bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimating optimal temperature conditions for growth, development, and reproduction of Tenebrio molitor (Coleoptera: Tenebrionidae)
Authors: Morales-Ramos Juan A , Macchiano Anthony , Rojas Maria Guadalupe
Published: December 2024

The yellow mealworm, Tenebrio molitor L., is one of the most important industrialized insects worldwide. As a poikilotherm, T. molitor requires a temperature-regulated environment for its farming. Currently, the farming of T. molitor uses temperatures between 29 and 31°C determined to be optimal for maximizing growth. This study was aimed to test and determine optimal temperature for T. molitor impacting all stages including their development, reproduction, and fitness. Pupae of T. molitor were exposed to 8 different temperatures (18, 21, 24, 27, 30, 33, 36, and 39°C). Developmental rates (=1/d to develop) were calculated at 8 temperatures and fitted in a poikilotherm model to determine the temperature with the highest developmental rate (developmental maximum, To). The developmental maximum was 33°C and the thermal maximum (tm) (lethal temperature) was 39°C. The biological and demographic parameters of T. molitor were compared at 3 favorable temperatures below the To (31, 29, and 27°C) to determine the fitness of T. molitor populations. Fecundity and egg viability were the highest at 27°C (5.25 eggs/female/d and 73.99%, respectively) and the lowest at 31°C (1.55 eggs/female/d and 27.14%, respectively). The shortest larval development time was observed at 27°C and the longest at 31°C (142.81 and 161.97 d, respectively). The highest fitness was observed at 27°C with a population doubling time of 32.78 d compared to 40.58 and 239.4 d at 29 and 31°C, respectively. In conclusion, 27°C is closer to the optimal temperature for T. molitor productivity than 29°C, thus reducing its farming energy needs.
Prevention of Torture: Between Playbooks and Real Life
Authors: Brzozowski Wojciech
Published: December 2024

This review considers Malcolm Evans’ Tackling Torture: Prevention in Practice and highlights its significance for both human rights scholars and practitioners. The strength of the book lies in the author’s extensive practical experience as the former Chair of the SPT, as well as his unique ability to approach torture prevention from a pragmatic perspective.
CALR frameshift mutation detection in myeloproliferative neoplasms by microfluidic chip analysis
Authors: Greenwood Michael P , Newton Keith M , Pepper Kristi L , Hendrickson Heather L , Olsen Randall J , Thomas Jessica S
Published: December 2024

Background

CALR mutation analysis is routinely used to diagnose BCR/ABL1-negative myeloproliferative neoplasms. The 2 most common CALR mutations are a 52–base pair (bp) deletion and a 5-bp insertion, which account for approximately 85% of cases.

Methods

To evaluate our new microfluidic chip assay, we tested CALR mutant and wild-type specimens that were previously analyzed using conventional methods at a reference laboratory. Samples included EDTA-anticoagulated peripheral blood and bone marrow specimens, air dried bone marrow aspirate smears, and formalin-fixed, paraffin-embedded bone marrow sections. CALR exon 9 was PCR amplified using 2 previously published primer pairs and a third unique primer pair designed for our new assay. Amplicons were sized using microfluidic chip analysis.

Results

Concordance with the reference method was 100% (42/42). Intra-run and inter-run reproducibility were also 100% (3/3 and 3/3, respectively). The limit of detection was confirmed to be 6% mutant alleles.

Conclusion

We determined that the microfluidic chip assay to detect CALR exon 9 mutations was acceptable for clinical use. Compared with the conventional method, the microfluidic analysis assay benefits from a streamlined workflow, faster turnaround, and a smaller instrument footprint.
Optimization of the preparation of a spiny spore high-concentrated Aspergillus brasiliensis suspension
Authors: Pisa Federica , Gionta Mirella , Biasi Antonio , Pizzuti Maura , Alt Jodi R , Zampaglione Imma
Published: December 2024

This work aimed to improve some steps of the existing guidelines of the European Standards to obtain an Aspergillus brasiliensis ATCC 16404 spore suspension with >75% spiny spores without mycelia and a concentration of at least 1.5 × 108 CFU ml−1. Several manufacturers’ combinations of “strain/medium” were assessed in terms of yield of spiny spores. Criteria to establish success included (i) the growth over different times of incubation (4, 7, and 10 days); (ii) the performance of two different filtration devices (fritted filters and cell strainers); and (iii) the fungal spores susceptibility after 4 days of incubation versus 7 days of incubation against a peracetic acid-based disinfectant. The best combination was “Microbiologics strain/Oxoid MEA” with 88.33% of spiny spores already after 4 days, and no statistical differences (P < .05) in terms of growth in the three time points were highlighted (from 1.85 × 108 CFU ml−1 to 2.21 × 108 CFU ml−1). Cell strainers gave a spore suspension much more concentrated (3.31 times) compared to fritted filters. Furthermore, the 4-day-old spore suspension showed the same susceptibility to disinfection when compared to a suspension whose culture was incubated for 7 days.
Outcomes and molecular profiles in sarcomatoid carcinoma of unknown primary: the Mayo Clinic experience
Authors: Fuentes Harry E , Suleiman Riham , Graham Rondell P , Villasboas Bisneto Jose C , Garcia Joaquin J , Halfdanarson Thorvardur R
Published: December 2024

Background

Sarcomatoid carcinomas (SC) are rare tumors with both epithelial and mesenchymal characteristics, linked to aggressive behavior and poor prognosis. Sarcomatoid carcinoma of unknown primary (SCUP) is an exceedingly rare subset with limited literature and no standardized management guidelines. This study aims to characterize the clinical presentations, treatment patterns, and genomic landscape of SCUP.

