Integrated epigenomic exposure signature discovery.

Aim: The epigenome influences gene regulation and phenotypes in response to exposures. Epigenome assessment can determine exposure history aiding in diagnosis.Materials & methods: Here we developed and implemented a machine learning algorithm, the exposure signature discovery algorithm (ESDA), to identify the most important features present in multiple epigenomic and transcriptomic datasets to produce an integrated exposure signature (ES).Results: Signatures were developed for seven exposures including Staphylococcus aureus, human immunodeficiency virus, SARS-CoV-2, influenza A (H3N2) virus and Bacillus anthracis vaccinations. ESs differed in the assays and features selected and predictive value.Conclusion: Integrated ESs can potentially be utilized for diagnosis or forensic attribution. The ESDA identifies the most distinguishing features enabling diagnostic panel development for future precision health deployment.

This article introduces ESDA, a new analytic tool for integrating multiple data types to identify the most distinguishing features following an exposure. Using the ESDA, we were able to identify signatures of infectious diseases. The results of the study indicate that integration of multiple types of large datasets can be used to identify distinguishing features for infectious diseases. Understanding the changes from different exposures will enable development of diagnostic tests for infectious diseases that target responses from the patient. Using the ESDA, we will be able to build a database of human response signatures to different infections and simplify diagnostic testing in the future.

Rational Design, Synthesis, and Structure-Activity Relationship of a Novel Isoquinolinone-Based Series of HBV Capsid Assembly Modulators Leading to the Identification of Clinical Candidate AB-836.

Inhibition of Hepatitis B Virus (HBV) replication by small molecules that modulate capsid assembly and the encapsidation of pgRNA and viral polymerase by HBV core protein is a clinically validated approach toward the development of new antivirals. Through definition of a minimal pharmacophore, a series of isoquinolinone-based capsid assembly modulators (CAMs) was identified. Structural biology analysis revealed that lead molecules possess a unique binding mode, exploiting electrostatic interactions with accessible phenylalanine and tyrosine residues. Key analogs demonstrated excellent primary potency, absorption, distribution, metabolism, and excretion (ADME) and pharmacokinetic properties, and efficacy in a mouse model of HBV. The optimized lead also displayed potent inhibition of capsid uncoating in HBV-infected HepG2 cells expressing the sodium-taurocholate cotransporting polypeptide (NTCP) receptor, affecting the generation of HBsAg and cccDNA establishment. Based on these results, isoquinolinone derivative AB-836 was advanced into clinical development. In Phase 1b trials, AB-836 demonstrated >3 log10 reduction in serum HBV DNA, however, further development was discontinued due to the observation of incidental alanine aminotransferase (ALT) elevations.

Characterizing emergency department surgical airway placement in the setting of trauma.

INTRODUCTION: Airway management is a key intervention during the resuscitation of critically ill trauma patients. Emergency surgical airway (ESA) placement is taught as a backup option when endotracheal intubation (ETI) fails. We sought to (1) describe the incidence of the emergency department (ED) ESA, (2) compare ESA versus ETI-only recipients, and (3) determine which factors were associated with receipt of an ESA. METHODS: We searched within the Trauma Quality Improvement Program datasets from 2017 to 2022 for all emergency department surgical airway placement and/or endotracheal intubations recipients. We compared ESA versus ETI-only recipients. RESULTS: From 2017 to 2022, there were 6,477,759 within the datasets, of which 238,128 met inclusion for this analysis. Within that, there were 236,292 ETIs, 2264 ESAs, with 428 (<1 %) having documentation of both. Of the ESAs performed, there were 82 documented in children <15 years of age with the youngest being 1 year of age. The ETI-only group had a lower proportion serious injuries to the head/neck (52 % versus 59 %), face (2 % versus 8 %), and skin (3 % versus 6 %). However, the ETI-only group had a higher proportion of serious injuries to the abdomen (15 % versus 9 %) and the extremities (19 % versus 12 %). Survival at 24-h was higher in the ETI-only group (83 % versus 76 %) as well as survival to discharge (70 % versus 67 %). In the subanaysis of children <15 years (n = 82), 34 % occurred in the 1-4 years age group, 35 % in the 5-9 years age group, and 30 % in the 10-14 years age group. In our multivariable logistic regression analysis, serious injuries to the head/neck (odds ratio [OR] 1.37, 95 % CI 1.23-1.54), face (OR 3.41, 2.83-4.11), thorax (OR 1.19, 1.06-1.33), and skin (OR 1.53, 1.15-2.05) were all associated with receipt of cricothyrotomy. Firearm (OR 3.62, 3.18-4.12), stabbing (2.85, 2.09-3.89), and other (OR 2.85, 2.09-3.89) were associated with receipt of ESA when using collision as the reference variable. CONCLUSIONS: ESA placement is a rarely performed procedure but frequently used as a primary airway intervention in this dataset. Penetrating mechanisms, and injuries to face were most associated with ESA placement. Our findings reinforce the need to maintain this critical airway skill for trauma management.

