bluuebunny/crossref_metadata_2025 huggingface dataset:
Fentanyl Deaths in Infants and Children
Authors: Monday Katrina , Shattuck Brandy , Barba Kristie , Revercomb Carolyn H.
Published: June 2024

Death due to fentanyl and its various analogs has resulted in an exponential rise in deaths throughout the United States, overwhelming many medical examiner offices for over a decade. Its potency and prevalence have caused fentanyl to become the most reported substance in overdose fatalities, with an accompanying increase in exposure of the most vulnerable, infants and children. This report provides information about fentanyl in the pediatric population, including case examples, proposed investigative practices, published therapeutic and lethal blood concentrations, and available resources for future cases. Nine cases of pediatric death between 2013 and 2023 due to fentanyl were reviewed. Five case summaries are presented that highlight classic features of fentanyl deaths in infants, children, and teenagers. Deaths due to fentanyl have continued to rise year after year. Infants and children, most of whom are opioid naive, are at ever increased risk for exposure to high levels of fentanyl. The legal ramifications of a positive fentanyl level in a child increase the need for caution on the part of the forensic pathologist. Understanding what can and cannot be proven by autopsy as well as what resources are available to strengthen one's justification for fentanyl being the primary cause of death is critical.
Delirium Screening in Critically Ill Children: Secondary Analysis of the Multicenter PICU Up! Pilot Trial Dataset, 2019–2020*
Authors: Azamfirei Razvan , Behrens Deanna , Padilla Sofia , Madden Kate , Goldberg Sarah , Geno Megan , Manning Mary-Jeanne , Piole Michelle , Madsen Erik , Maue Danielle , Abu-Sultaneh Samer , Awojoodu Ronke , Wang Nae-Yuh , Needham Dale M. , Neufeld Karin , Kudchadkar Sapna R.
Published: June 2024

OBJECTIVES:

To determine the patient-level factors associated with performing daily delirium screening in PICUs with established delirium screening practices.

DESIGN:

A secondary analysis of 2019–2020 prospective data from the baseline phase of the PICU Up! pilot stepped-wedge multicenter trial (NCT03860168).

SETTING:

Six PICUs in the United States.

PATIENTS:

One thousand sixty-four patients who were admitted to a PICU for 3 or more days.

INTERVENTIONS:

None.

MEASUREMENTS AND MAIN RESULTS:

Of 1064 patients, 74% (95% CI, 71–76%) underwent delirium screening at least once during their PICU stay. On 57% of the 8965 eligible patient days, screening was conducted. The overall prevalence of delirium was 46% across all screened days, and 64% of screened patients experienced delirium at some point during their PICU stay. Factors associated with greater adjusted odds ratio (aOR) of increased daily delirium screening included PICU stay longer than 15 days compared with 1–3 days (aOR 3.36 [95% CI, 2.62–4.30]), invasive mechanical ventilation as opposed to room air (aOR 1.67 [95% CI, 1.32–2.12]), dexmedetomidine infusions (aOR 1.23 [95% CI, 1.04–1.44]) and propofol infusions (aOR 1.55 [95% CI, 1.08–2.23]). Conversely, decreased aOR of daily delirium screening was associated with female gender (aOR 0.78 [95% CI, 0.63–0.96]), and the administration of continuous infusions of opioids (aOR 0.75 [95% CI, 0.63–0.90]) or ketamine (aOR 0.48 [95% CI, 0.29–0.79]). Neither patient age, the presence of family or physical restraints, or benzodiazepine infusions were associated with daily delirium screening rates.

CONCLUSIONS:

In the 2019–2020 PICU UP! cohort, across six PICUs, delirium screening occurred on only 57% of days, despite the presence of established practices. Female gender, patients in the early stages of their PICU stay, and patients not receiving mechanical ventilation were associated with lower odds of daily delirium screening. Our results highlight the need for structured quality improvement processes to both standardize and increase the frequency of delirium screening.
Stromal p16 and SATB2 Expression Does Not Distinguish Atypical Polypoid Adenomyoma (APA) From its Benign Mimics
Authors: Bui Chau Minh , Azimpouran Mahzad , Balzer Bonnie , Maluf Horacio , Medeiros Fabiola
Published: June 2024

Atypical polypoid adenomyoma (APA) is a polypoid biphasic lesion of low malignant potential that arises in the lower uterine segment and uterine corpus. The diagnosis of APA is often challenging on biopsy and curettage specimens, and both benign and malignant processes need to be considered in the differential. Stromal expression of p16 and SATB2 have recently been shown to distinguish APA from myoinvasive endometrioid carcinoma. The authors hypothesized that p16 and SATB2 immunohistochemistry could also aid in the distinction of APA from benign adenomyomatous polyp and endometrioid adenomyoma. The study comprised 10 APAs, 7 adenomyomatous polyps, 11 endometrioid adenomyomas, and 10 myoinvasive endometrioid carcinomas. The majority of APAs showed moderate to strong, diffuse p16 and stromal expression. However, most adenomyomatous polyps and endometrioid adenomyomas also exhibited moderate to strong, focal to diffuse p16 stromal expression. SATB2 showed weak to moderate, focal to diffuse expression in the majority of APAs, adenomyomatous polyps and endometrioid adenomyomas. In contrast, p16 and SATB2 were negative to weak and focal in 90% of myoinvasive endometrioid carcinomas. Our findings demonstrate that p16 and SATB2 may be helpful in the differential diagnosis of myoinvasive endometrioid carcinoma and APA while not useful in separating APA from adenomyomatous polyp and endometrioid adenomyoma.
A predictive model for HIV-related lymphoma
Authors: Kurosawa Shuhei , Yoshimura Yukihiro , Takada Yusuke , Yokota Takako , Hibi Masaki , Hirahara Ayumi , Yoshida Tsutomu , Okubo So , Masuda Moe , So Yuna , Miyata Nobuyuki , Nakayama Hitomi , Sakurai Aki , Sato Kosuke , Ito Chisako , Aisa Yoshinobu , Nakazato Tomonori
Published: June 2024

Objectives:

To address the paucity of HIV-related lymphoma (HRL)–specific prognostic scores for the Japanese population by analyzing domestic cases of HRL and constructing a predictive model.