Patients and Methods

Data were retrospectively collected from the Mayo Clinic Rochester Cancer of Unknown Primary Registry. Patients included had biopsy-proven SC with no identifiable primary tumor despite comprehensive diagnostic evaluations. Baseline characteristics, immunohistochemistry (IHC) results, next-generation sequencing (NGS) data, and treatment outcomes were analyzed. Statistical analyses included descriptive statistics, Kaplan–Meier survival estimates, and Cox proportional hazards regression.

Results

Fifty-two SCUP patients were identified, with a median age of 60 years. Most patients presented with widely metastatic disease, particularly lytic bone lesions. Elevated alkaline phosphatase (ALP) was noted in nearly half of the patients. IHC showed high positivity for AE1/AE3 and OSCAR antibodies. Tumor NGS revealed 247 alterations, with TP53 being the most common mutation. Patients receiving definitive therapy had a median overall survival (OS) of 72 months, significantly longer than those receiving systemic therapy (14 months). Immunotherapy was a significant prognostic factor, reducing the risk of death by 90%.

Conclusions

This study provides essential insights into the clinical and genomic characteristics of SCUP, advocating for the integration of definitive therapy and immunotherapy in treatment protocols. Further prospective studies are needed to validate these findings and improve patient outcomes.
Bacillus amyloliquefaciens promotes cluster root formation of white lupin under low phosphorus by mediating auxin levels
Authors: Yang Jinyong , Li Shenglan , Zhou Xiangxue , Du Chongxuan , Fang Ju , Li Xing , Zhao Jun , Ding Fan , Wang Yue , Zhang Qian , Wang Zhengrui , Liu Jianping , Dong Gangqiang , Zhang Jianhua , Xu Feiyun , Xu Weifeng
Published: December 2024

White lupin (Lupinus albus L.) produces cluster roots to acquire more phosphorus under phosphorus deficiency. Bacillus amyloliquefaciens SQR9 contributes to plant growth, but whether and how it promotes cluster root formation in white lupin remain unclear. Here, we investigated the roles of SQR9 in cluster root formation under low phosphorus conditions using a microbial mutant and virus-induced gene silencing (VIGS) in white lupin. SQR9 substantially enhanced cluster root formation under low phosphorus conditions. The ysnE gene encodes an auxin biosynthesis enzyme in SQR9 and was associated with cluster root formation, as ysnE-defective SQR9 did not trigger cluster root formation. SQR9 inoculation induced the expression of PIN-formed2 (LaPIN2, encoding an auxin transporter) and YUCCA4 (LaYUC4, encoding an auxin biosynthesis enzyme) in white lupin roots. VIGS-mediated knockdown of LaPIN2 and LaYUC4 prevented wild-type SQR9-induced cluster root formation in white lupin. Finally, white lupin LaYUC4-derived auxin and SQR9-derived auxin pools were both transported by LaPIN2, promoting cluster root formation under low phosphorus conditions. Taken together, we propose that B. amyloliquefaciens promotes cluster root formation in white lupin under low phosphorus conditions by stimulating auxin biosynthesis and transport. Our results provide insights into the interplay between bacteria and root auxin in crop phosphorus use efficiency.
Copper homeostasis; A rapier between mycobacteria and macrophages
Authors: Hu Di , Yang Zisha , Zhang Jun‐ai , Liu Ganbin , Pi Jiang , Xu Junfa , Wang Yan , Zhao Yi
Published: December 2024

Copper is a vital trace element crucial for mediating interactions between Mycobacterium and macrophages. Within these immune cells, copper modulates oxidative stress responses and signaling pathways, enhancing macrophage immune functions and facilitating Mycobacterium clearance. Conversely, copper may promote Mycobacterium escape from macrophages through various mechanisms: inhibiting macrophage activity, diminishing phagocytic and bactericidal capacities, and supporting Mycobacterium survival and proliferation. This paradox has intensified research focus on the regulatory role of copper in immune cell–pathogen interactions. Interactions among metal ions can affect Mycobacterium concentration, distribution, and activity within an organism. In this review, we have elucidated the role of copper in these interactions, focusing on the mechanisms by which this metal influences both the immune defense mechanisms of macrophages and the survival strategies of Mycobacterium. The findings suggest that manipulating copper levels could enhance macrophage bactericidal functions and potentially limit Mycobacterium resistance. Therefore, elucidating the regulatory role of copper is pivotal for advancing our understanding of metal homeostasis in immune cell–pathogen dynamics and TB pathogenesis. Furthermore, we recommend further investigation into the role of copper in TB pathogenesis to advance tuberculosis diagnosis and treatment and gain comprehensive insights into metal homeostasis in infectious disease contexts.
Effect of Nicotine Replacement Therapy on Perioperative Pain Management and Opioid Requirement in Abstinent Tobacco Smokers Undergoing Spinal Fusion: A Double-blind Randomized Controlled Trial
Authors: Maheshwari Ankita , Gupta Manish , Garg Bhavuk , Singh Akhil Kant , Khanna Puneet
Published: December 2024

Background:

Smoking negatively impacts postoperative outcomes but acute abstinence from smoking during hospitalization can increase postoperative pain, lower pain thresholds, disrupt pain management, and trigger hyperalgesia due to abrupt nicotine withdrawal in tobacco users. Nicotine replacement therapy has been recommended to minimize these complications. We hypothesized that a high dose (21 mg/24 h) transdermal nicotine (TDN) patch would reduce postoperative pain and opioid requirements.