Clinical course of atypical parathyroid neoplasm with soft tissue extension.

BACKGROUND AND OBJECTIVES: The American Joint Committee on Cancer (AJCC) TNM staging system defines atypical parathyroid neoplasia (APN) as tumor in situ (Tis) and reserves the definition of parathyroid carcinoma (PC) to parathyroid tumor with invasion into surrounding structures. Because the parathyroid gland has no true capsule, "extension" with APN versus microscopic "invasion" of surrounding soft tissue can be difficult and confusing for clinicians. We aimed to determine the clinical course of atypical parathyroid neoplasm with and without soft tissue extension and parathyroid carcinoma with only soft tissue invasion (pT1) and to report the outcomes. METHODS: Following an IRB-approved protocol, we identified all patients treated for parathyroid neoplasm or cancer at our single tertiary care cancer center from 1990 to 2021. We excluded all patients with evidence of clinical or pathologic gross invasion into surrounding structures (pT2 or higher), lymph node involvement, or metastatic disease. By definition, this excluded all cases where the distinction was clinically evident to the surgeon at the time of the operation based on finding a hard, firm, sticky, or discolored parathyroid gland. Only patients with pathologic T1 (pT1) parathyroid carcinoma or APN were included. All pathologic examinations were independently re-reviewed by a single designated expert senior endocrine pathologist. The definition of APN strictly followed the WHO definition of a clinically worrisome lesion having features including fibrous bands or increased mitotic rate, necrosis, or trabecular growth that did not meet robust criteria for frank invasion. Pathologic T1 disease was defined as invasion limited to soft tissue. Analyses were performed using R version 4.0.2 and Jamovi. RESULTS: Of all PC patients at our institution, only 71 met the strict inclusion criteria of APN or pT1. Forty-four patients had pT1 disease and 27 had APN: 12 of the APN had soft tissue extension, and 15 had no soft tissue extension. The groups were similar with regard to age at diagnosis (p = 0.328). The average follow-up duration was 84 months from initial surgical intervention. Of the 12 with APN, one patient (1/12; 8%) with soft tissue extension recurred, developed distant metastases, and subsequently died during follow up. Of the 44 patients with pT1 PC, six developed distant metastases and 13 (13/44; 30%) died during the follow-up period. One patient with APN and soft tissue extension recurred and died and no patient with APN and no soft tissue extension died. CONCLUSIONS: Patients with APN and extension into soft tissue have a clinical course similar to that of APN without soft tissue extension. APN with soft tissue extension is a different disease from pT1 disease with invasion of soft tissue. The pTis classification appears justified for APN with and without soft tissue extension.

Identification of 43 novel HLA alleles by PacBio single molecule real-time sequencing in haematopoietic cell donors.

A total of 43 novel HLA alleles detected in haematopoietic cell donors using single molecule real-time DNA sequencing.

Erratum: Geometrical analysis of sand piles on small platforms [Phys. Rev. E 68, 011303 (2003)].

This corrects the article DOI: 10.1103/PhysRevE.68.011303.

Re/connecting with "home": a mixed methods study of service provider and patient perspectives to facilitate implementing rehabilitation in the home for reconditioning.