Design:

A single-center retrospective study coupled with a review of case reports of HRL.

Methods:

We reviewed all patients with HRL treated at our hospital between 2007 and 2023 and conducted a comprehensive search for case reports of HRL from Japan using public databases. A multivariate analysis for overall survival (OS) was performed using clinical parameters, leading to the formulation of the HIV-Japanese Prognostic Index (HIV-JPI).

Results:

A total of 19 patients with HRL were identified in our institution, whereas the literature review yielded 44 cases. In the HIV-JPI, a weighted score of 1 was assigned to the following factors: age at least 45 years, HIV-RNA at least 8.0×104 copies/ml, Epstein–Barr virus-encoded small RNA positivity, and Ann Arbor classification stage IV. The overall score ranged from 0 to 4. We defined the low-risk group as scores ranging from 0 to 2 and the high-risk group as scores ranging from 3 to 4. The 3-year OS probability of the high-risk group [30.8%; 95% confidence interval (CI): 9.5–55.4%) was significantly poorer than that of the low-risk group (76.8%; 95% CI: 52.8–89.7%; P < 0.01).

Conclusion:

This retrospective analysis established pivotal prognostic factors for HRL in Japanese patients. The HIV-JPI, derived exclusively from Japanese patients, highlights the potential for stratified treatments and emphasizes the need for broader studies to further refine this clinical prediction model.
Predicting Reduction Mammaplasty Total Resection Weight With Machine Learning
Authors: Seu Michelle Y. , Rezania Nikki , Murray Carolyn E. , Qiao Mark T. , Arnold Sydney , Siotos Charalampos , Ferraro Jennifer , Jazayeri Hossein E. , Hood Keith , Shenaq Deana , Kokosis George
Published: June 2024

Background

Machine learning (ML) is a form of artificial intelligence that has been used to create better predictive models in medicine. Using ML algorithms, we sought to create a predictive model for breast resection weight based on anthropometric measurements.

Methods

We analyzed 237 patients (474 individual breasts) who underwent reduction mammoplasty at our institution. Anthropometric variables included body surface area (BSA), body mass index, sternal notch–to–nipple (SN-N), and nipple–to–inframammary fold values. Four different ML algorithms (linear regression, ridge regression, support vector regression, and random forest regression) either including or excluding the Schnur Scale prediction for the same data were trained and tested on their ability to recognize the relationship between the anthropometric variables and total resection weights. Resection weight prediction accuracy for each model and the Schnur scale alone were evaluated based on using mean absolute error (MAE).

Results

In our cohort, mean age was 40.36 years. Most patients (71.61%) were African American. Mean BSA was 2.0 m2, mean body mass index was 33.045 kg/m2, mean SN-N was 35.0 cm, and mean nipple–to–inframammary fold was 16.0 cm. Mean SN-N was found to have the greatest variable importance. All 4 models made resection weight predictions with MAE lower than that of the Schnur Scale alone in both the training and testing datasets. Overall, the random forest regression model without Schnur scale weight had the lowest MAE at 186.20.

Conclusion

Our ML resection weight prediction model represents an accurate and promising alternative to the Schnur Scale in the setting of reduction mammaplasty consultations.
Effects of the March 2021 Allocation Policy Change on Key Deceased-donor Kidney Transplant Metrics
Authors: Cutrone Alissa M. , Rega Scott A. , Feurer Irene D. , Karp Seth J.
Published: June 2024

Background.

A major change to deceased-donor kidney allocation in the United States, Kidney Allocation System 250 (KAS250), was implemented on March 15, 2021. Evaluating the consequences of this policy on critical system performance metrics is critical to determining its success.

Methods.

We performed a retrospective analysis of critical performance measures of the kidney transplant system by reviewing all organs procured during a 4-y period in the United States. To mitigate against possible effects of the COVID-19 pandemic, Scientific Registry of Transplant Recipients records were stratified into 2 pre- and 2 post-KAS250 eras: (1) 2019; (2) January 1, 2020–March14, 2021; (3) March 15, 2021–December 31, 2021; and (4) 2022. Between-era differences in rates of key metrics were analyzed using chi-square tests with pairwise z-tests. Multivariable logistic regression and analysis of variations methods were used to evaluate the effects of the policy on rural and urban centers.

Results.

Over the period examined, among kidneys recovered for transplant, nonuse increased from 19.7% to 26.4% (all between-era P < 0.05) and among all Kidney Donor Profile Index strata. Cold ischemia times increased (P < 0.001); however, the distance between donor and recipient hospitals decreased (P < 0.05). Kidneys from small-metropolitan or nonmetropolitan hospitals were more likely to not be used over all times (P < 0.05).

Conclusions.

