bluuebunny/crossref_metadata_2025 huggingface dataset:
Within-visit Blood Pressure Variability in Children and Adolescents in the National Health and Nutrition Examination Survey (2013-2020)
Authors: Riar Sandeep K , Gillespie Scott , South Andrew M
Published: August 2024

Background

It is assumed that BP decreases with repeat measurements and multiple readings are recommended. There is limited information about within-visit BP variability (BPV) in healthy children.

Methods

We used NHANES data (2013-2020) to measure BPV in subjects 8-17 years old with three BP readings. During 2013 to 2016, auscultatory BP was obtained (manual protocol, MP). Subsequently, oscillometric BP was measured (automated protocol, AP). We excluded subjects with diastolic BP ‘zero’.

Results

We included a total 5656 subjects with 3365 (59.5%) in the MP and 2291 (40.5%) in the AP group. A ΔBP (individual-level difference between the highest and lowest of three BP readings) ≥5 mmHg was noted in 49.1% and 60.7% subjects for systolic BP (SBP) and diastolic BP (DBP) respectively. A ΔDBP ≥10 mmHg and DBP average real variability ≥10 mmHg was twice as common in the MP than AP group. A ΔBP ≥20 mmHg was noted in 1.3% and 4.4% subjects for SBP and DBP respectively. The first SBP and DBP reading was ≥5 mmHg higher or lower than the averaged second and third SBP and DBP readings in 24.9% and 34.5% of subjects respectively. The first SBP and DBP reading was the highest of three BP readings in 44.2% and 42.4% subjects respectively.

Conclusions

There is significant BPV in children and adolescents. Diastolic BPV is more common in MP than AP groups. Initial BP is not always the highest and inclusion of second and third BP reading may be more representative of patient’s actual BP.
Heparanase 2 regulates endothelial permeability and prevents from proteinuria via VEGFA and FGF signaling
Authors: Becker Yannic , Tkachuk Sergey , Jörns Anne , Alwakaa Ahmad , Hegermann Jan , Schenk Heiko , Kiyan Yulia , Haller Hermann
Published: August 2024

Background

Heparan sulfates (HS) attached to the apical surface of vascular endothelial cells (ECs) play an important role in regulating endothelial permeability and ligand recognition by cell-surface receptors. Shedding of heparan sulfate (HS) from the EC surface increases vascular leakage and is associated with vascular diseases. Recently, heparanase 2 (Hpa2) was described as a novel regulatory molecule that controls HS shedding. However, its role in regulating HS physiology in the vascular endothelium is largely unknown. Here, we characterize the role of endogenous Hpa2 in the vertebrate vascular system.

Methods

We use zebrafish larvae as our primary animal model. Hpa2 expression and localization was examined byin situhybridization and immunofluorescence. Hpa2 loss-of-function (LOF) was induced by CRISPR-Cas9 or morpholino antisense strategies. We assessed vascular permeability, blood vessel architecture, and EC morphology using transgenic zebrafish and transmission electron microscopy. EC expression profiles and HS quantity were analyzed in Hpa2-LOF larvae. The capacity of recombinant Hpa2 to modulate signaling in ECs by the HS-binding growth factors fibroblast growth factor 2 (FGF2) and vascular endothelial growth factor A165(VEGFA165) was tested by western blotting and immunofluorescence. Attenuation of the Hpa2-LOF phenotype was testedin vivoin zebrafish larvae via use of recombinant Hpa2 and pharmacological inhibition of FGF and VEGFA signaling.

Results

We detectedhpse2expression in hepatic tissue and localized the protein in blood vessels. Hpa2-LOF larvae exhibited increased vascular permeability, occasional hypersprouting, and altered EC and extracellular matrix (ECM) morphology. Hpa2-LOF also reduced HS levels and caused changes in the endothelial transcriptome characterized by dysregulated genes involved in ECM-receptor interaction and signal transduction regulation. Recombinant hHpa2 rescued the Hpa2-LOF phenotype in zebrafish. We showedin vitrothat Hpa2 competes with FGF2 and VEGFA165for binding on the EC surface and consequently reduces the cellular response these factors elicit. Pharmacological inhibition of these pathways alleviated the Hpa2-LOF phenotype in zebrafish.

Conclusion

We conclude that Hpa2 is a circulating molecule that maintains vascular integrity by regulating HS-dependent processes on the EC surface. These results may translate into novel strategies applying recombinant Hpa2 to treat microvascular diseases.
Global genomic surveillance of monkeypox virus
Authors: Otieno James R. , Ruis Christopher , Onoja Bernard A. , Kuppalli Krutika , Hoxha Ana , Nitsche Andreas , Brinkmann Annika , Michel Janine , Mbala-Kisengeni Placide , Mukadi-Bamuleka Daniel , Osman Muntasir Mohammed , Hussein Hanadi Elawad , Raja Muhammad Ali , Fotsing Richard , Herring Belinda L. , Keita Mory , Rico Jairo Mendez , Gresh Lionel , Barakat Amal , Katawera Victoria , Nahapetyan Karen , Naidoo Dhamari , Floto R. Andres , Cunningham Jane , Van Kerkhove Maria D. , Lewis Rosamund , Subissi Lorenzo
Published: August 2024