PURPOSE: To explore the views of healthcare professionals and patients about the advantages and disadvantages of rehabilitation in the home (RITH) for reconditioning, and identify factors that should contribute to the successful implementation of a consensus-based RITH model for reconditioning. MATERIALS AND METHODS: Interviews with 24 healthcare professionals and 21 surveys (comprising Likert scale and free text responses) of inpatients undergoing rehabilitation for reconditioning provided study data. Interpretive thematic analysis was used to analyse interview data; descriptive statistics analysed Likert scale responses; patient written responses assisted with the interpretation of themes developed from the interview data. RESULTS: Two major themes were elicited in this study: the home is a physical setting and the home is a lived space. Advantages and disadvantages of RITH for patients, carers and healthcare professionals were identified within these themes. Appropriate patient selection; effective communication with patients and carers, and within RITH teams; adequate patient and carer support; ensuring the safety of patients and staff; and education of patients, carers and healthcare professionals are essential for the satisfactory implementation of RITH. CONCLUSION: The concept of home shapes the delivery of RITH. Recognising the advantages and disadvantages of RITH highlights important considerations needed to successfully implement RITH for reconditioning.

The home setting facilitates a person-centred approach to care, especially when staff consider patients to be equal partners in their care.Home offers an opportunity to negotiate contextually relevant rehabilitation goals with patients.Effective communication between patients, their local doctor, family, and rehabilitation staff is essential for the successful delivery of rehabilitation in the home.Safety concerns (for patients and staff) and the shift in the burden of care from hospital staff to family must be adequately addressed prior to the commencement of rehabilitation in the home.

Hyperdiluting Calcium Hydroxylapatite With Platelet-Rich Plasma and Hyaluronidase for Improving Neck Laxity and Wrinkle Severity.

The two cases discussed in this report investigate the efficacy and safety of a novel injectable therapy for treating neck wrinkles and skin laxity, utilizing a combination of hyperdiluted calcium hydroxylapatite (CaHA), platelet-rich plasma (PRP), and hyaluronidase. Two patients presenting with moderate neck wrinkles and laxity underwent treatment and were evaluated several months later. The combined therapy demonstrated improvements in skin texture and laxity following a single treatment. The rationale behind incorporating PRP and hyaluronidase was their potential to amplify the regenerative effects of CaHA. PRP contains growth factors that stimulate collagen production and tissue regeneration while hyaluronidase facilitates the breakdown of hyaluronic acid, promoting better diffusion and more even product dispersion. The findings from these cases provide emerging preliminary evidence supporting the safety and efficacy of this innovative combination therapy for addressing neck wrinkles and laxity. This is the first documented instance of skin priming CaHA with hyaluronidase and PRP. Future investigations are warranted to explore the application of this treatment for other anatomical regions and to delineate the role of each injected component.

HLA typing: A review of methodologies and clinical impact on haematopoietic cell transplantation.

The importance of the HLA gene system in haematopoietic cell transplant outcomes was established early on and advances in both fields have led to ever increasing success of this clinical therapy. In large part, improvements in the understanding of HLA have been driven by the advancement in typing technologies. Each iteration of typing technology has improved the resolution of HLA typing, and often enabled the identification of polymorphism within the HLA loci. The discovery of the enormous amount of variation in the HLA genes, and the need to be able to characterise this for clinical HLA typing, has often resulted in a move away from one typing method to another more suited to typing of this complexity. Today, the gold standard for HLA typing are methods that can produce definitive HLA typing results.

Mechanisms and efficacy of small molecule "latency promoting agents" to inhibit HIV reactivation ex vivo.