Methods:

One hundred abstinent tobacco smokers undergoing single-level spinal fusion were randomized into placebo (n=50) and nicotine treatment (n=50) groups. Placebo and TDN patches were applied 24 hours before surgery until 48 hours after surgery. Primary outcomes were postoperative pain scores and opioid (morphine) consumption, and serum nicotine levels. The relationship between daily tobacco use and pain and opioid requirements, and between serum nicotine levels and morphine consumption, were assessed.

Results:

Postoperative pain scores at rest and on movement were lower in the nicotine group than in the placebo group at 6 hours, 12 hours, and 24 hours after surgery (P<0.05). Postoperative morphine consumption was lower in the nicotine group than in the placebo group (9.92 ± 4.0 vs. 15.9 ± 5.0 mg, respectively; P=0.0002). There was a positive correlation between the number of cigarettes smoked per day and postoperative pain scores at rest (r = 0.4553; P = 0.0001) and during movement and a negative correlation between serum nicotine concentration and postoperative morphine consumption (r =−0.3664; P = 0.0089)

Conclusions:

TDN patches (21 mg/24 h) reduced postoperative pain and opioid requirements in abstinent tobacco smokes undergoing spinal fusion.
Mechanism of action of the nucleotide-binding oligomerization domain-like receptor protein 3 inflammasome and its regulation in liver injury
Authors: Lu Yifan , Wang Tianyu , Yu Bo , Xia Kang , Guo Jiayu , Liu Yiting , Ma Xiaoxiong , Zhang Long , Zou Jilin , Chen Zhongbao , Zhou Jiangqiao , Qiu Tao
Published: December 2024

Nucleotide-binding oligomerization domain (NOD)-like receptor protein 3 (NLRP3) is a cytosolic pattern recognition receptor that recognizes multiple pathogen-associated molecular patterns and damage-associated molecular patterns. It is a cytoplasmic immune factor that responds to cellular stress signals, and it is usually activated after infection or inflammation, forming an NLRP3 inflammasome to protect the body. Aberrant NLRP3 inflammasome activation is reportedly associated with some inflammatory diseases and metabolic diseases. Recently, there have been mounting indications that NLRP3 inflammasomes play an important role in liver injuries caused by a variety of diseases, specifically hepatic ischemia/reperfusion injury, hepatitis, and liver failure. Herein, we summarize new research pertaining to NLRP3 inflammasomes in hepatic injury, hepatitis, and liver failure. The review addresses the potential mechanisms of action of the NLRP3 inflammasome, and its regulation in these liver diseases.
Artificial intelligence-enabled discovery of a RIPK3 inhibitor with neuroprotective effects in an acute glaucoma mouse model
Authors: Tu Xing , Zou Zixing , Li Jiahui , Zeng Simiao , Luo Zhengchao , Li Gen , Gao Yuanxu , Zhang Kang
Published: December 2024

Background:

Retinal ganglion cell (RGC) death caused by acute ocular hypertension is an important characteristic of acute glaucoma. Receptor-interacting protein kinase 3 (RIPK3) that mediates necroptosis is a potential therapeutic target for RGC death. However, the current understanding of the targeting agents and mechanisms of RIPK3 in the treatment of glaucoma remains limited. Notably, artificial intelligence (AI) technologies have significantly advanced drug discovery. This study aimed to discover RIPK3 inhibitor with AI assistance.

Methods:

An acute ocular hypertension model was used to simulate pathological ocular hypertension in vivo. We employed a series of AI methods, including large language and graph neural network models, to identify the target compounds of RIPK3. Subsequently, these target candidates were validated using molecular simulations (molecular docking, absorption, distribution, metabolism, excretion, and toxicity [ADMET] prediction, and molecular dynamics simulations) and biological experiments (Western blotting and fluorescence staining) in vitro and in vivo.

Results:

AI-driven drug screening techniques have the potential to greatly accelerate drug development. A compound called HG9-91-01, identified using AI methods, exerted neuroprotective effects in acute glaucoma. Our research indicates that all five candidates recommended by AI were able to protect the morphological integrity of RGC cells when exposed to hypoxia and glucose deficiency, and HG9-91-01 showed a higher cell survival rate compared to the other candidates. Furthermore, HG9-91-01 was found to protect the retinal structure and reduce the loss of retinal layers in an acute glaucoma model. It was also observed that the neuroprotective effects of HG9-91-01 were highly correlated with the inhibition of PANoptosis (apoptosis, pyroptosis, and necroptosis). Finally, we found that HG9-91-01 can regulate key proteins related to PANoptosis, indicating that this compound exerts neuroprotective effects in the retina by inhibiting the expression of proteins related to apoptosis, pyroptosis, and necroptosis.