Monkeypox virus (MPXV) is endemic in Western and Central Africa and, in May 2022, a clade IIb lineage (B.1) caused a global outbreak outside Africa, resulting in its detection in 117 countries/territories. To understand the global phylogenetics of MPXV, we carried out the first analysis of all available MPXV sequences, including 10,670 sequences from 65 countries collected between 1958 and 2024. Our analysis reveals high mobility of clade I viruses within Central Africa, sustained human-to-human transmission of clade IIb lineage A viruses within the Eastern Mediterranean region, and distinct mutational signatures that can distinguish sustained human-to-human from animal-to-animal transmission. Moreover, distinct clade I sequences from Sudan suggest local MPXV circulation in areas of Eastern Africa over the past four decades. Our study underscores the importance of genomic surveillance in tracking spatiotemporal dynamics of MXPV clades and the need to strengthen such surveillance, including in some parts of Eastern Africa.
Prognostic frailty-based determinants of long-term mortality in older patients with newly diagnosed multiple myeloma
Authors: Muzyka Mariya , Ottaviani Silvia , Caffa Irene , Bonfiglio Tommaso , Parisi Erica , Guijarro Ana , Tagliafico Luca , Lemoli Roberto , Ponzano Marta , Marelli Cristina , Signori Alessio , Nencioni Alessio , Cea Michele , Monacelli Fiammetta
Published: August 2024

Introduction

Multiple myeloma (MM) is a plasma cell neoplasm predominantly diagnosed in older adults. However, the significance of defining patient frailty, as well as identifying the most suitable and reliable tools for its assessment, remains to be firmly established.

Materials and Methods

This retrospective observational study investigated 36 patients, aged 65 or older, who underwent Comprehensive Geriatric Assessment (CGA). The average patient age was 76 (SD 6.22), with 33.3% being female. Patients were evaluated using the International Myeloma Working Group Frailty Index (IMWG-FI) and the 40-item Rockwood’s Frailty Index (FI) at the Oncogeriatrics clinic of the IRCCS Polyclinic San Martino Hospital, Genoa, Italy, between December 2017 and August 2021. Laboratory, cancer-specific, demographic, and clinical variables were collected. Survival analysis and frailty comparison were conducted using Stata version 17.0.

Results

Stepwise multivariate analysis identified Numerical Rating Scale (NRS) (HR 1.40, 95% CI 1.09-1.78, p=0.008) and Rockwood’s Frailty Index (FI) (HR 2.23, 95% CI 1.29-3.87, p=0.004) as significant prognostic predictors, adjusted for sex, ISS stage, and multimorbility. Comparison between Rockwood’s FI and IMWG-FI using Spearman correlation coefficient showed no statistically significant correlation (r=0.268, p=0.114). Multivariate Cox model, adjusting for sex, International Staging System (ISS) stage, and Cumulative Illness Rating Scale (CIRS) comorbidity index, demonstrated the superior predictive ability of Rockwood’s FI over IMWG-FI (C-index 0.775 vs 0.749).

Discussion

the 40-item Rockwood FI emerges as a valuable tool for prognostication in old MM patients, surpassing the traditional IMWG-FI in predictive accuracy, emphasizing the importance of a comprehensive approach considering both disease-specific and patient-related factors.
Emergency Care in India: A Retrospective Cross-sectional Analysis of Health Management and Information System and Global Burden of Disease
Authors: Urs Gaurav , Zadey Siddhesh , Kumar Padmavathy Krishna , Gangane Tejali , Nimkar Pushkar , Staton Catherine , Vissoci Joao Ricardo Nickenig
Published: August 2024

Background

To understand the utilization and burden of emergency medical conditions (EMCs), we assessed EM Department (EMD) data from the Health Management and Information System (HMIS) of India and EMC from the Global Burden of Diseases (GBD).

Methods

This was a retrospective cross-sectional analysis of HMIS and GBD data for 2019. We extracted EMD registrations, admissions, and deaths from HMIS and incidence, deaths, and DALYs from GBD for 31 EMCs at the national and state levels. We analyzed HMIS and GBD data for proportions and rates of registrations, deaths, and incident cases relative to population counts and hospital admission numbers.

Results

In 2019, 119,103,358 patients (8,935.66 per 100,000 people) were registered at EMDs. The national EMD registration rate was 6,744.21 per 100,000 hospital admissions and the EMD death rate was 43,939.49 per 100,000 inpatient deaths. Only 12.14% of all HMIS registrations had cause-specific data. GBD estimated 2,047,175,737 EMC incident cases nationally, accounting for 27.22% of all-cause incidence, 51.71% of all-cause mortality, and 42.30% of all-cause DALYs. Trauma-related registrations were 9.27% in HMIS while injuries in GBD accounted for 7% of EMCs. Overall, HMIS EMD registrations were lower than GBD EMC incidence numbers, with regional variations.

Conclusions

The study reveals gaps in the EMD utilization as per HMIS data compared to the EMC burden estimates from GBD. Improved data integration and reporting can address regional disparities.
Simultaneous Heart and Kidney Transplantation utilizing Circulatory Death Donors in the United States
Authors: Tavolacci Sooyun C. , Okumura Kenji , Isath Ameesh , Rodriguez Gabriel B. , De La Pena Corazon , Shimamura Junichi , Lansman Steven L. , Ohira Suguru
Published: August 2024

Objective

Heart transplants utilizing donors from circulatory death (DCD) allografts are rapidly growing with the potential to expand the donor pool. However, little is known about the use of DCD donors for simultaneous heart and kidney transplants (SHKT) compared to SHKT using brain death donors (DBD).

Methods

From May 22, 2020, to September 30, 2023, 1,129 adult patients received SHKT (DCD, N=91 vs. DBD, N=1,038), identified using the United Network for Organ Sharing database, excluding other multi-organ transplants and re-transplants. A 1:3 ratio propensity score matching was performed using 17 recipient characteristics and 7 donor characteristics. A total of 91 DCD and 273 DBD matched cases were compared.