HIV infection cannot be cured due to the persistence of a reservoir of latently infected cells. Furthermore, virally suppressed individuals experience chronic immune activation from ongoing low-level viral expression. Drugs that inhibit HIV transcription and/or reactivation of latent HIV have been proposed as a strategy to reduce HIV-associated immune activation and/or to achieve a functional cure. We evaluated 26 small molecules, both previously reported drugs and new drug candidates, for their ability to act as "latency promoting/silencing agents (LPAs)" that can reduce or prevent HIV expression after T cell activation. Using a panel of RT-ddPCR assays, we measured the progression through HIV transcription and pinpointed the step at which each of those drugs inhibited HIV transcription, with and without prior activation. While some drugs primarily inhibited one or two steps in HIV reactivation, other drugs (CDK inhibitors, splicing inhibitors, tanespimycin, and triptolide) inhibited multiple stages of HIV transcription and blocked the production of supernatant viral RNA. Dinaciclib, AZD4573, and pladienolide B also appeared to inhibit HIV splicing in unstimulated PBMC. By selecting drugs with known mechanisms of action, we specifically identified cellular factors and pathways that may be involved in regulation of HIV expression. These drugs/targets deserve further study in strategies aimed at reducing HIV-associated immune activation or achieving a functional cure.

Pediatric Papillary Thyroid Carcinoma: Outcomes After Surgery Without Adjuvant Radioactive Iodine.

CONTEXT: Pediatric papillary thyroid carcinoma (PTC) is usually treated with total thyroidectomy followed by radioactive iodine (RAI). Recently, RAI is being used more selectively based on surgical pathology and postoperative dynamic risk stratification (DRS). OBJECTIVE: To describe patients with pediatric PTC not initially treated with RAI and their disease outcomes. METHODS: This was an ambispective study at a tertiary cancer center of patients < 19 years diagnosed from 1/1/1990 to 12/31/2021 with stage I PTC who intentionally were not treated with RAI within a year of diagnosis. We assessed clinical characteristics, management, and disease outcomes using DRS. RESULTS: Of 490 PTC patients, we identified 93 eligible patients (median age at diagnosis 16y; 87% female), including 46 (49%) with cervical lymph node metastases. Initial management included: total thyroidectomy ± neck dissection (n=69, 75%), lobectomy ± neck dissection (n=20, 21%), or a Sistrunk procedure for ectopic PTC (n=4, 4%). After a median follow-up of 5.5 years (range 1-26), most patients (85/93; 91%) remained disease-free with no further therapy. Persistent (n=5) or recurrent (n=3) disease was found in 9% of the entire cohort. Four patients ultimately received RAI, of which only one clearly benefited, and additional surgery was performed or planned in four patients, two of whom had an excellent response at last follow-up. CONCLUSIONS: Selected pediatric PTC patients, even those with lymph node metastases, may not require therapeutic 131I and can avoid the unnecessary risks of RAI while still benefitting from the excellent long-term outcomes that are well-described for this disease.

Venous thromboembolic events associated with blood product administration in an era of whole blood use.

BACKGROUND: The risks associated with blood product administration and venous thromboembolic events remains unclear. We sought to determine which blood products were associated with the development of deep vein thrombosis (DVT) and pulmonary embolism (PE). METHODS: We analyzed data from patients ≥18 years of age in the Trauma Quality Improvement Program (TQIP) database that received ≥1 blood product and survived ≥24 â€‹h. RESULTS: There were 42,399 that met inclusion, of whom, 2086 had at least one VTE event. In our multivariable logistic regression model, we found that WB had a unit odds ratio (uOR) of 1.05 (95 â€‹% CI 1.02-1.08) for DVT and 1.08 (1.05-1.12) for PE. Compared to WB, platelets had a higher uOR for DVT of 1.09 (1.04-1.13) but similar uOR for PE of 1.08 (1.03-1.14). CONCLUSIONS: We found an association of both DVT and PE with early whole blood and platelets.

A review of CD4+ T cell differentiation and diversity in dogs.

