevorgyan Arman , Mikhaylova Yulia , Akimkin Vasiliy 
Published: August 2024

ABSTRACT

The rate of polymyxin-resistant
Enterobacteriaceae
, as well as human and animal infections caused by them, is increasing worldwide, posing a high epidemiological threat since colistin represents a last-resort antibiotic to treat complicated infections. The study of environmental niches, in particular, aquatic ecosystems in terms of genome analysis of inhabiting antimicrobial-resistant (AMR) microorganisms as reservoirs of acquired resistance determinants (AMR genes), represents a specific concern from a One Health approach. Here, we present a phenotypic AMR analysis and molecular characterization of
Escherichia coli
isolate found in municipal drinking water after an accident in the water supply system of a residential building in Armenia in 2021. CrieF1144
E. coli
isolate was resistant to ampicillin, ampicillin/sulbactam, cefuroxime, ciprofloxacin, levofloxacin, trimethoprim/sulfamethoxazole, colistin, and tigecycline, whereas whole genome sequencing (WGS) revealed
blaTEM-1B
,
tet(A
), and a combination of
dfrA14
with
sul1
resistance determinants, which corresponds well with phenotypic resistance above. Moreover, the multidrug-resistant isolate studied harbored
mcr-1.1
gene on a conjugative 251 Kb IncHI2 plasmid, whose structure was determined using hybrid short- and long-reads assembly. CrieF1141_p1 plasmid carried all antimicrobial resistance genes revealed in the isolate and did not harbor any virulence determinants, so it could contribute to the spread of AMR genes in the bacterial population. Two copies of ISApl1 transposase-encoding element, which is likely to mediate
mcr-1.1
gene mobilization, were revealed surrounding this gene in a plasmid.

IMPORTANCE

Evolutionary patterns of
Escherichia coli
show that they usually develop into highly pathogenic forms by acquiring fitness advantages such as antimicrobial resistance (AMR) and various virulence factors through horizontal gene transfer mediated by mobile elements. This has led to high prevalence of multidrug-resistant (MDR) strains, which highlights the relevancy of enhanced surveillance to monitor and prevent transmission of the MDR bacteria to human and animal populations. However, the limited number of reports regarding the whole genome sequencing (WGS) investigation of MDR
E. coli
strains isolated from drinking water and harboring
mcr
genes hampers the adoption of a comprehensive approach to address the relationship between environmental
E. coli
populations and human and veterinary infections. Our results highlight the relevance of analyzing the environment, especially water, as a part of the surveillance programs to understand the origins and dissemination of antimicrobial resistance within the One Health concept.
Clostridioides difficile
exploits xanthine and uric acid as nutrients by utilizing a selenium-dependent catabolic pathway
Authors: Johnstone Michael A. , Self William T. 
Published: August 2024

ABSTRACT

Selenium is a trace element that plays critical roles in redox biology; it is typically incorporated into “selenoproteins” as the 21st amino acid selenocysteine. Additionally, selenium exists as a labile non-selenocysteine cofactor in a small subset of selenoproteins known as selenium-dependent molybdenum hydroxylases (SDMHs). In purinolytic clostridia, SDMHs are implicated in the degradation of hypoxanthine, xanthine, and uric acid for carbon and nitrogen. While SDMHs have been biochemically analyzed, the genes responsible for the insertion and maturation of the selenium cofactor lack characterization. In this study, we utilized the nosocomial pathogen
Clostridioides difficile
as a genetic model to begin characterizing this poorly understood selenium utilization pathway and its role in the catabolism of host-derived purines. We first observed that
C. difficile
could utilize hypoxanthine, xanthine, or uric acid to overcome a growth defect in a minimal medium devoid of glycine and threonine. However, strains lacking selenophosphate synthetase (
selD
mutants) still grew poorly in the presence of xanthine and uric acid, suggesting a selenium-dependent purinolytic process. Previous computational studies have identified
yqeB
and
yqeC
as potential candidates for cofactor maturation, so we subsequently deleted each gene using CRISPR-Cas9 technology. We surprisingly found that the growth of the Δ
yqeB
mutant in response to each purine was similar to the behavior of the
selD
mutants, while the Δ
yqeC
mutant exhibited no obvious phenotype. Our results suggest an important role for YqeB in selenium-dependent purine catabolism and also showcase
C. difficile
as an appropriate model organism to study the biological use of selenium.

IMPORTANCE

The apparent modification of bacterial molybdenum hydroxylases with a catalytically essential selenium cofactor is the least understood mechanism of selenium incorporation. Selenium-dependent molybdenum hydroxylases play an important role in scavenging carbon and nitrogen from purines for purinolytic clostridia. Here, we used
Clostridioides difficile
as a genetic platform to begin dissecting the selenium cofactor trait and found genetic evidence for a selenium-dependent purinolytic pathway. The absence of
selD
or
yqeB
—a predicted genetic marker for the selenium cofactor trait—resulted in impaired growth on xanthine and uric acid, known substrates for selenium-dependent molybdenum hydroxylases. Our findings provide a genetic foundation for future research of this pathway and suggest a novel metabolic strategy for
C. difficile
to scavenge host-derived purines from the gut.
Airway consequences of alendronic acid aspiration
Authors: Lonsdale Henry , Sawant Rupali , Kinshuck Andrew , Fleming Jason 
Published: August 2024