Implementation of KAS250 was associated with increased nonuse rates across all Kidney Donor Profile Index strata, increased cold ischemic times, and shorter distance traveled.
Expanding Selection Criteria in Deceased Donor Liver Transplantation for Hepatocellular Carcinoma: Long-term Follow-up of a National Registry and 2 Transplant Centers
Authors: Wehrle Chase J. , Kusakabe Jiro , Akabane Miho , Maspero Marianna , Zervos Bobby , Modaresi Esfeh Jamak , Whitsett Linganna Maureen , Imaoka Yuki , Khalil Mazhar , Pita Alejandro , Kim Jaekeun , Diago-Uso Teresa , Fujiki Masato , Eghtesad Bijan , Quintini Cristiano , Kwon Choon David , Pinna Antonio , Aucejo Federico , Miller Charles , Mazzaferro Vincenzo , Schlegel Andrea , Sasaki Kazunari , Hashimoto Koji
Published: June 2024

Background.

This study compares selection criteria for liver transplant (LT) for hepatocellular carcinoma (HCC) for inclusivity and predictive ability to identify the most permissive criteria that maintain patient outcomes.

Methods.

The Scientific Registry of Transplant Recipients (SRTR) database was queried for deceased donor LT’s for HCC (2003–2020) with 3-y follow-up; these data were compared with a 2-center experience. Milan, University of California, San Francisco (UCSF), 5-5-500, Up-to-seven (U7), HALT-HCC, and Metroticket 2.0 scores were calculated.

Results.

Nationally, 26 409 patients were included, and 547 at the 2 institutions. Median SRTR-follow-up was 6.8 y (interquartile range 3.9–10.1). Three criteria allowed the expansion of candidacy versus Milan: UCSF (7.7%, n = 1898), Metroticket 2.0 (4.2%, n = 1037), and U7 (3.5%, n = 828). The absolute difference in 3-y overall survival (OS) between scores was 1.5%. HALT-HCC (area under the curve [AUC] = 0.559, 0.551–0.567) best predicted 3-y OS although AUC was notably similar between criteria (0.506 < AUC < 0.527, Mila n = 0.513, UCSF = 0.506, 5-5-500 = 0.522, U7 = 0.511, HALT-HCC = 0.559, and Metroticket 2.0 = 0.520), as was Harrall’s c-statistic (0.507 < c-statistic < 0.532). All scores predicted survival to P < 0.001 on competing risk analysis. Median follow-up in our enterprise was 9.8 y (interquartile range 7.1–13.3). U7 (13.0%, n = 58), UCSF (11.1%, n = 50), HALT-HCC (6.4%, n = 29), and Metroticket 2.0 (6.3%, n = 28) allowed candidate expansion. HALT-HCC (AUC = 0.768, 0.713–0.823) and Metroticket 2.0 (AUC = 0.739, 0.677–0.801) were the most predictive of recurrence. All scores predicted recurrence and survival to P < 0.001 using competing risk analysis.

Conclusions.

Less restrictive criteria such as Metroticket 2.0, UCSF, or U7 allow broader application of transplants for HCC without sacrificing outcomes. Thus, the criteria for Model for End-stage Liver Disease-exception points for HCC should be expanded to allow more patients to receive life-saving transplantation.
Erysipelothrix spp. and other Erysipelotrichales detected by 16S rRNA microbial community profiling in samples from healthy conventionally reared chickens and their environment
Authors: Wattrang Eva , Sørensen Dalgaard Tina , Eriksson Helena , Söderlund Robert
Published: June 2024

Outbreaks of erysipelas, a disease caused by infection with Erysipelothrix rhusiopathiae (ER), is a re-emerging problem in cage-free laying hen flocks. The source of ER infection in hens is usually unknown and serological evidence has also indicated the presence of ER or other antigenically related bacteria in healthy flocks. The aim of the present study was to evaluate sample collection, culture methods and DNA-based methodology to detect ER and other Erysipelotrichales in samples from healthy chickens and their environment. We used samples from a research facility with conventionally reared chickens with no history of erysipelas outbreaks where hens with high titres of IgY recognising ER previously have been observed. Microbial DNA was extracted from samples either directly or after pre-culture in nonselective or ER-selective medium. Real-time PCR was used for detection of Erysipelothrix spp. and high-throughput amplicon sequencing of 16S rRNA sequencing was used for detection of Erysipelotrichales. A pilot serological analysis of some Erysipelotrichales members with IgY from unvaccinated and ER-vaccinated high-biosecurity chickens, as well as conventionally reared chickens, was also performed. All samples were negative for ER, E. tonsillarum and E. piscisicarius by PCR analysis. However, 16S rRNA community profiling indicated the presence of several Erysipelotrichales genera in both environmental samples and chicken intestinal samples, including Erysipelothrix spp. that were detected in environmental samples. Sequences from Erysipelothrix spp. were most frequently detected in samples pre-cultured in ER-selective medium. At species level the presence of Erysipelothrix anatis and/or Erysipelothrix aquatica was indicated. Serological results indicated that IgY raised to ER showed some cross-reactivity with E. anatis. Hence, environmental samples pre-cultured in selective medium and analysis by 16S rRNA sequencing proved a useful method for detection of Erysipelotrichales, including Erysipelothrix spp., in chicken flocks. The observation of such bacteria in environmental samples offers a possible explanation for the observation of high antibody titres to ER in flocks without a history of clinical erysipelas.
The effect of daily usage of Listerine Cool Mint mouthwash on the oropharyngeal microbiome: a substudy of the PReGo trial
Authors: Laumen J.G.E. , Van Dijck C. , Manoharan-Basil S.S. , de Block T. , Abdellati S. , Xavier B.B. , Malhotra-Kumar S. , Kenyon C.
Published: June 2024

Introduction. Listerine is a bactericidal mouthwash widely used to prevent oral health problems such as dental plaque and gingivitis. However, whether it promotes or undermines a healthy oral microbiome is unclear.