Conclusion:

AI‐enabled drug discovery revealed that HG9-91-01 could serve as a potential treatment for acute glaucoma.
DEK::AFF2 Fusion Sinonasal and Skull Base Nonkeratinizing Squamous Cell Carcinoma
Authors: Hart Stephanie A. , Hang Jen-Fan , Chernock Rebecca D. , Mikula Michael W. , Rooper Lisa , Amin Sara E. , Saluja Karan , Bishop Justin A. , Chen Yu Hsiu , Cipriani Nicole A. , David Stephanie N. , Dupont William D. , Plummer W. Dale , Ferrer Karen T. , Geromes Ariana , Hsieh Min-Shu , Hernandez-Prera Juan C. , Kuo Ying-Ju , Sasaki Eiichi , Shi Qiuying , Truong Tra , Velez Torres Jaylou M. , Lewis James S.
Published: December 2024

DEK::AFF2 fusion nonkeratinizing squamous cell carcinoma (NKSCC) is an emerging entity in the sinonasal tract, temporal bone, and skull base. However, the clinical behavior of these tumors has not been well studied. Here, we report the largest cohort of DEK::AFF2 carcinomas to determine if morphology, mitotic rate, and/or Ki-67 IHC are associated with patient outcomes, including a comparison with high-risk human papillomavirus (HPV)-associated and independent patients. We solicited cases of molecularly or AFF2 immunohistochemistry (IHC) proven DEK::AFF2 SCC from surgical pathologists to collect patient demographic, clinical, and outcome data. Using representative H&E slides, we characterized the morphology and counted mitoses. Ki-67 immunohistochemistry was performed. We also compared the DEK::AFF2 survival rates to those in a cohort of AFF2 IHC-negative HPV-associated and HPV-independent SCC. DEK::AFF2 carcinomas most commonly arose in the nasal cavity (13/30, 43%), and the average number of recurrences was 1.8 (range: 0 to 10). At the last follow-up, most patients were disease free (19/30, 63%) or were alive with disease (9/30, 30%). There was an average mitotic rate of 2 per 2 mm2 (range: 0 to 9) and Ki-67 proliferation rate of 26% (range: 3% to 60%). Local recurrence was common, but morphology, mitotic activity, and Ki-67 index were not associated with recurrence or survival. On Kaplan-Meier survival analysis, DEK::AFF2 patients had lower disease-free survival but otherwise had similar outcomes to conventional SCC patients. Our multi-institutional study shows that local recurrence is common in DEK::AFF2 fusion nonkeratinizing SCC patients, but patients have survival rates similar to conventional SCC. Despite showing a range of different features and proliferation rates, traditional grading by morphology, mitotic rate, and/or Ki-67 activity does not seem to be predictive of outcome.
Long-term Changes in Pain, Depression, Function and Informal Caregiving after Major Elective Surgeries Among Seriously Ill Older Adults
Authors: Min Jolene Wong Si , Wang Yihan , Bollens-Lund Evan , Reich Amanda J. , Dhanani Hiba , Ankuda Claire K. , Lipsitz Stuart , Gray Tamryn F. , Kim Dae Hyun , Ritchie Christine S. , Kelley Amy S. , Cooper Zara
Published: December 2024

Objective:

To compare differences in pain, depression, function, and informal caregiving pre-and-post major elective surgery among older adults with and without serious illness; and determine if serious illness was independently associated with increasing pain, depression, assistance in activities of daily living (ADLs) and informal caregiving post-surgery.

Background:

The American College of Surgeons has endorsed the integration of palliative care (PC) into surgical care in adults with serious illness but targets for PC during surgical episodes such as pain, depression, function, and informal caregiving are understudied.

Methods:

We used Health and Retirement Study-linked Medicare data (2008-2018) to identify older (≥66 y) adults with and without serious illness who had major elective surgery. We performed difference-in-difference analysis to measure changes in pain, depression, function and informal caregiving pre-and-post-surgery between groups. We tested associations between serious illness and changes in pain, depression, function and informal caregiving using multivariable regression.

Results:

Among 1896 adults who had major surgery, 1139 (60%) were seriously ill. Compared to adults without serious illness, those with serious illness had greater baseline pain (43 vs. 38%), depression (22 vs.13%), assistance with ADLs(12 vs.0%) and informal caregiving (18 vs.4%); and, greater increases in assistance with ADLs pre-and-post-surgery(DID 6%, 95%CI 3.7-8.3). Serious illness was independently associated with increasing pain (OR 1.6, 95%CI 1.1-2.2), depression (OR 1.5, 95%CI 1.1-2.2), assistance with ADLs (OR 2.1, 95%CI 1.3-3.4) and informal caregiving (OR 2.1, 95%CI 1.4-3.1) post-surgery.

Conclusions:

Most older adults having elective surgery are seriously ill. Pain, depression, function, and caregiving are targets for PC to improve post-surgical outcomes.
Automating Candidate Gene Prioritization with Large Language Models: Development and Benchmarking of an API-Driven Workflow Leveraging GPT-4
Authors: Khan Taushif , Toufiq Mohammed , Yurieva Marina , Indrawattana Nitaya , Jittmittraphap Akanitt , Kosoltanapiwat Nathamon , Pumirat Pornpan , Sukphopetch Passanesh , Vanaporn Muthita , Palucka Karolina , Kabeer Basirudeen , Rinchai Darawan , Chaussabel Damien
Published: December 2024

In this exploratory study, we developed an automated workflow that leverages Large Language Models, specifically GPT-4, to prioritize candidate genes for targeted assay development. The workflow automates interaction with OpenAI models and enables prompt creation, submission. It features customizable prompts designed to evaluate candidate genes based on criteria such as association with biological processes, biomarker potential, and therapeutic implications, which can be tailored for specific diseases or processes. Benchmarking experiments comparing the performance of the Application Programming Interface (API)-based automated prompting approach with manual prompting demonstrated high consistency and reproducibility in gene prioritization results. The automated method exhibited scalability by successfully prioritizing genes relevant to sepsis from the BloodGen3 repertoire, comprising 11,465 genes, distributed among 382 modules. The workflow efficiently identified sepsis-associated genes across the repertoire, revealing distinct gene clusters and providing insights into their distribution within module aggregates and individual modules. This proof-of-concept study demonstrates how LLMs can enhance gene prioritization, streamlining the identification process for targeted assays across various biological contexts. However, it also reveals the need for further validation and highlights the exploratory nature of this work due to scoring inconsistencies and the necessity for manual fact-checking. Despite these challenges, the automated workflow holds promise for accelerating targeted assay development for disease management and paves the way for future research.
A Model of Place Field Reorganization During Reward Maximization
Authors: Kumar M Ganesh , Bordelon Blake , Zavatone-Veth Jacob A. , Pehlevan Cengiz
Published: December 2024