Bisphosphonates are commonly prescribed medications to prevent and treat osteoporosis. Although possessing low side effect profiles, the potential for severe topical effects is rare but important. Irritation of the upper gastrointestinal tract is well documented; however, the risk and effects of accidental aspiration are rarely reported.Attention is drawn to a case recently managed at a tertiary head and neck centre where a patient in their 70s was admitted in respiratory distress 3 days after aspirating alendronic acid. This case highlights the potential risk of topical chemical injury posed to the airway by bisphosphonates.Bisphosphonates should be prescribed with detailed and specific counselling regarding this risk. Pharmacological product literature should be updated to reflect the risk. Clinical teams should be aware of and vigilant for the delayed presentation and prolonged symptom course of such injuries. Prompt airway intervention and techniques to minimise further mucosal trauma ensure optimal outcomes.
Large language models: a new frontier in paediatric cataract patient education
Authors: Dihan Qais , Chauhan Muhammad Z , Eleiwa Taher K , Brown Andrew D , Hassan Amr K , Khodeiry Mohamed M , Elsheikh Reem H , Oke Isdin , Nihalani Bharti R , VanderVeen Deborah K , Sallam Ahmed B , Elhusseiny Abdelrahman M 
Published: August 2024

Background/aimsThis was a cross-sectional comparative study. We evaluated the ability of three large language models (LLMs) (ChatGPT-3.5, ChatGPT-4, and Google Bard) to generate novel patient education materials (PEMs) and improve the readability of existing PEMs on paediatric cataract.MethodsWe compared LLMs’ responses to three prompts. Prompt A requested they write a handout on paediatric cataract that was ‘easily understandable by an average American.’ Prompt B modified prompt A and requested the handout be written at a ‘sixth-grade reading level, using the Simple Measure of Gobbledygook (SMOG) readability formula.’ Prompt C rewrote existing PEMs on paediatric cataract ‘to a sixth-grade reading level using the SMOG readability formula’. Responses were compared on their quality (DISCERN; 1 (low quality) to 5 (high quality)), understandability and actionability (Patient Education Materials Assessment Tool (≥70%: understandable, ≥70%: actionable)), accuracy (Likert misinformation; 1 (no misinformation) to 5 (high misinformation) and readability (SMOG, Flesch-Kincaid Grade Level (FKGL); grade level <7: highly readable).ResultsAll LLM-generated responses were of high-quality (median DISCERN ≥4), understandability (≥70%), and accuracy (Likert=1). All LLM-generated responses were not actionable (<70%). ChatGPT-3.5 and ChatGPT-4 prompt B responses were more readable than prompt A responses (p<0.001). ChatGPT-4 generated more readable responses (lower SMOG and FKGL scores; 5.59±0.5 and 4.31±0.7, respectively) than the other two LLMs (p<0.001) and consistently rewrote them to or below the specified sixth-grade reading level (SMOG: 5.14±0.3).ConclusionLLMs, particularly ChatGPT-4, proved valuable in generating high-quality, readable, accurate PEMs and in improving the readability of existing materials on paediatric cataract.
Impact of multiple obesity metrics on hypertensive disorders of pregnancy: a meta-analysis and Mendelian randomisation study
Authors: Sun Mengting , Gao Ming , Luo Manjun , Wang Tingting , Ruan Xiaorui , Tang Jiapeng , Chen Qian , Liu Hanjun , Li Liuxuan , Qin Jiabi 
Published: August 2024

BackgroundThe relationships between various obesity measures and hypertensive disorders of pregnancy (HDP) remain inadequately explored, and their causal links are not well understood. This study aims to clarify these associations and investigate the mediating role of triglycerides.MethodsWe conducted a comprehensive meta-analysis of observational studies alongside Mendelian randomisation (MR) analysis to assess the impact of 10 obesity measures on HDP risk. Additionally, we evaluated the mediating effect of triglycerides.ResultsOur meta-analysis revealed significant associations between maternal prepregnancy overweight/obesity and increased risks of gestational hypertension (GH) (overweight: OR=1.98, 95% CI 1.83 to 2.15; obesity: OR=3.77, 95% CI 3.45 to 4.13) and pre-eclampsia (overweight: OR=1.78, 95% CI 1.67 to 1.90; obesity: OR=3.46, 95% CI 3.16 to 3.79). Higher maternal waist circumference (WC) was also linked to increased pre-eclampsia risk (OR=1.45, 95% CI 1.14 to 1.83). MR analyses indicated that each 1-SD increase in genetically predicted obesity measures (whole body fat mass, body fat percentage, trunk fat mass, trunk fat percentage, body mass index, WC, hip circumference) was associated with higher risks of GH and pre-eclampsia. Triglycerides mediated 4.3%–14.1% of the total genetic effect of these obesity measures on GH and pre-eclampsia risks.ConclusionsThis study demonstrates that various obesity measures are causally linked to increased HDP risk and highlights the mediating role of triglycerides. These findings could inform clinical practices and public health strategies aimed at reducing HDP through targeted obesity and triglyceride management.