Hypothesis/Gap Statement. We hypothesized that the daily use of Listerine Cool Mint would have a significant impact on the oropharyngeal microbiome.

Aim. We aimed to assess if daily usage of Listerine Cool Mint influenced the composition of the pharyngeal microbiome.

Methodology. The current microbiome substudy is part of the Preventing Resistance in Gonorrhoea trial. This was a double-blind single-centre, crossover, randomized controlled trial of antibacterial versus placebo mouthwash to reduce the incidence of gonorrhoea/chlamydia/syphilis in men who have sex with men (MSM) taking HIV pre-exposure prophylaxis (PrEP). Fifty-nine MSM taking HIV PrEP were enrolled. In this crossover trial, participants received 3 months of daily Listerine followed by 3 months of placebo mouthwash or vice versa. Oropharyngeal swabs were taken at baseline and after 3 months use of each mouthwash. DNA was extracted for shotgun metagenomic sequencing (Illumina Inc.). Non-host reads were taxonomically classified with MiniKraken and Bracken. The alpha and beta diversity indices were compared between baseline and after each mouthwash use. Differentially abundant bacterial taxa were identified using ANOVA-like differential expression analysis.

Results.
Streptococcus was the most abundant genus in most samples (n = 103, 61.7 %) with a median relative abundance of 31.5% (IQR 20.6–44.8), followed by Prevotella [13.5% (IQR 4.8–22.6)] and Veillonella [10.0% (IQR 4.0–16.8)]. Compared to baseline, the composition of the oral microbiome at the genus level (beta diversity) was significantly different after 3 months of Listerine (P = 0.006, pseudo-F = 2.29) or placebo (P = 0.003, pseudo-F = 2.49, permutational multivariate analysis of variance) use. Fusobacterium nucleatum and Streptococcus anginosus were significantly more abundant after Listerine use compared to baseline.

Conclusion. Listerine use was associated with an increased abundance of common oral opportunistic bacteria previously reported to be enriched in periodontal diseases, oesophageal and colorectal cancer, and systemic diseases. These findings suggest that the regular use of Listerine mouthwash should be carefully considered.
Systematic search for new HLA alleles in 4195 human 30x WGS samples
Authors: Albert EA , Deviatkin AA , Smirnova DI , Woroncow M. , Zobkova G.Y , Smirnova A.V , Volchkov PY
Published: June 2024

HLA (Human Leukocyte Antigens) is a highly polymorphic locus in the human genome which also has a high clinical significance. New alleles of HLA genes are constantly being discovered but mostly through the efforts of laboratories which primarily focus on HLA typing and are using field-specific experimental and data processing techniques, like enrichment of HLA region in high-throughput sequencing data. Nevertheless, a vast amount of whole genome sequencing (WGS) data was accumulated over the past years and continues to expand rapidly. Therefore it is an appealing possibility to identify new HLA alleles and refine the information on known alleles from already available WGS data. Currently there are many tools designed for HLA typing, e.g. assigning known alleles, from non HLA enriched WGS data, but none of them specifically tailored towards identification and immediate thorough description of new HLA alleles. Here we are presenting a pipeline HLAchecker, which is specifically designed to identify potentially new HLA alleles based on discrepancies between predicted HLA types, made by any other dedicated tool, and underlying raw 30x WGS data. HLAchecker reports structured in a way which simplifies further validation of potentially new HLA alleles and streamlines submission of alleles to appropriate databases. We validated this tool on 4195 30x WGS samples typed by HLA-HD, discovered 17 potentially new HLA alleles with substitutions in exonic regions and validated five randomly chosen alleles by Sanger sequencing.
Respiratory mucosal administration of DNA aptamer nanomaterials protects against antigenically diverse SARS-CoV-2 variants
Authors: D’Agostino Michael R. , Li Jiuxing , Zhang Zijie , Gu Jimmy , Marzok Art , Ang Jann , Bujold Katherine E. , Afkhami Sam , Xia Xiaohu , Li Yingfu , Miller Matthew S.
Published: June 2024

The ongoing COVID-19 pandemic has highlighted the need for innovative therapeutic strategies to combat rapidly evolving pathogens that challenge the efficacy of traditional vaccines and monoclonal antibody treatments. Here, we explored the potential of TMSA52, a previously described homotrimeric DNA aptamer as a universal prophylactic and therapeutic agent against SARS-CoV-2. TMSA52 demonstrates exceptional binding affinities and broad neutralization against diverse SARS-CoV-2 variant spike proteins that are further enhanced through multimerization onto lamellar iridium nanoplates. Respiratory mucosal delivery of TMSA52 nanomaterials was well-tolerated. Surprisingly, TMSA52 offered potent protection from infection with ancestral SARS-CoV-2 on-par with monoclonal antibodies, and superior protection against antigenically distant SARS-CoV-2 variants. These findings establish DNA aptamers as a promising, cost-effective, and scalable alternative to traditional monoclonal antibody therapies. This study underscores the potential of aptamer-based platforms as a next-generation strategy to enhance global pandemic preparedness and expand our arsenal of infectious disease countermeasures.
Three families of CD4-induced antibodies are associated with the capacity of plasma from people living with HIV to mediate ADCC in presence of CD4-mimetics
Authors: Tauzin Alexandra , Marchitto Lorie , Bélanger Étienne , Benlarbi Mehdi , Beaudoin-Bussières Guillaume , Prévost Jérémie , Yang Derek , Chiu Ta-Jung , Chen Hung-Ching , Bourassa Catherine , Medjahed Halima , Korzeniowski Marek K , Gottumukkala Suneetha , Tolbert William D. , Richard Jonathan , Smith Amos B , Pazgier Marzena , Finzi Andrés
Published: June 2024