CD4+ T cells are an integral component of the adaptive immune response, carrying out many functions to combat a diverse range of pathogenic challenges. These cells exhibit remarkable plasticity, differentiating into specialized subsets such as T helper type 1 (TH1), TH2, TH9, TH17, TH22, regulatory T cells (Tregs), and follicular T helper (TFH) cells. Each subset is capable of addressing a distinct immunological need ranging from pathogen eradication to regulation of immune homeostasis. As the immune response subsides, CD4+ T cells rest down into long-lived memory phenotypes-including central memory (TCM), effector memory (TEM), resident memory (TRM), and terminally differentiated effector memory cells (TEMRA) that are localized to facilitate a swift and potent response upon antigen re-encounter. This capacity for long-term immunological memory and rapid reactivation upon secondary exposure highlights the role CD4+ T cells play in sustaining both adaptive defense mechanisms and maintenance. Decades of mouse, human, and to a lesser extent, pig T cell research has provided the framework for understanding the role of CD4+ T cells in immune responses, but these model systems do not always mimic each other. Although our understanding of pig immunology is not as extensive as mouse or human research, we have gained valuable insight by studying this model. More akin to pigs, our understanding of CD4+ T cells in dogs is much less complete. This disparity exists in part because canine immunologists depend on paradigms from mouse and human studies to characterize CD4+ T cells in dogs, with a fraction of available lineage-defining antibody markers. Despite this, every major CD4+ T cell subset has been described to some extent in dogs. These subsets have been studied in various contexts, including in vitro stimulation, homeostatic conditions, and across a range of disease states. Canine CD4+ T cells have been categorized according to lineage-defining characteristics, trafficking patterns, and what cytokines they produce upon stimulation. This review addresses our current understanding of canine CD4+ T cells from a comparative perspective by highlighting both the similarities and differences from mouse, human, and pig CD4+ T cell biology. We also discuss knowledge gaps in our current understanding of CD4+ T cells in dogs that could provide direction for future studies in the field.

Genome-Wide Association Study and transcriptome analysis reveals a complex gene network that regulates opsin gene expression and cell fate determination in Drosophila R7 photoreceptor cells.

Background: An animal's ability to discriminate between differing wavelengths of light (i.e., color vision) is mediated, in part, by a subset of photoreceptor cells that express opsins with distinct absorption spectra. In Drosophila R7 photoreceptors, expression of the rhodopsin molecules, Rh3 or Rh4, is determined by a stochastic process mediated by the transcription factor spineless. The goal of this study was to identify additional factors that regulate R7 cell fate and opsin choice using a Genome Wide Association Study (GWAS) paired with transcriptome analysis via RNA-Seq. Results: We examined Rh3 and Rh4 expression in a subset of fully-sequenced inbred strains from the Drosophila Genetic Reference Panel and performed a GWAS to identify 42 naturally-occurring polymorphisms-in proximity to 28 candidate genes-that significantly influence R7 opsin expression. Network analysis revealed multiple potential interactions between the associated candidate genes, spineless and its partners. GWAS candidates were further validated in a secondary RNAi screen which identified 12 lines that significantly reduce the proportion of Rh3 expressing R7 photoreceptors. Finally, using RNA-Seq, we demonstrated that all but four of the GWAS candidates are expressed in the pupal retina at a critical developmental time point and that five are among the 917 differentially expressed genes in sevenless mutants, which lack R7 cells. Conclusions: Collectively, these results suggest that the relatively simple, binary cell fate decision underlying R7 opsin expression is modulated by a larger, more complex network of regulatory factors. Of particular interest are a subset of candidate genes with previously characterized neuronal functions including neurogenesis, neurodegeneration, photoreceptor development, axon growth and guidance, synaptogenesis, and synaptic function.

The perceptual span in dyslexic reading and visual search.

Many studies have attempted to identify the root cause of dyslexia. Different theories of dyslexia have proposed either a phonological, attentional, or visual deficit. While research has used eye-tracking to study dyslexia, only two previous studies have used the moving-window paradigm to explore the perceptual span in dyslexic reading, and none have done so in visual search. The present study analysed the perceptual span using both reading and visual search tasks to identify language-independent attentional impairments in dyslexics. We found equivocal evidence that the perceptual span was impaired in dyslexic reading and no evidence of impairment in visual search. However, dyslexic participants did show deficits in the visual search task, with lower search accuracy and shorter saccades compared with controls. These results lend support for a visual, rather than attentional or phonological, account of dyslexia.

Magnetic sphincter augmentation vs subtotal gastrectomy with Roux-en-Y reconstruction for the treatment of postsleeve gastrectomy gastroesophageal reflux disease.