Results

In the unmatched cohort, DCD recipients were older (DCD: 60 vs. DBD: 58 years, p=0.03) and had a lower rate of dialysis at transplant (27% vs. 40%, p=0.03) and status 1 to 2 patients (43% vs. 72%, p<.001). Donors were younger (30 vs. 32 years, p=0.02) in the DCD group. In the matched cohort, kidney delayed graft function (27% vs. 22%, p=0.29) was comparable, as were recipient survival (p=0.19), heart graft survival (p=0.19), and kidney graft survival (p=0.17). In multivariate Cox proportional hazards analysis, donor type (DCD) was not associated with an increased risk of mortality (HR=1.69, 95% Cl 0.90-3.16, p=0.10). Sub-group analysis showed that survival and freedom from graft failures were comparable between different modes of DCD recovery. The centers performing both DCD- and DBD-SHKT showed significantly shorter waitlist days with comparable transplant outcomes compared to centers that only performed DBD-SHKT.

Conclusions

SHKT using DCD donors yields comparable survival and graft outcomes to those using DBD donors. These findings will guide treatment strategies for heart transplant candidates with kidney dysfunction, including the selection of donors and patients and safety net policy options.
Normalization of Single-cell RNA-seq Data Using Partial Least Squares with Adaptive Fuzzy Weight
Authors: Singh Vikas , Kirtipal Nikhil , Lim Songwon , Lee Sunjae
Published: August 2024

Normalization of single-cell RNA-seq (scRNA-seq) is a crucial step in downstream analysis, where raw data are adjusted to correct unwanted factors that prevent the direct comparison of expression measures. scRNA-seq data exhibits a multivariate relationship between transcript-specific expression and sequencing depth that a single scale factor cannot address. A partial least squares (PLS) regression was performed to accommodate the variability of gene expression in each condition, and upper and lower quantiles with adaptive fuzzy weights were utilized to correct unwanted biases in scRNA-seq data. The present approach was compared using real and simulated datasets across various state-of-the-art performance measures.
Different treatment durations of loperamide in preventing pyrotinib-induced diarrhea: A randomized, parallel-group sub-study of the phase II PHAEDRA trial
Authors: Wang Changjun , Lin Yan , Xu Ying , Mao Feng , Guan Jinghong , Wang Xuejing , Zhang Yanna , Zhang Xiaohui , Shen Songjie , Zhong Ying , Pan Bo , Peng Li , Huang Xin , Cao Xi , Yao Ru , Zhou Xintong , He Zecheng , Liu Yuhan , Lang Jie , Li Chenggang , Zhou Yidong , Sun Qiang
Published: August 2024

Background: Pyrotinib, a pan-HER tyrosine kinase inhibitor, demonstrates efficacy in the treatment of HER2-positive breast cancer. However, the frequent occurrence of treatment-emergent diarrhea necessitating discontinuation, impacts patient outcomes. Methods: In this multicenter, open-label, phase II PHAEDRA study enrolling early stage HER2-positive patients for postoperative treatment with nab-paclitaxel and pyrotinib, 120 patients were included for a sub-study and randomly divided into two groups to receive 21 days and 42 days of loperamide for primary prophylaxis of diarrhea, followed by as-needed usage. The primary outcome was the incidence of grade ≥3 diarrhea. Results: Fifty-eight patients in the 21-day group and 59 patients in the 42-day group received at least one dose of pyrotinib. With a median follow-up of 12.1 months, all patients experienced diarrhea of any grade, with grade ≥3 events in 39.7% of the 21-day group and 42.4% of the 42-day group (relative risk: 0.94; 95% confidence interval: 0.61-1.45). The most common treatment-emergent adverse events, other than diarrhea, were hypoesthesia, vomiting, nausea, and rash, mostly grade 1-2, except for one case of grade ≥3 decreased neutrophil count in each group. Conclusion: No significant differences were observed between 21-day and 42-day loperamide durations in preventing grade ≥3 diarrhea. Considering the economic cost and patient compliance, 21-day loperamide prophylaxis might represent a more pragmatic and appropriate approach for clinical application.
Large-scale CSF proteome profiling identifies biomarkers for accurate diagnosis of Frontotemporal Dementia
Authors: Hok-A-Hin Yanaika S. , Vermunt Lisa , Peeters Carel F.W. , van der Ende Emma L. , de Boer Sterre C.M. , Meeter Lieke H. , van Swieten John C. , Hu William T. , Lleó Alberto , Alcolea Daniel , Engelborghs Sebastiaan , Sieben Anne , Chen-Plotkin Alice , Irwin David J. , van der Flier Wiesje M. , Pijnenburg Yolande A.L. , Teunissen Charlotte E. , del Campo Marta
Published: August 2024

Diagnosis of Frontotemporal dementia (FTD) and the specific underlying neuropathologies (frontotemporal lobar degeneration; FTLD-Tau and FTLD-TDP) is challenging, and thus fluid biomarkers are needed to improve diagnostic accuracy. We used proximity extension assays to analyze 665 proteins in cerebrospinal fluid (CSF) samples from a multicenter cohort including patients with FTD (n = 189), Alzheimer’s Disease dementia (AD; n = 232), and cognitively unimpaired individuals (n = 196). In a subset, FTLD neuropathology was determined based on phenotype or genotype (FTLD-Tau = 87 and FTLD-TDP = 68). Forty three proteins were differentially regulated in FTD compared to controls and AD, reflecting axon development, regulation of synapse assembly, and cell-cell adhesion mediator activity pathways. Classification analysis identified a 14- and 13-CSF protein panel that discriminated FTD from controls (AUC: 0.96) or AD (AUC: 0.91). Custom multiplex panels confirmed the highly accurate discrimination between FTD and controls (AUCs > 0.96) or AD (AUCs > 0.88) in three validation cohorts, including one with autopsy confirmation (AUCs > 0.90). Six proteins were differentially regulated between FTLD-TDP and FTLD-Tau, but no reproducible classification model could be generated (AUC: 0.80). Overall, this study introduces novel FTD-specific biomarker panels with potential use in diagnostic setting.
Psychometric Evaluation of the Japanese Yale-Brown Obsessive Compulsive Scale Modified for Olfactory Reference Disorder (ORD-YBOCS-J)
Authors: Sano Nanako , Greenberg Jennifer L. , Yoshida Saran
Published: August 2024