When rodents learn to navigate in a novel environment, a high density of place fields emerges at reward locations, fields elongate against the trajectory, and individual fields change spatial selectivity while demonstrating stable behavior. Why place fields demonstrate these characteristic phenomena during learning remains elusive. We develop a normative framework using a reward maximization objective, whereby the temporal difference (TD) error drives place field reorganization to improve policy learning. Place fields are modeled using Gaussian radial basis functions to represent states in an environment, and directly synapse to an actorcritic for policy learning. Each field’s amplitude, center, and width, as well as downstream weights, are updated online at each time step to maximize cumulative reward. We demonstrate that this framework unifies three disparate phenomena observed in navigation experiments. Furthermore, we show that these place field phenomena improve policy convergence when learning to navigate to a single target and relearning multiple new targets. To conclude, we develop a normative model that recapitulates several aspects of hippocampal place field learning dynamics and unifies mechanisms to offer testable predictions for future experiments.
Pre-trained protein language model for codon optimization
Authors: Pathak Shashank , Lin Guohui
Published: December 2024

Motivation

Codon optimization of Open Reading Frame (ORF) sequences is essential for enhancing mRNA stability and expression in applications like mRNA vaccines, where codon choice can significantly impact protein yield which directly impacts immune strength. In this work, we investigate the use of a pre-trained protein language model (PPLM) for getting a rich representation of amino acids which could be utilized for codon optimization. This leaves us with a simpler fine-tuning task over PPLM in optimizing ORF sequences.

Results

The ORFs generated by our proposed models outperformed their natural counterparts encoding the same proteins on computational metrics for stability and expression. They also demonstrated enhanced performance against the benchmark ORFs used in mRNA vaccines for the SARS-CoV-2 viral spike protein and the varicella-zoster virus (VZV). These results highlight the potential of adapting PPLM for designing ORFs tailored to encode target antigens in mRNA vaccines.
Targeted Culture-Independent Sequencing Identifies Emergence of Macrolide-ResistantBordetella Pertussisin Australia
Authors: Fong Winkie , Rockett Rebecca J , Tam Kingsley King-Gee , Nguyen Trang , Sim Eby M , Tay Enoch , Suster Carl J.E. , Agius Jessica E , Chandra Shona , Watt Anne E , Speers David , Graham Maryza , Tran Thomas , Lim Chuan Kok , Wehrhahn Michael C , Ginn Andrew N , Gray Darcy , Robson Jennifer , Gardner Indya , McDougall Rodney , Papanicolas Lito , Howard-Jones Annaleise R , Outhred Alexander C , Kennedy Karina , Cooley Louise , Wang Qinning , Jeoffreys Neisha , Chen Sharon C-A , Basile Kerri , Golubchik Tanya , Kok Jen , Sintchenko Vitali
Published: December 2024

Bordetella pertussiscontinues to circulate globally despite wide-spread vaccination, with an emergent international epidemic in 2024. The resurgence of disease is confounded by the emergence of pertactin-deficient, macrolide-resistantB. pertussis(MRBP) strains in Asia and Europe, which are under-recognised using traditional diagnostic and surveillance methods. This study addressed these gaps by applying a probe-capture hybridisation technique, which enables targeted culture-independent sequencing of genomes (tNGS) directly from respiratory specimens. Seven co-circulating lineages ofB. pertussiswere identified in Australia, including two associated with MRBP. Eight epidemiologically unrelated and geographically dispersed cases of MRBP in Australia with a A2037G mutation in all three copies of 23S rRNA were documented, three of which were confirmed by phenotypic testing and sequencing of corresponding isolates. The estimated rate of MRBP amongB. pertussisPCR positive cases was 4.4%. This study demonstrated the value of tNGS based on target enrichment and probe capture sets designed for respiratory pathogens for public health laboratory surveillance of pertussis. This approach can improve the resolution and completeness ofB. pertussissurveillance given the increasing diversity and vaccine evasion capability of this pathogen.
Evaluating the Quality of Mental Health Information Generated by Large Language Model Chatbots
Authors: Porwal Gargi , Jeenger Jitendra
Published: December 2024