BACKGROUND: Obesity affects more than one-third of Americans and can be treated with bariatric surgery, most commonly sleeve gastrectomy (SG). SG has been shown to increase the incidence of gastroesophageal reflux disease (GERD) in some patients, which can be refractory to medical management. Surgical options for post-SG GERD include magnetic sphincter augmentation (MSA) and subtotal gastrectomy with Roux-en-Y reconstruction (SGRY). A comparative analysis of MSA and SGRY for post-SG GERD was performed to evaluate postoperative outcomes. METHODS: A retrospectively maintained prospectively gathered database from 2018 to 2023 was used to identify patients who underwent MSA or SGRY for the indication of GERD after SG. Differences among patient characteristics; GERD assessments, including the health-related quality of life (HRQL) questionnaire and the reflux symptom index (RSI); and procedure outcomes were collected and analyzed according to surgery type. RESULTS: A total of 92 patients (85 females and 7 males) met the inclusion criteria. The study included 17 patients in the MSA group, 71 patients in the SGRY group, and 4 patients who underwent both procedures. The average preoperative body mass index (BMI) of all patients was 33.3. Compared with patients who underwent MSA, those who underwent SGRY presented with higher BMI (29.4 vs 34.2, respectively; P = .013), preoperative GERD-HRQL (35 vs 52, respectively; P = .046), and RSI (14 vs 28, respectively; P = .017). Postoperatively, patients who underwent SGRY demonstrated a higher decrease in mean postoperative DeMeester score than those who underwent MSA (44.2 vs 13.9, respectively; P = .040), with 22 patients (50%) in the SGRY group vs 10 patients (20%) in the MSA group achieving normalization. CONCLUSION: Although MSA remains a viable surgical alternative, our study indicated that SGRY can produce better symptom control and decrease acid exposure compared with MSA in patients with post-SG GERD.

Global patterns in the growth potential of soil bacterial communities.

Despite the growing catalogue of studies detailing the taxonomic and functional composition of soil bacterial communities, the life history traits of those communities remain largely unknown. This study analyzes a global dataset of soil metagenomes to explore environmental drivers of growth potential, a fundamental aspect of bacterial life history. We find that growth potential, estimated from codon usage statistics, was highest in forested biomes and lowest in arid latitudes. This indicates that bacterial productivity generally reflects ecosystem productivity globally. Accordingly, the strongest environmental predictors of growth potential were productivity indicators, such as distance to the equator, and soil properties that vary along productivity gradients, such as pH and carbon to nitrogen ratios. We also observe that growth potential was negatively correlated with the relative abundances of genes involved in carbohydrate metabolism, demonstrating tradeoffs between growth and resource acquisition in soil bacteria. Overall, we identify macroecological patterns in bacterial growth potential and link growth rates to soil carbon cycling.

A Fluorogenic Pseudoinfection Assay to Probe Transfer and Distribution of Influenza Viral Contents to Target Vesicles.

Fusion of enveloped viruses with endosomal membranes and subsequent release of the viral genome into the cytoplasm are crucial to the viral infection cycle. It is often modeled by performing fusion between virus particles and target lipid vesicles. We utilized fluorescence microscopy to characterize the kinetic aspects of the transfer of influenza viral ribonucleoprotein (vRNP) complexes to target vesicles and their spatial distribution within the fused volumes to gain deeper insight into the mechanistic aspects of endosomal escape. The fluorogenic RNA-binding dye QuantiFluor (Promega) was found to be well-suited for direct and sensitive microscopic observation of vRNPs which facilitated background-free detection and kinetic analysis of fusion events on a single particle level. To determine the extent to which the viral contents are transferred to the target vesicles through the fusion pore, we carried out virus-vesicle fusion in a side-by-side fashion. Measurement of the Euclidean distances between the centroids of superlocalized membrane and content dye signals within the fused volumes allowed determination of any symmetry (or the lack thereof) between them as expected in the event of transfer (or the lack thereof) of vRNPs, respectively. We found that, in the case of fusion between viruses and 100 nm target vesicles, ∼39% of the events led to transfer of viral contents to the target vesicles. This methodology provides a rapid, generic, and cell-free way to assess the inhibitory effects of antiviral drugs and therapeutics on the endosomal escape behavior of enveloped viruses.