Objective

The Yale-Brown Obsessive Compulsive Scale Modified for Olfactory Reference Syndrome (ORS-YBOCS) is a self-rated measure for assessing the severity of current olfactory reference disorder (ORD) symptoms. This scale has been translated into multiple languages and used in previous studies. However, its psychometric properties have not been investigated. The present study aimed to develop a Japanese ORS-YBOCS (newly named the ORD-YBOCS) and examine its reliability and validity.

Methods

A total of 104 individuals with self-reported ORD symptoms were included (mean age = 30.20 years,SD= 10.25). Internal consistency and factor structure were assessed by calculating Cronbach’s alpha and conducting confirmatory factor analysis (CFA) respectively. Convergent and divergent validity were examined via correlations with measures of Jikoshu-Kyofu symptoms, body image concerns, depression, and fear of negative evaluation.

Results

The Japanese ORD-YBOCS had good internal consistency (α= .81) and acceptable construct validity (r= .43 with Jikoshu-Kyofu symptoms,r= .20 with body image concerns,r= .56 with depression, andr= .27 with fear of negative evaluation). The scree plot suggested a one-factor model, but the CFA results did not support this (CFI = 0.76, TLI = 0.70, RMSEA = 0.14, and SRMR = 0.10).

Conclusion

This is the first study to examine the psychometric properties of the self-report ORS-YBOCS. The linguistically validated Japanese ORD-YBOCS showed good internal consistency and acceptable validity. These results suggest that the Japanese ORD-YBOCS is a valid and reliable tool to measure ORD symptom severity.
Considerations for Equitable Distribution of Digital Healthcare for People Who Use Drugs
Authors: Papalamprakopoulou Zoi , Roussos Sotirios , Ntagianta Elisavet , Triantafyllou Vasiliki , Kalamitsis George , Dharia Arpan , Sypsa Vana , Hatzakis Angelos , Talal Andrew H.
Published: August 2024

Background

Telehealth holds the potential to expand healthcare access for people who use drugs (PWUD). However, approaches to increase PWUDs’ access to digital healthcare are not well-understood. We studied digital healthcare accessibility among PWUD.

Methods

We employed respondent-driven sampling to recruit 162 PWUD in Athens, Greece to collect data via a structured questionnaire. Participants were aged at least 18 years and had an injection drug use (IDU) history. We assessed current internet and computer access, and experience with telemedicine. We utilized logistic regression to evaluate sociodemographic associations.

Results

Participants’ mean (standard deviation) age was 45.9 (8.8) years, 84.0% were male, 90.1% Greek, 77.8% reported IDU within the past year, 85.2% were not linked to opioid treatment, and 50.0% were currently experiencing homelessness. Only 1.9% had experience and 46.3% had familiarity with telemedicine. Internet and computer access were reported by 66.0% and 31.5% of participants, respectively. Compared to participants with secure housing, those currently experiencing homelessness reported decreased internet (50.6% vs 81.5%, p<0.001) and computer access (11.1% vs 51.9%, p<0.001). Multivariable analyses revealed that older age (per 1-year increase: odds ratio [OR]=0.94, 95% confidence interval [CI] [0.89, 0.99], p=0.03), IDU within the past year (0.29 [0.10, 0.88], p=0.03), and homelessness (0.29, [0.13, 0.65], p=0.003) were associated with lower odds of internet access. Homelessness was associated with lower odds of computer access (0.17, [0.07, 0.41], p<0.001).

Conclusions

Internet and infrastructure challenges, homelessness, and digital literacy gaps should be considered to bridge the digital divide and ensure equitable digital healthcare distribution for PWUD.

Clintrials.govregistration number:NCT05794984
Altered neural recruitment despite dual task performance recovery in athletes with repeat concussion
Authors: Hagen Andrew C. , Tracy Brian L , Stephens Jaclyn A.
Published: August 2024

Sports-related concussions (SRCs) pose significant challenges to college-aged athletes, eliciting both immediate symptoms and subacute cognitive and motor function impairment. While most symptoms and impairments resolve within weeks, athletes with repeat SRCs may experience heightened risk for prolonged recovery trajectories, future musculoskeletal injuries, and long-term neurocognitive deficits. This includes impaired dual task performance and altered neurophysiology that could persist across the lifespan and elicit future pathophysiology and neurodegeneration. Thus, it is imperative to improve our understanding of neurophysiology after SRC. This study aimed to investigate the impact of repeat SRCs on dual task performance and associated neural recruitment using functional near-infrared spectroscopy (fNIRS).

A total of 37 college-aged athletes (ages 18-24) participated in this cross-sectional observational study. Among these athletes, 20 had a history of two or more SRCs, while 17 had never sustained a SRC and served as controls. Participants completed the Neuroimaging-Compatible Dual Task Screen (NC-DTS) while fNIRS measured neural recruitment in the frontoparietal attention network and the primary motor and sensory cortices.