CD4-mimetics (CD4mcs) are small molecule compounds that mimic the interaction of the CD4 receptor with HIV-1 envelope glycoproteins (Env). Env from primary viruses normally samples a “closed” conformation which occludes epitopes recognized by CD4-induced (CD4i) non-neutralizing antibodies (nnAbs). CD4mcs induce conformational changes on Env resulting in the exposure of these otherwise inaccessible epitopes. Here we evaluated the capacity of plasma from a cohort of 50 people living with HIV to recognize HIV-1-infected cells and eliminate them by antibody-dependent cellular cytotoxicity (ADCC) in the presence of a potent indoline CD4mc. We observed a marked heterogeneity among plasma samples. By measuring the levels of different families of CD4i Abs, we found that the levels of anti-cluster A, anti-coreceptor binding site and anti-gp41 cluster I antibodies are responsible for plasma-mediated ADCC in presence of CD4mc.

IMPORTANCE

There are several reasons that make it difficult to target the HIV reservoir. One of them, is the capacity of infected cells to prevent the recognition of HIV-1 envelope glycoproteins (Env) by commonly-elicited antibodies in people living with HIV. Small CD4-mimetic compounds expose otherwise occluded Env epitopes, thus enabling their recognition by non-neutralizing antibodies. A better understanding of the contribution of these antibodies to eliminate infected cells in presence of CD4mc could lead to the development of therapeutic cure strategies.
Hepatic Macrophage Migration Inhibitory Factor Promotes Pancreatic Cancer Liver Metastasis in NAFLD
Authors: Yu Qian , Song Hui , Zhu Liang , Shi Xiao-ya , Wang Hai-zhen , Wang Ying-luo , Gong Rui-ning , Cui Jiu-fa , Yang Xiao-nan , Wang Ji-gang , Liang Yu , Chen Ying , Dong Xiao-wu , Lu Guo-tao , Li Chang , Zhang Huan , Tian Yan-tao , Hu Hai-tao , Shao Xin-xin , Hu Ya-bin , Saluja Ashok K. , Li Yue , Mo Ming-guang , Ren He
Published: June 2024

How pathological livers shape tumors, thereby driving pancreatic ductal adenocarcinoma (PDAC) metastasis to the liver, is poorly understood. In the present study, we focus on examining key molecules implicated in this process and assessing their translational significance. We demonstrated that patients with combined non-alcoholic fatty liver disease (NAFLD) have approximately a ninefold increased risk of developing liver metastasis compared to those without NAFLD. In mice model, NAFLD fosters an immunosuppressive microenvironment with increased tumor cell pluripotency and focal adhesion. Mechanistically, NAFLD-induced MIF mediated the progression of PDAC liver metastasis by attracting CD44 positive pancreatic cells. Hepatic MIF knockdown significantly reduced metastases burden with decreased stem-like cancer cells, tumor associated macrophages (TAMs) infiltration and focal adhesion. Targeting the MIF-CD44 axis by either a MIF tautomerase inhibitor, IPG1576, or by CD44 knockdown in tumor cells significantly attenuate liver metastasis of PDAC within the NAFLD context. Patients with PDAC liver metastasis and NAFLD had elevated hepatic MIF expression and increased number of stem-cell like cancer cells. Collectively, our study highlights a pivotal role for MIF-CD44 axis in cancer stemness and offer novel avenues for tailoring therapeutic strategies to individual patients with NAFLD as an underlying condition.
Unraveling Alzheimer’s Disease: Investigating Dynamic Functional Connectivity in the Default Mode Network through DCC-GARCH Modeling
Authors: Yue Kun , Webster Jason , Grabowski Thomas , Jahanian Hesamoddin , Shojaie Ali
Published: June 2024

Alzheimer’s disease (AD) has a prolonged latent phase. Sensitive biomarkers of amyloid beta (Aβ), in the absence of clinical symptoms, offer opportunities for early detection and identification of patients at risk. CurrentAβbiomarkers, such as CSF and PET biomarkers, are effective but face practical limitations due to high cost and limited availability. Recent blood plasma biomarkers, though accessible, still incur high costs and lack physiological significance in the Alzheimer’s process. This study explores the potential of brain functional connectivity (FC) alterations associated with AD pathology as a non-invasive avenue forAβdetection. While current stationary FC measurements lack sensitivity at the single-subject level, our investigation focuses on dynamic FC using resting-state functional MRI (rs-fMRI) and introduces the Generalized Auto-Regressive Conditional Heteroscedastic Dynamic Conditional Correlation (DCC-GARCH) model. Our findings demonstrate the superior sensitivity of DCC-GARCH to CSFAβstatus, and offer key insights into dynamic functional connectivity analysis in AD.
Assessment of Ontario-purchased commercially available milk products for the presence of influenza A viral RNA
Authors: Blais-Savoie Juliette , Yim Winfield , Kotwa Jonathon D. , Yip Lily , Kozak Robert , McGeer Allison , Mubareka Samira
Published: June 2024

Given the widespread presence of influenza A(H5N1) viral RNA in pasteurized milk in the United States, we tested 117 samples of pasteurized cow’s milk purchased from retail outlets in Ontario, Canada in April 2024 for the presence of influenza A viral RNA. No influenza A viral RNA was detected.
Distinct Perception Mechanisms of BACH1 Quaternary Structure Degrons by Two F-box Proteins under Oxidative Stress
Authors: Cao Shiyun , Shi Huigang , Garcia Sheena Faye , Kito Yuki , Shi Hui , Goldberg Hailey V. , Ponce Jackeline , Ueberheide Beatrix , Lignitto Luca , Pagano Michele , Zheng Ning
Published: June 2024