Artificial intelligence (AI) large language models (LLMs) hold great potential to transform psychiatry and mental health care by delivering relevant and tailored mental health information. This study aimed to evaluate the quality of mental health information generated by LLMs by determining their level of accessibility, reliability, and interpreting any bias present. Generative Pre-trained Transformer-4 (GPT-4) (San Francisco, California: Open AI), Gemini 1.5 Flash (Mountain View, California: Google LLC), and Large Language Model Meta AI 3.2 (Llama 3.2) (Menlo Park, California: Meta Inc.) were prompted with 20 questions commonly asked about anxiety and depression. The responses were evaluated using Flesch-Kincaid readability tests to quantify their ease of understanding through grade level and reading ease score measures. The text was subsequently analyzed using a modern DISCERN score to assess the reliability of the health-related information presented. Finally, the LLM responses were evaluated for stigmatizing language using communication and language guidelines for mental health. A significant difference in grade levels and reading ease scores was observed between GPT-4 and Llama (p < 0.01) and Gemini and Llama(p < 0.01), with both GPT-4 and Gemini having higher readability scores. No significant difference was observed in the grade level and reading ease scores between GPT-4 and Gemini (p > 0.05). All three models reported moderate reliability scores but no significant differences were observed (p > 0.05). GPT-4, Gemini, and Llama included stigmatizing phrases in 10%, 15%, and 20% of their responses respectively. These phrases were attributed to descriptions of mental health conditions and substance use; however, no significant differences were observed in the proportions of stigmatizing phrases present across the three models (p > 0.05). Furthermore, comparisons between anxiety and depression responses for each model revealed no significant differences in readability, reliability, or bias. All models demonstrated the ability to generate mental health information that generally satisfied criteria for accessibility, reliability, and minimal bias, with GPT-4 and Gemini reporting higher readability than Llama. However, the lack of additional resources cited in responses and the occasional presence of certain stigmatizing phrases, indicate that additional model training and fine-tuning, specifically for mental health applications, may be necessary before these tools can be deployed on a large scale for mental health care.
Technical Feasibility Study for a Retinal Camera System
Authors: Makedonsky Katherine , Patwardhan Anil , Kim Angela , Silvestrini Matthew , Lui Clarissa , Kavusi Sam
Published: December 2024

Background/Objectives

Improvements in diabetic retinopathy (DR) screening could boost early detection rates and contribute to better patient outcomes. The availability of primary care-based DR screening could address this issue, although operational challenges remain. This study represents a preliminary evaluation of the feasibility and operational performance of a retinal screening system suitable for integration into a primary care setting.

Methods

This was a multi-center, data collection study for a non-mydriatic retinal camera system, conducted in 4 iterative development phases; phase 4 simulated a clinical workflow. Study endpoints evaluated image quality (gradability) and operational characterization in phase 4 (time to complete image capture). Participants were required to be at least 22 years of age, and separate participant pools were recruited throughout study phases. In each phase, multiple images per eye were collected, and graded independently by sponsor-employed and external graders.

Results

The study included 212 participants. In phases 1-3 (n=192), evaluation of the first image captured per eye for all participants (k=383) by non-sponsor graders showed 93.7% of images (359/383) as gradable; in phase 4 (n=20; k=55), there were 81.8% (45/55) gradable images. Regarding operational results, 90.1% of first-attempts trigger times were less than 30 seconds; by the third attempt, 96.7% were less than 30 seconds,

Conclusions

These are encouraging preliminary results in terms of performance and usability for the retinal camera system in this study, which may have potential application in primary care clinics.
Texture-Analysis Classification of Intraductal Carcinoma of the Prostate Using Label-Free Multimodal Nonlinear Optical Imaging
Authors: Gagnon Justin R. , Allen Christian Harry , Diop Mame-Kany , Dallaire Frédérick , Leblond Frédéric , Trudel Dominique , Murugkar Sangeeta
Published: December 2024

Intraductal carcinoma of the prostate (IDC-P) is a very aggressive histopathological subtype of prostate cancer (PCa) for which no accurate biomarkers exist. In our work, we apply a multimodal nonlinear optical imaging approach that uses second-harmonic generation (SHG) and stimulated Raman scattering (SRS) imaging to distinguish IDC-P from regular PCa and benign prostate tissue. Images from each tissue type were classified using support vector machine (SVM). The technique classified the images from each region based on first-order statistics and texture-based second-order statistics derived from the gray-level co-occurrence matrix (GLCM) of the images. Our results demonstrate that SVM models trained on either SHG or SRS images accurately classify IDC-P as well as high-grade PCa, low-grade PCa, and benign tissue with a mean classification accuracy of over 89%. Furthermore, a classification model combining both SHG and SRS imaging modalities can accurately classify all tissue types with a mean classification accuracy of 98%.
Ilastik: a machine learning image analysis platform to interrogate stem cell fate decisions across multiple vertebrate species
Authors: Munoz Alma Zuniga , Soni Kartik , Li Angela , Lakkundi Vedant , Iyer Arundati , Adler Ari , Kirkendall Kathryn , Petrigliano Frank , Benayoun Bérénice A. , Lozito Thomas P. , Almada Albert E.
Published: December 2024

Stem cells are the key cellular source for regenerating tissues and organs in vertebrate species. Historically, the investigation of stem cell fate decisionsin vivohas been assessed in tissue sections using immunohistochemistry (IHC), where a trained user quantifies fluorescent signal in multiple randomly selected images using manual counting—which is prone to inaccuracies, bias, and is very labor intensive. Here, we highlight the performance of a recently developed machine-learning (ML)-based image analysis program called Ilastik using skeletal muscle as a model system. Interestingly, we demonstrate that Ilastik accurately quantifies Paired Box Protein 7 (PAX7)-positive muscle stem cells (MuSCs) before and during the regenerative process in whole muscle sections from mice, humans, axolotl salamanders, and short-lived African turquoise killifish, to a precision that exceeds human capabilities and in a fraction of the time. Overall, Ilastik is a free user-friendly ML-based program that will expedite the analysis of stained tissue sections in vertebrate animals.
DOC2b enrichment mitigates proinflammatory cytokine-induced CXCL10 expression by attenuating IKKβ and STAT-1 signaling in human islets
Authors: Chatterjee Bhowmick Diti , Ahn Miwon , Bhattacharya Supriyo , Aslamy Arianne , Thurmond Debbie C.
Published: December 2024

Introduction

Type 1 diabetic human islet β-cells are deficient in double C 2 like domain beta (DOC2b) protein. Further, DOC2b protects against cytokine-induced pancreatic islet β-cell stress and apoptosis. However, the mechanisms underpinning the protective effects of DOC2b remain unknown.