Behavioral analysis revealed that athletes with repeat SRCs exhibited comparable single task and dual task performance to control athletes. Additionally, dual task effects (DTE), which capture performance declines in dual tasks versus single tasks, did not significantly differ between groups. Notably, the cohort of athletes with repeat SRC in this study had a longer time since their last SRC (mean = 1.75 years) than majority of previous SRC studies. Neuroimaging results indicated altered neural recruitment patterns in athletes with multiple repeat SRCs during both single and dual tasks. Specifically, athletes with repeat SRCs demonstrated increased prefrontal cortex (PFC) activation during single motor tasks compared to controls (P< 0.001,d= 0.47). Conversely, during dual tasks, these same athletes exhibited reduced PFC activation (P< 0.001,d= 0.29) and primary motor cortex (M1) activation (P= 0.038,d= 0.16) compared to their single task activation.

These findings emphasize the complex relationship between SRC history, dual task performance, and changes in neurophysiology. While athletes with repeat SRCs demonstrate recovery in behavioral dual task performance, persistent alterations in neural recruitment patterns suggest ongoing neurophysiological changes, possibly indicating compensatory neural strategies and inefficient neural resource allocation, even beyond symptom resolution and medical clearance. Understanding the compensatory neural recruitment strategies that support behavioral performance following repeat SRCs can inform return-to-play decisions, future musculoskeletal injury risk, and the long-term impact of SRCs on neurocognitive function.
The Detection of Xylazine in Tijuana, Mexico: Triangulating Drug Checking and Clinical Urine Testing Data
Authors: Friedman Joseph R. , Montoya Alejando González , Ruiz Carmina , González Tejeda Mariana Alejandra , Segovia Luis A. , Godvin Morgan E. , Sisco Edward , Pyfrom Elise M. , Appley Meghan G. , Shover Chelsea L. , Bufanda Lilia Pacheco
Published: August 2024

Introduction

Xylazine is a veterinary anesthetic increasingly present alongside illicit fentanyl in the US and Canada, presenting novel health risks. Although xylazine remains less common in the Western US, Mexican border cities serve as key trafficking hubs and may have higher prevalence of novel substances, but surveillance has been limited.

Methods

We examined deidentified records from the Prevencasa harm reduction clinic in Tijuana, describing urine and paraphernalia testing from patients reporting using illicit opioids within 24 hr. Xylazine (two types), fentanyl, opiate, methamphetamine, amphetamine, benzodiazepine, and nitazene test strips were used to test urine and paraphernalia samples. Paraphernalia samples were also analyzed with mass spectrometry.

Results

The study consisted of 23 participants that provided both urine and paraphernalia samples. Of the participants studied, 100 %, 91.3 %, and 69.6 % reported using China White/fentanyl, methamphetamine, and tar heroin, respectively. The mean age was 41.7 years, 95.7 % were male, 65.2 % were unhoused, and 30.4 % had skin wounds at the time of sample collection.

Xylazine positivity in urine, for the two types used, was 82.6 % and 65.2 %. For paraphernalia testing, the xylazine positivity was 65.2 % and 47.8 %. Confirmatory testing of paraphernalia samples by mass spectrometry indicated a 52.2 % xylazine positivity. This testing also revealed positivity rates for fentanyl (73.9 %), fluorofentanyl (30.4 %), tramadol (30.4 %), and lidocaine (30.4 %).

The mass spectrometry results suggest lidocaine triggeredn= 3 andn= 0 false positives among the xylazine test strip types. A total ofn= 0 andn= 1 false negatives were also observed.

Discussion

Xylazine is present on the U.S.-Mexico border, requiring public health intervention. High lidocaine positivity complicates the clinical detection of xylazine via testing strips. Xylazine was found to be more prevalent in urine than in paraphernalia samples. Confirmatory urine studies are needed to better understand possible complications of using test strips for toxicological testing.
Enhanced Diversifying Selection on Polymerase Genes in H5N1 Clade 2.3.4.4b: A Key Driver of Altered Species Tropism and Host Range Expansion
Authors: Misra Sougat , Gilbride Elizabeth , Ramasamy Santhamani , Pond Sergei L. Kosakovsky , Kuchipudi Suresh V.
Published: August 2024

Highly pathogenic avian influenza H5N1 clade 2.3.4.4b viruses have shown unprecedented host range and pathogenicity, including infections in cattle, previously not susceptible to H5N1. We investigated whether selection pressures on clade 2.3.4.4b viral genes could shed light on their unique epidemiological features. Our analysis revealed that while the gene products of clade 2.3.4.4b H5N1 primarily undergo purifying selection, there are notable instances of episodic diversifying selection. Specifically, the polymerase genes PB2, PB1, and PA exhibit significantly greater selection pressures in clade 2.3.4.4b than all earlier H5N1 virus clades. Polymerases play critical roles in influenza virus adaptation, including viral fitness, interspecies transmission, and virulence. Our findings provide evidence that significant selection pressures have shaped the evolution of the H5N1 clade 2.3.4.4b viruses, facilitating their expanded host tropism and the potential for further adaptation to mammalian hosts. We discuss how exogenous factors, such as altered bird migration patterns and increased host susceptibility, may have contributed to the expanded host range. As H5N1 viruses continue to infect new hosts, there is a greater risk of emergent novel variants with increased pathogenicity in humans and animals. Thus, comprehensive One Health surveillance is critical to monitor transmission among avian and mammalian hosts.
mobileRNA: a tool for efficient analysis of mobile RNA molecules in multiple genomes
Authors: Jeynes-Cupper Katie , Catoni Marco
Published: August 2024