The transcription factor BACH1 regulates heme homeostasis and oxidative stress responses and promotes cancer metastasis upon aberrant accumulation. Its stability is controlled by two F-box protein ubiquitin ligases, FBXO22 and FBXL17. Here we show that the homodimeric BTB domain of BACH1 functions as a previously undescribed quaternary structure degron, which is deciphered by the two F-box proteins via distinct mechanisms. After BACH1 is released from chromatin by heme, FBXO22 asymmetrically recognizes a cross-protomer interface of the intact BACH1 BTB dimer, which is otherwise masked by the co-repressor NCOR1. If the BACH1 BTB dimer escapes the surveillance by FBXO22 due to oxidative modifications, its quaternary structure integrity is probed by a pair of FBXL17, which simultaneously engage and remodel the two BTB protomers into E3-bound monomers for ubiquitination. By unveiling the multifaceted regulatory mechanisms of BACH1 stability, our studies highlight the abilities of ubiquitin ligases to decode high-order protein assemblies and reveal therapeutic opportunities to block cancer invasion via compound-induced BACH1 destabilization.
Loopsim: Enrichment Analysis of Chromosome Conformation Capture with Fast Empirical Distribution Simulation
Authors: Shaked Gideon , Zhang Haihan , Zhang Zhaolin , Gudjonsson Johann E. , Elder James T. , Patrick Matthew T. , Tsoi Lam C.
Published: June 2024

Gene regulation is intricately influenced by the three-dimensional organization of the genome. In particular, chromatin can exist in loop structures that enable long-range regulatory interactions. By utilizing chromosome conformation capture techniques such as Hi-C, valuable information regarding the organization of these loop structures in 3D space can be obtained. While functional/feature enrichment has become a standard downstream analysis for different genomic data to provide biological context, tools that developed specifically for high throughput assays capturing chromosome conformation are relatively limited. Here, we present Loopsim, a command-line application that performs enrichment analysis on Hi-C loop profiles against user-defined regions. Loopsim efficiently simulates a background distribution using a distinctive sampling approach that considers loop size, intervals, loop-loop distances, and structure; it then computes loop-level statistics based on the empirical null distribution.

Availability

Loopsim is a Python package available via PyPI (https://pypi.org/project/loopsim) and the source code is available on GitHub (https://github.com/CutaneousBioinf/Loopsim) under the MIT license.
The TyphiNET data visualisation dashboard: UnlockingSalmonellaTyphi genomics data to support public health
Authors: Dyson Zoe A. , Cerdeira Louise , Sharma Vandana , Carey Megan E. , Holt Kathryn E. ,   Global Typhoid Genomics Consortium
Published: June 2024

Background

Salmonella entericasubspeciesentericaserovar Typhi (abbreviated as ‘Typhi’) is the bacterial agent of typhoid fever. Effective antimicrobial therapy reduces complications and mortality; however, antimicrobial resistance (AMR) is a major problem in many endemic countries. Prevention through vaccination is possible through recently-licensed Gavi-supported typhoid conjugate vaccines (TCVs), and national immunisation programs are currently being considered or deployed in several countries where AMR prevalence is known to be high. Pathogen whole genome sequence data are a rich source of information on Typhi variants (genotypes or lineages), AMR prevalence, and mechanisms. However, this information is currently not readily accessible to non-genomics experts, including those driving vaccine implementation or empirical therapy guidance.

Results

We developed TyphiNET (https://www.typhi.net), an interactive online dashboard for exploring Typhi genotype and AMR distributions derived from publicly available pathogen genome sequences. TyphiNET allows users to explore country-level summaries such as the frequency of pathogen lineages, temporal trends in resistance to clinically relevant antimicrobials, and the specific variants and mechanisms underlying emergent AMR trends. User-driven plots and session reports can be downloaded for ease of sharing. Importantly, TyphiNET is populated by high-quality genome data curated by the Global Typhoid Pathogen Genomics Consortium, analysed using the Pathogenwatch platform, and identified as coming from non-targeted sampling frames that are suitable for estimating AMR prevalence amongst Typhi infections (no personal data is included in the platform). As of February 2024, data from a total of n=11,836 genomes from 101 countries are available in TyphiNET. We outline case studies illustrating how the dashboard can be used to explore these data and gain insights of relevance to both researchers and public health policy-makers.

Conclusions

The TyphiNET dashboard provides an interactive platform for accessing genome-derived data on pathogen variant frequencies to inform typhoid control and intervention strategies. The platform is extensible in terms of both data and features, and provides a model for making complex bacterial genome-derived data accessible to a wide audience.
Amygdala circuit mechanisms underlying alcohol seeking
Authors: Suh Junghyup , Pasqualini Amanda L. , Zambrano Maria A. , Ressler Kerry J.
Published: June 2024