Methods

Biochemical studies, qPCR, proteomics, and immuno-confocal microscopy were conducted to determine the underlying protective mechanisms of DOC2b in β-cells. DOC2b- enriched or-depleted primary islets (human and mouse) and β-cell lines challenged with or without proinflammatory cytokines, global DOC2b heterozygous knockout mice subjected to multiple-low-dose-streptozotocin (MLD-STZ), were used for these studies.

Results

A significant elevation of stress-induced CXCL10 mRNA was observed in DOC2b- depleted β-cells and primary mouse islets. Further, DOC2b enrichment markedly attenuated cytokine-induced CXCL10 levels in primary non-diabetic human islets and β-cells. DOC2b enrichment also reduced total-NF-κB p65 protein levels in human islets challenged with T1D mimicking proinflammatory cytokines. IKKβ, NF-κB p65, and STAT-1 are capable of associating with DOC2b in cytokine-challenged β-cells. DOC2b enrichment in cytokine-stressed human islets and β-cells corresponded with a significant reduction in activated and total IKKβ protein levels. Total IκBβ protein was increased in DOC2b-enriched human islets subjected to acute cytokine challenge. Cytokine-induced activated and total STAT-1 protein and mRNA levels were markedly reduced in DOC2b-enriched human islets. Intriguingly, DOC2b also prevents ER-stress-IKKβ and STAT-1 crosstalk in the rat INS1-832/13 β-cell line.

Conclusion

The mechanisms underpinning the protective effects of DOC2b involve attenuation of IKKβ-NF-κB p65 and STAT-1 signaling, and reduced CXCL10 expression.

Graphical abstract
Comprehensive analysis of macrophages infected with avirulent and virulentMycobacterium tuberculosisuncovers distinct immune mechanisms and anti-TB effect of treated exosomes
Authors: Yang Li , Lyu Lingna , Li Cuidan , Zhang Xiuli , Ju Yingjiao , Zhang Ju , Liu Jie , Yue Liya , Zhang Xiangli , Lu Dandan , Yang Tingting , Wang Peihan , Wang Jie , Wang Xiaotong , Xu Sihong , Sheng Yongjie , Jiang Chunlai , Wang Jing , Hu Xin , Bahetibieke Tuohetaerbaike , Zhang Zongde , Chen Fei
Published: December 2024

Tuberculosis (TB) is now the world’s second deadliest infectious killer after COVID-19. Human-macrophages and their secreted exosomes play important roles in combating invadingMtb. However, the panoramic analysis of the underlying immune mechanism for the infected macrophages, package or secretion mechanism, and anti-TB effect ofMtbtreated exosomes remain poorly understood. Here we conducted comprehensive analyses of the macrophages infected with avirulent and virulentMtb(H37Ra & H37Rv) and their secreted exosomes, collected cells and corresponding exosomes for omics and phenotypic analysis. The results showed that avirulentMtbstimulated robust immune-responses and apoptosis in macrophages to eliminate the invadingMtb; virulentMtbinduced severe necrosis and immune-escape for survival. The HMGB1 signaling pathway andTNFRSF1Bplays important roles in the immune escape of virulentMtb. Interestingly, our results suggest that macrophages killMtbin an IFN-γ independent but simulative way, highlighting the central role of IFN signaling pathway in anti-TB immune response. Moreover, we observed selective transport of host andMtbRNAs from macrophages to exosomes. Notably, “H37Ra-treated exosomes” displayed a higher anti-TB effect than “H37Rv-treated exosomes” due to some enriched pro-inflammation and immune-escape relatedMtbproteins in these two exosomes, respectively. Conclusively, our findings shed new light on the immune mechanism of macrophages in response toMtbinfection, offering a new TB-treatment strategy and some promising vaccine candidates.
“Let’s stick together”: toward a serial mediation model about the impact of relational leadership on workers’ employability
Authors: Hoedemakers Joost , Vanderstukken Arne , Stoffers Jol , Van der Heijden Beatrice
Published: December 2024

Purpose

This paper explores whether relational leadership enhances nurses’ employability. An empirical study was conducted to investigate associations between relational leadership, perceived supervisory support, perceived opportunities for competence development and employability.

Design/methodology/approach

A serial mediation model was constructed to investigate our hypothesized relationships. We applied a two-wave panel design and collected self-reported survey data from 109 nurses who worked in a Dutch homecare organization. Relationships were tested using PLS-SEM.

Findings

Our findings suggest no direct association between relational leadership and employability. However, we found support for a serial mediation model, in which perceived supervisory support and perceived opportunities for competence development fully mediated the relationship between relational leadership and employability.

Research limitations/implications

This scholarly work contributes to the employability literature; a supervisor who fosters high-quality relationships with nurses communicates a willingness to support their development and provides them competence development opportunities, which, in turn, fosters nurses’ employability.

Practical implications

HR managers and supervisors in homecare organizations should create leadership development policies and practices that encourage relational leadership, particularly empowering leadership.