In plants, mobile RNA molecules play a significant role in long distance signalling, with evidence of transport mechanisms and functional roles for both mobile messenger RNA (mRNA) and small RNA (sRNA) molecules. The movement of RNAs between distant tissues can be revealed in plant grafting experiments involving different genotypes (hetero-grafting) associated to genomic analysis, using the natural polymorphisms between the genotypes to discriminate between RNAs produced in the sampled tissue from those which have travelled from distant organs. However, the hight level of noise in the analyses of RNA sequencing datasets involving two different genotypes, and the lack of a standardised pipeline for the analysis of grafted plants, make the identification of natural mobile RNA molecules a challenge. Here, we introduce a pipeline integrated into an R package,mobileRNA, which performs simultaneous alignment of RNA sequencing samples on a merged reference genome. Using simulated datasets, we show thatmobileRNAcan identify putative mobile RNAs with unprecedented efficiency in absence of post-processing steps.
Using Functional Genomic Data in Monocytes/Macrophages and Genotyping to Nominate Disease-Driving Single Nucleotide Polymorphisms and Target Genes in Juvenile Idiopathic Arthritis
Authors: Haley Emma K. , Barshad Gilad , He Adam , Rice Edward , Sudman Marc , Thompson Susan D. , Crinzi Elizabeth A. , Jiang Kaiyu , Danko Charles G. , Jarvis James N.
Published: August 2024

Introduction

GWAS have identified multiple regions that confer risk for juvenile idiopathic arthritis (JIA). However, identifying the single nucleotide polymorphisms (SNPs) that drive disease risk is impeded by the SNPs’ that identify risk loci being in linkage disequilibrium (LD) with hundreds of other SNPs. Since the causal SNPs remain unknown, it is difficult to identify target genes and use genetic information to inform patient care. We used genotyping and functional data in primary human monocytes/macrophages to nominate disease-driving SNPs on JIA risk haplotypes and identify their likely target genes.

Methods

We identified JIA risk haplotypes using Immunochip data from Hinks et al (Nature Gen 2013) and the meta-analysis from McIntosh et al (Arthritis Rheum 2017). We used genotyping data from 3,939 children with JIA and 14,412 healthy controls to identify SNPs that: (1) were situated within open chromatin in multiple immune cell types and (2) were more common in children with JIA than the controls (p< 0.05). We intersected the chosen SNPs (n=846) with regions of bi-directional transcription initiation characteristic of non-coding regulatory regions detected using dREG to analyze GRO-seq data. Finally, we used MicroC data to identify gene promoters interacting with the regulatory regions harboring the candidate causal SNPs.

Results

We identified 190 SNPs that overlap with dREG peaks in monocytes and126 SNPs that overlap with dREG peaks in macrophages. Of these SNPs, 101 were situated within dREG peaks in both monocytes and macrophages, suggesting that these SNPs exert their effects independent of the cellular activation state. MicroC data in monocytes identified 20 genes/transcripts whose promoters interact with the enhancers harboring the SNPs of interest.

Conclusion

SNPs in JIA risk regions that are candidate causal variants can be further screened using functional data such as GRO-seq. This process identifies a finite number of candidate causal SNPs, the majority of which are likely to exert their biological effects independent of cellular activation state in monocytes. Three-dimensional chromatin data generated with MicroC identifies genes likely to be influenced by these SNPs. These studies demonstrate the importance of investigations into the role of innate immunity in JIA.
Molecular Visualization of Neuronal TDP43 PathologyIn Situ
Authors: Erwin Amanda L. , Chang Matthew L. , Fernandez Martin G. , Attili Durga , Russ Jennifer E. , Sutanto Renaldo , Pinarbasi Emile S. , Bekier Michael , Brant Tyler S. , Hahn Terry , Dykstra Megan , Thomas Dafydd , Li Xingli , Baldridge Ryan D. , Tank Elizabeth M. H. , Barmada Sami J. , Mosalaganti Shyamal
Published: August 2024

Nuclear exclusion and cytoplasmic accumulation of the RNA-binding protein TDP43 are characteristic of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Despite this, the origin and ultrastructure of cytosolic TDP43 deposits remain unknown. Accumulating evidence suggests that abnormal RNA homeostasis can drive pathological TDP43 mislocalization, enhancing RNA misprocessing due to loss of nuclear TDP43 and engendering a cycle that ends in cell death. Here, we show that adding small monovalent oligonucleotides successfully recapitulates pathological TDP43 mislocalization and aggregation in iPSC-derived neurons (iNeurons). By employing a multimodalin situcryo-correlative light and electron microscopy pipeline, we examine how RNA influences the localization and aggregation of TDP43 in near-native conditions. We find that mislocalized TDP43 forms ordered fibrils within lysosomes and autophagosomes in iNeurons as well as in patient tissue, and provide the first high-resolution snapshots of TDP43 aggregatesin situ. In so doing, we provide a cellular model for studying initial pathogenic events underlying ALS, FTLD, and related TDP43-proteinopathies.
Towards Digital Quantification of Ploidy from Pan-Cancer Digital Pathology Slides using Deep Learning
Authors: Carrillo-Perez Francisco , Cramer Eric M. , Pizurica Marija , Andor Noemi , Gevaert Olivier
Published: August 2024