Alcohol seeking during abstinence is mediated in part by strong associations between the pharmacological effects of alcohol and the environment within which alcohol is administered. The amygdala, particularly the basolateral amygdala (BLA), is a key neural substrate of environmental cue and reward associations since it is involved in associative learning and memory recall. However, we still lack a clear understanding of how the activity of molecularly distinct BLA neurons is affected by alcohol and encodes information that drives environmental cue-dependent, alcohol-related behaviors. We previously demonstrated that a subset of BLA neurons which express the CaMKII and Thy1 markers project preferentially to the nucleus accumbens (NAcc), rather than the central amygdala; and these neurons mediate fear inhibition rather than fear acquisition or expression, suggesting a specific role in positive valence processing. We now demonstrate that Pavlovian conditioning with alcohol administration increases the activity of these Thy1-expressing (Thy1+) excitatory neurons in mouse BLA, which is necessary for the conditioned appetitive response.In vivocalcium imaging indicates that the temporal activity profile of these neurons is also correlated with alcohol seeking behavior in response to environmental cues. Optogenetic inhibition of BLA Thy1+ neuronal activity disrupts both the formation and recall of alcohol conditioned place preference. Furthermore, selective axonal inhibition of BLA-Thy1+ neurons reveals that the activity of their NAcc and prefrontal cortex (PFC) projections are differentially necessary for alcohol cueassociationvs.recall, respectively. Together, these findings provide insights into a molecularly distinct subset of BLA neurons that regulates environmental cue-reward associations and drives alcohol seeking behaviors in a projection-specific manner.

Disclosures

KJR has received consulting income from Acer, Bionomics, and Jazz Pharma; serves on Scientific Advisory Boards for Sage, Boehringer Ingelheim, Senseye, the Brain and Behavior Research Foundation, and the Brain Research Foundation, and he has received sponsored research support from Alto Neuroscience. None of this work is directly related to the work presented here.
DICE: Fast and Accurate Distance-Based Reconstruction of Single-Cell Copy Number Phylogenies
Authors: Weiner Samson , Bansal Mukul S.
Published: June 2024

Somatic copy number alterations (sCNAs) are valuable phylogenetic markers for inferring evolutionary relationships among tumor cell subpopulations. Advances in single-cell DNA sequencing technologies are making it possible to obtain such sCNAs datasets at ever-larger scales. However, existing methods for reconstructing phylogenies from sCNAs are often too slow for large datasets. Moreover, the accuracies of many existing methods are highly sensitive to error and other features of the analyzed datasets.

In this work, we propose two new distance-based approaches for reconstructing single-cell tumor phylogenies from sCNA data. The new methods,DICE-barandDICE-star, are based on novel, easy-to-compute distance measures and drastically outperform the current state-of-the-art in terms of both accuracy and scalability. Using carefully simulated datasets, we find that DICE-bar and DICE-star significantly improve upon the accuracies of existing methods across a wide range of experimental conditions and error rates while simultaneously being orders of magnitude faster. Our experimental analysis also reveals how noise/error in copy number inference, as expected for real datasets, can drastically impact the accuracies of many existing methods. We apply DICE-star, the most accurate method on error-prone datasets, to two real single-cell breast cancer datasets and find that it helps identify previously unreported rare cell populations.
Genomic regions of current low hybridisation mark long-term barriers to gene flow in scarce swallowtail butterflies
Authors: Ebdon Sam , Laetsch Dominik R. , Vila Roger , Baird Stuart J.E. , Lohse Konrad
Published: June 2024

Many closely related species continue to hybridise after millions of generations of divergence. However, the extent to which current patterning in hybrid zones connects back to the speciation process remains unclear: does evidence for current multilocus barriers support the hypothesis of speciation due to multilocus divergence? We analyse whole-genome sequencing data to investigate the speciation history of the scarce swallowtailsIphiclides podaliriusandI. feisthamelii, which abut at a narrow (∼25 km) contact zone north of the Pyrenees. We first quantify the heterogeneity of effective migration rate under a model of isolation with migration, using genomes sampled across the range to identify long-term barriers to gene flow. Secondly, we investigate the recent ancestry of individuals from the hybrid zone using genome polarisation and estimate the coupling coefficient under a model of a multilocus barrier. We infer a low rate of long-term gene flow fromI. feisthameliiintoI. podaliriusthe direction of which matches the admixture across the hybrid zone and complete reproductive isolation across≈33% of the genome. Our contrast of recent and long-term gene flow shows that regions of low recent hybridisation are indeed enriched for long-term barriers which maintain divergence between these hybridising sister species. This paves the way for future analysis of the evolution of reproductive isolation along the speciation continuum.

Author summary

Efforts to understand how new species evolve typically approach the problem through either: 1) investigating patterns of genetic exchange across ’hybrid zones’ — where closely related species interbreed — or 2) modelling the demographic history of closely related species. Both approaches are capable of quantifying variation in genetic exchange, or ’gene flow’, along the genome to identify regions of reproductive isolation; yet they leverage genetic signatures across vastly different timescales. The former exploits very recent signatures, while the latter averages long-term signatures over the history of divergence. Hence, we can contrast the genomic distribution of barriers acting on these very different timescales to test how patterns of gene flow change across the speciation continuum. Here we use this strategy to capture the speciation dynamics of a pair of hybridising papilionid butterflies. Our results show that not only are these species continuing to produce hybrids after more than a million years since the onset of divergence, but there is a significant degree of concordance between patterns of gene flow observed along the genome across time scales.
QTL mapping in field plant populations reveals a genetic basis for frequency- and spatially-specific fungal pathosystem resistance
Authors: Baraniecka Patrycja , Gase Klaus , Pradhan Maitree , Baldwin Ian T. , McGale Erica , Valim Henrique F.
Published: June 2024

Fungal pathogens pose significant challenges to agro-ecosystem productivity. The wild tobacco,Nicotiana attenuata, has been grown for over two decades at an experimental field station in its native habitat, leading to the emergence of a high-mortality sudden wilt disease caused by aFusarium-Alternariapathosystem. By using an Advanced Intercross Recombinant Inbred Line (AI-RIL) mapping population ofN. attenuataplanted in the infected field site, we found two significant loci associated with plant susceptibility to the fungi. A functional characterization of several genes in these loci identifiedRLXL(intracellular ribonuclease LX-like) as an important factor underlying plant pathogen resistance. Virus-induced silencing ofRLXLreduced leaf wilting in plants inoculated with anin vitroculture ofFusariumspecies. Assessing the significance of theRLXL-associated allele in mixed field populations indicated that, among 4-plant subpopulations, those harboring a single plant with theRLXL-deficiency allele exhibited the highest survival rates. Within these populations, a livingRLXL-deficient plant improved the survival ofRLXL-producing plants located diagonally, while the mortality of the adjacent plants remained as high as in all other subpopulations. Taken together, these findings provide evidence for the genetic basis for a frequency- and spatially-dependent population pathogen resistance mechanism.