Originality/value

To the best of our knowledge, up until now, this study is the first to use supervisors’ relational leadership to predict employees’ employability.
Differential Expression Spectrum of circRNA in Plasma Exosomes in Dilated Cardiomyopathy With Heart Failure
Authors: Xu Shuai , Zhang Ge , Tan Xin , Zeng Yiyao , Fan Huimin , Gao Jiamin , Qin Zhen , Yu Fengyi , Ma Bin , Zhang Ting , Jiang Hezi , Li Xian , Wang Xiangyu , Fan Jili , Bo Xiaohong , Zhou Yafeng , Tang Junnan
Published: December 2024

Dilated cardiomyopathy (DCM), a form of non‐ischaemic myocardial disease, is characterised by structural and functional cardiac abnormalities. As defined by the World Health Organisation, DCM constitutes a significant cardiac pathology, leading to increased morbidity and mortality due to complications such as heart failure and arrhythmias. The diagnostic process for DCM predominantly employs echocardiography and MRI, with biomarkers like NT‐pro BNP and troponin providing supportive, yet non‐specific, evidence. Exosomes, small extracellular vesicles, play a critical role in intercellular communications by transferring biomolecules including lipids, proteins, messenger RNA (mRNA) and non‐coding RNA (ncRNA) to target cells, thereby influencing key cellular processes such as proliferation, differentiation, apoptosis, angiogenesis and immune modulation. Within the ncRNA category, circular RNAs (circRNAs) are notable for their cellular specificity and evolutionary conservation and are often implicated in the regulatory mechanisms underlying DCM and heart failure. This investigation employed next‐generation sequencing technology to analyse plasma exosomal circRNA profiles in DCM patients with chronic heart failure (CHF), compared to healthy controls. The analysis revealed distinct circRNA expression patterns, identifying 49 uniquely expressed circRNAs in the DCM cohort with CHF. These circRNAs were associated with several critical biological pathways, including the sequestration of extracellular ligands from receptors, N‐acetyltransferase activity, histone acetyltransferase activity and endocytic vesicle membrane composition. The findings of this study provide valuable insights into the pathophysiological mechanisms of DCM and offer evidence for improving clinical diagnostic methodologies.
CCL2/CCR2 Signalling in Mesenchymal Stem/Progenitor Cell Recruitment and Fracture Healing in Mice
Authors: Kannan Rahasudha , Koh Amy J. , Kent Robert N. , Bhutada Kaira , Wasi Fatima , Wagner Leon , Kozloff Kenneth , Baker Brendon M. , Roca Hernan , McCauley Laurie K.
Published: December 2024

Macrophage efferocytosis (clearance of apoptotic cells) is crucial for tissue homeostasis and wound repair, where macrophages secrete factors that promote resolution of inflammation and regenerative signalling. This study examined the role of efferocytic macrophage‐associated CCL2 secretion, its influence on mesenchymal stem/progenitor cell (MSPC) chemotaxis, and in vivo cell recruitment using Ccr2−/− (KO) mice with disrupted CCL2 receptor signalling in two regenerative models: ossicle implants and ulnar stress fractures. Single cell RNA sequencing and PCR validation indicated that efferocytosis of various apoptotic cells at bone injury sites (osteoblasts, pre‐osteoblasts, MSPC) upregulated CCL2. CCL2 gradients enhanced MSPC migration through type I collagen matrices. In vivo, MSPC (LepR+) infiltration was significantly reduced while macrophage (F4/80+) infiltration increased in KO ossicle implants versus WT. In ulnar stress fractures, micro‐CT revealed increased mineralized callus incidence in CCR2 KO male mice 5 days post injury (dpi) versus WT. By 7‐dpi callus fractional bone volume, trabecular thickness, and bone mineral density were increased versus WT. Immunohistochemistry of mice 5‐dpi confirmed an increase in callus area (including soft tissue); however, the percent of osteoprogenitors (%Osx+) within the callus was not different. These findings suggest that CCL2 differentially impacts MSPC recruitment depending on bone wound healing model.
Myeloperoxidase and Thyrotropin‐Releasing Hormone Within Leukaemia Stem Cells Increased Chemosensitivity in Acute Myeloid Leukaemia
Authors: Chen Chung‐Hsing , Chen Tsung‐Chih , Wu Ting‐Shuan , Hsiao Tzu‐Hung , Chen Jo‐Mei Maureen , Huang Chi‐Ying F. , Cheng Po‐Liang , Tsai Jia‐Rung , Teng Chieh‐Lin Jerry
Published: December 2024

Leukaemia stem cells (LSCs) are major contributors to chemoresistance in acute myeloid leukaemia (AML). Identifying potential biomarkers within LSCs that can predict chemosensitivity in AML is key. This prospective study involved 20 consecutive de novo AML patients who underwent ‘7 + 3’ induction therapy. The patients were divided into CR (n = 15) and non‐CR (n = 5) groups. Using single‐cell RNA sequencing, we examined the cellular states of bone marrow mononuclear cells from AML patients at diagnosis and identified LSC among these cells. Our results showed that in non‐CR AML patients, a significant increase in the proportion of immature cells during haematopoiesis within the AML cell populations was observed. Moreover, the expression of myeloperoxidase (MPO) (log2 fold‐change = 0.89; adjusted p < 0.0001) and thyrotropin‐releasing hormone (TRH) (log2 fold‐change = 0.65; adjusted p < 0.0001) was higher within LSCs in the CR group than in the non‐CR group. Furthermore, patients with higher expression of MPO and TRH demonstrated improved relapse‐free survival (p = 0.002 for MPO; p = 0.009 for TRH) and overall survival (p = 0.002 for MPO; p < 0.001 for TRH). The connection between MPO or TRH and chemosensitivity could be linked with the downregulation of transforming growth factor and the upregulation of interferon‐α. In conclusion, MPO and TRH in LSCs could serve as chemosensitivity biomarkers in AML.