Abnormal DNA ploidy, found in numerous cancers, is increasingly being recognized as a contributor in driving chromosomal instability, genome evolution, and the heterogeneity that fuels cancer cell progression. Furthermore, it has been linked with poor prognosis of cancer patients. While next-generation sequencing can be used to approximate tumor ploidy, it has a high error rate for near-euploid states, a high cost and is time consuming, motivating alternative rapid quantification methods. We introduce PloiViT, a transformer-based model for tumor ploidy quantification that outperforms traditional machine learning models, enabling rapid and cost-effective quantification directly from pathology slides. We trained PloiViT on a dataset of fifteen cancer types from The Cancer Genome Atlas and validated its performance in multiple independent cohorts. Additionally, we explored the impact of self-supervised feature extraction on performance. PloiViT, using self-supervised features, achieved the lowest prediction error in multiple independent cohorts, exhibiting better generalization capabilities. Our findings demonstrate that PloiViT predicts higher ploidy values in aggressive cancer groups and patients with specific mutations, validating PloiViT potential as complementary for ploidy assessment to next-generation sequencing data. To further promote its use, we release our models as a user-friendly inference application and a Python package for easy adoption and use.
The consequences of mismatched buffers in spectral cell sorting
Authors: Dapaah Rita A. S. , Ferrer-Font Laura , Shi Xiaoshan , Hall Christopher , Thompson Sam , Costa Larissa Catharina , Mage Peter L. , Tyznik Aaron J. , Lundsten Kelly , Walker Rachael V
Published: August 2024

Although spectral flow cytometry has become a ubiquitous tool for cell analysis, the use of spectral cytometry on cell sorters requires additional considerations arising from the unique requirements of sorting workflows. Here, we show that care should be taken when ascertaining the purity of a sort on a spectral cell sorter, as the mismatch of buffers used for initial sample suspension and the buffers used for sort collection can affect the unmixing of the data, potentially giving rise to erroneous purity check results.
Cell size and selection for stress-induced cell fusion in unicellular eukaryotes
Authors: Liu Xiaoyuan , Pitchford Jonathan W. , Constable George W. A.
Published: August 2024

In unicellular organisms, sexual reproduction typically begins with the fusion of two cells (plasmogamy) followed by the fusion of their two haploid nuclei (karyogamy) and finally meiosis. Most work on the evolution of sexual reproduction focuses on the benefits of the genetic recombination that takes place during meiosis. However, the selection pressures that may have driven the early evolution of binary cell fusion, which sets the stage for the evolution of karyogamy by bringing nuclei together in the same cell, have seen less attention. In this paper we develop a model for the coevolution of cell size and binary cell fusion rate. The model assumes that larger cells experience a survival advantage from their larger cytoplasmic volume. We find that under favourable environmental conditions, populations can evolve to produce larger cells that undergo obligate binary cell fission. However, under challenging environmental conditions, populations can evolve to subsequently produce smaller cells under binary cell fission that nevertheless retain a survival advantage by fusing with other cells. The model thus parsimoniously recaptures the empirical observation that sexual reproduction is typically triggered by adverse environmental conditions in many unicellular eukaryotes and draws conceptual links to the literature on the evolution of multicellularity.

Author summary

Sexual reproduction is commonly observed, both in eukaryotic microorganisms and in higher multicellular organisms. Sex has evolved despite numerous apparent costs, including investment in finding a partner and the energetic requirements of sexual reproduction. Binary cell fusion is a process that sets the stage for sexual reproduction by bringing nuclei from different cells into contact. Here, we provide a mathematical explanation of the advantage conferred by binary cell fusion due to increased cell mass. We show that when unicellular organisms have the option to invest in either cell fusion or cell mass, they can evolve to fuse together as rapidly as possible in the face of adverse environments, instead of increasing their mass. These results are consistent with the empirical observation that sexual reproduction is often triggered by environmental stress in unicellular eukaryotes. Our results imply an advantage to cell fusion, which helps to shed light on the early evolution of sexual reproduction itself.
SegFinder: an automated tool for identifying RNA virus genome segments through co-occurrence in multiple sequenced samples
Authors: Liu Xue , Kong Jianbin , Shan Yongtao , Yang Ziyue , Miao Jiafan , Pan Yuanfei , Luo Tianyang , Shi Zhiyuan , Wang Yingmei , Gou Qinyu , Yang Chunhui , Li Chunmei , Li Shaochuan , Zhang Xu , Sun Yanni , Holmes Edward C. , Guo Deyin , Shi Mang
Published: August 2024

Metagenomic sequencing has expanded the RNA virosphere, but many identified viral genomes remain incomplete, especially for segmented viruses. Traditional methods relying on sequence homology struggle to identify highly divergent segments and group them confidently within a single virus species. To address this, we developed a new bioinformatic tool – SegFinder – that identifies virus genome segments based on their common co-occurrence at similar abundance within segmented viruses. SegFinder successfully re-discovered all segments from a test data set of individual mosquito transcriptomes, which was also used to establish parameter thresholds for reliable segment identification. Using these optimal parameters, we applied SegFinder to 858 libraries from eight metagenomic sequencing projects, including vertebrates, invertebrates, plants, and environmental samples. Furthermore, we identified 108 (excluding RdRP) unique viral genome segments, of which 55 were novel and 32 showed no recognizable sequence homology to known sequences but which were verified by the presence of conserved sequences at the genome termini. SegFinder is also able to identify segmented genome structures in viruses previously considered to be predominantly unsegmented, and in doing so expanded the number of known families and orders of segmented RNA viruses, making it a valuable tool in an era of large-scale parallel sequencing.
Blockade of rheumatoid arthritis synovial fluid-induced sensory neuron activation by JAK inhibitors
Authors: Li Yuening , Gray Elizabeth H. , Ross Rosie , Zebochin Irene , Lock Amy , Fedele Laura , Kamajaya Louisa Janice , Marrow Rebecca J. , Ryan Sarah , Röderer Pascal , Brüstle Oliver , John Susan , Denk Franziska , Taams Leonie S.
Published: August 2024

Objective

Clinical studies suggest that compared to anti-TNF treatment, JAK inhibitors (JAKi) are superior in reducing pain in rheumatoid arthritis (RA). The underlying mechanisms for this observation are still unknown. Sensory neurons transmit noxious signals from inflamed joints to the central nervous system, where a pain percept is generated. We investigated whether JAKi exert direct effects on sensory neurons.