Significance statement

Plant pathogen resistance studies predominantly focus on single genes that reduce pathogenicity in individual plants, aiming to apply these findings to agricultural monocultures. On the other hand, ecologists have observed for decades that greater diversity drives plant population resistance and resilience to pathogens. More studies are needed to identify and characterize loci with positive effects conferred through their frequency in plant populations. We combine quantitative genetics, molecular techniques, and ecologically-informed mixed field populations to identify a novel intracellular ribonuclease LX-like (RLXL) gene with a frequency- and position-dependent effect for plant resistance. To our knowledge, this is the first detailed link between plant population protection and various percentages of plants with an allele representingRLXLpresence or absence.
A new level of RNA-based plant protection - dsRNAs designed from functionally characterized siRNAs highly effective against Cucumber Mosaic Virus
Authors: Knoblich Marie , Gursinsky Torsten , Gago-Zachert Selma , Weinholdt Claus , Grau Jan , Behrens Sven-Erik
Published: June 2024

RNA-mediated crop protection increasingly becomes a viable alternative to agrochemicals that threaten biodiversity and human health. Pathogen-derived double-stranded dsRNAs are processed into small interfering RNAs (siRNAs), which can then induce silencing of target RNAs,e.g.viral genomes. However, with currently used dsRNAs, which largely consist of undefined regions of the target RNAs, silencing is often ineffective: processing generates siRNA pools that contain only a few functionally effective siRNAs (here calledesiRNAs). Using a recently developedin vitroscreen that reliably identifiesesiRNAs from siRNA pools, we identifiedesiRNAs against Cucumber Mosaic Virus (CMV), a devastating plant pathogen. Topical application ofesiRNAs to plants resulted in highly effective protection against massive CMV infection. However, optimal protection was achieved with newly designed multivalent “effective dsRNAs” (edsRNAs), which contain the sequences of severalesiRNAs and are preferentially processed into precisely theseesiRNAs. TheesiRNA components can attack one or more target RNAs at different sites, be active in different silencing complexes and provide cross-protection against different viral variants, important properties for combating rapidly mutating pathogens such as CMV.esiRNAs andedsRNAs have thus been established as a new class of “RNA actives” that significantly increase the efficacy and specificity of RNA-mediated plant protection.
Florfenicol administration in piglets co-selects for multiple antimicrobial resistance genes
Authors: Holman Devin B. , Gzyl Katherine E. , Kommadath Arun
Published: June 2024

Florfenicol is a broad-spectrum phenicol antibiotic used in swine for various indications. However, information regarding its effect on the pig gut microbiome and resistome is lacking. Therefore, this study investigated those effects by treating piglets with an intramuscular injection of florfenicol at 1 and 7 days of age. Fecal samples were collected from treated (n =30) and untreated (n = 30) pigs at nine different time points up until 140 days of age and their microbiomes were profiled using both 16S rRNA gene and shotgun metagenomic sequencing. The gut microbiomes of the two groups of piglets were most dissimilar in the immediate period following florfenicol administration. These differences were driven in part by an enrichment inClostridium scindens,Enterococcus faecalis, andEscherichiaspp. in the florfenicol-treated piglets andFusobacteriumspp.,Pauljensenia hyovaginalis,andRuminococcus gnavusin the control piglets. In addition to florfenicol resistance genes includingfloR,fexA, andfexB, florfenicol also selected for genes conferring resistance to the aminoglycosides, beta-lactams, peptides, or sulfonamides up until weaning at 21 days of age. Florfenicol-resistantEscherichia coliisolated from these piglets were found to carry a plasmid with afloR, alongtet(A),aph(6)-Id,aph(3’’)-Ib,sul2, andblaTEM-1/blaCMY-2. A plasmid carryingfexBandpoxtAwas identified in florfenicol-resistantEnterococcus avium,Enterococcus faecium, andE.faecalisisolates from the treated piglets. This study highlights the potential for co-selection and perturbation of the gut microbial community in pre-weaned piglets administered florfenicol.

Importance

Antimicrobial use and resistance remain a serious challenge in food-animal production systems. Understanding how specific antimicrobials affect the gut microbiome and resistome is an important step in reducing antimicrobial use and resistance. Florfenicol is an antimicrobial used in swine production, yet very little is known about its effect on the pig gut microbiome and resistome. In this study, we administered florfenicol to piglets at 1 and 7 days of age and characterized their fecal metagenomes through to 140 days of age. Florfenicol altered the fecal microbiome and selected for many unrelated antimicrobial resistance genes up until weaning at 21 days of age. Part of this co-selection process appeared to involve anEscherichia coliplasmid carrying a florfenicol resistance gene along with genes conferring resistance to at least four other antimicrobial classes. These results demonstrate the potential for certain antimicrobials to co-select for multiple, unrelated antimicrobial resistance genes in pigs.