Methods

In-house and public RNA sequencing datasets of sensory neurons were analysed for relevant JAK/STAT and cytokine-receptor gene expression. Human induced pluripotent stem cell (IPSC)-derived sensory neurons were stimulated with serum and synovial fluid (SF) from individuals with RA, or with selected cytokines that were found in RA SF by Luminex. Phosphorylation of STAT3 (pSTAT3) was assessed by Western blot. Sensory neuron activation was examined by recording neuronal firing using multi-electrode array and measuring expression levels of pain-relevant genes with STAT3-binding sites.

Results

Cell-free RA synovial fluid induced pSTAT3 in IPSC-derived sensory neurons, an effect which was completely blocked by the JAKi tofacitinib. Compared to paired serum, RA SF was enriched for the JAK/STAT cytokines IL-6, IL-11, LIF, IFN-alpha and IFN-beta, with their requisite receptors present on sensory neurons. Stimulation of IPSC- derived sensory neurons with these recombinant cytokines recapitulated pSTAT3 induction in these cells. Furthermore, IL-6+sIL-6R or LIF upregulated expression of pain-relevant genes which was blocked by tofacitinib. Finally, we provided evidence that LIF can induce neuronal sensitisation.

Conclusion

Our data indicate that JAKi can act directly on sensory neurons, providing a potential mechanistic explanation for their suggested superior analgesic properties.
Comparative effects of proton and photon irradiation on the molecular and cellular profiles of triple-negative breast cancer: the crucial impact of VEGFC on tumor microenvironment remodeling
Authors: Sarlak Saharnaz , Marotte Delphine , Morfoisse Florent , Pierantoni Alessandra , Sirera Jessy , Tsai Meng-Chen , Vidal Marie , Hérault Joël , Garmy-Susini Barbara , Doyen Jérôme , Luciano Frédéric , Pagès Gilles
Published: August 2024

Metastatic triple-negative breast cancers (TNBC) are among the most aggressive types of breast cancer and are often treated with adjuvant radiotherapy and chemotherapy. Despite initial efficacy, relapses are common, leading to poor prognosis. Understanding the response of tumor microenvironment to radiotherapy is crucial, particularly comparing photon (X) and proton (P) radiotherapy due to proton radiation’s reduced side effects.

Methods

We investigated the effects of single and multiple X and P irradiations on various cell types within the tumor microenvironment, including vascular and lymphatic endothelial cells, fibroblasts, and TNBC tumor cells. VEGFC, a key factor in lymphatic vessel formation and metastasis, was a primary focus. We used protein arrays to evaluate the effects of irradiation and examined the impact of VEGFC inactivation on the sensitivity to X and P radiation. Additionally, we tested tumor-forming capabilities of irradiated cells and assessed the impact of genetic or therapeutic VEGFC inhibition on TNBC growth. Transcriptomic and proteomic analyses further characterized the differences between X and P tumors, providing deeper insights into their distinct molecular profiles.

Results

Both X and P irradiations caused a transient increase in VEGFC levels, along with other pro-angiogenic, pro-lymphangiogenic, and pro-fibrotic factors, such as angiopoietin 2, artemin, endostatin, IGFBP2, serpinE1, PDGFA, and DPPIV. Endothelial cells exposed to multiple rounds of radiation showed enhanced proliferation but lost the ability to form pseudo vessels, indicating an endothelial-mesenchymal transition. Tumor cells lacking VEGFC were more sensitive to radiation, and anti-VEGFC antibodies significantly suppressed TNBC cells’ proliferation, both naïve and multi-irradiated. Tumor xenografts formed by multi-irradiated cells grew larger in nude mice, particularly following proton irradiation, while X-irradiated tumors exhibited a more pro-lymphangiogenic phenotype compared to P-irradiated tumors.

Conclusions

Our findings show that while P multi-irradiated TNBC cells form larger tumors, X multi-irradiated tumors are more aggressive, with elevated expression of genes linked to angiogenesis, lymphangiogenesis, and endothelial-mesenchymal transition. Targeting VEGFC during photon or proton radiotherapy could reduce metastasis and improve TNBC prognosis.
Human PC4 supports telomere stability and viability in cells utilizing the alternative lengthening of telomeres mechanism
Authors: Salgado Sara , Abreu Patricia L. , Moleirinho Beatriz , Larcombe Lee , Azzalin Claus M.
Published: August 2024

Cancer cells with an activated Alternative Lengthening of Telomeres (ALT) mechanism elongate telomeres via homology-directed repair. Sustained telomeric replication stress is an essential trigger of ALT activity; however, it can lead to cell death if not properly restricted. By analyzing publicly available data from genome-wide CRISPR KO screenings, we have identified the multifunctional protein PC4 as a novel factor essential for ALT cell viability. Depletion of PC4 using siRNAs results in rapid ALT cell death, while telomerase-positive cells show minimal effects. PC4 depletion induces replication stress and telomere fragility primarily in ALT cells, and increases ALT activity. PC4 binds to telomeric DNA in cells, and its binding is enhanced by telomeric replication stress. Finally, a mutant PC4 with partly impaired single stranded DNA binding activity is capable to localize to telomeres and suppress ALT activity and telomeric replication stress. We propose that PC4 supports ALT cell viability, at least partly, by averting telomere dysfunction. Targeted inhibition of PC4 holds promise for innovative therapies to eradicate ALT cancers.