Prokrustean Graph: A substring index supporting rapid enumeration across a range of k-mer sizes.

Despite the widespread adoption of k -mer-based methods in bioinformatics, a fundamental question persists: How can we quantify the influence of k sizes in applications? With no universal answer available, choosing an optimal k size or employing multiple k sizes remains application-specific, arbitrary, and computationally expensive. The assessment of the primary parameter k is typically empirical, based on the end products of applications which pass complex processes of genome analysis, comparison, assembly, alignment, and error correction. The elusiveness of the problem stems from a limited understanding of the transitions of k -mers with respect to k sizes. Indeed, there is considerable room for improving both practice and theory by exploring k -mer-specific quantities across multiple k sizes. This paper introduces an algorithmic framework built upon a novel substring representation: the Prokrustean graph. The primary functionality of this framework is to extract various k -mer-based quantities across a range of k sizes, but its computational complexity depends only on maximal repeats, not on the k range. For example, counting maximal unitigs of de Bruijn graphs for k = 10 , … , 100 takes just a few seconds with a Prokrustean graph built on a read set of gigabases in size. This efficiency sets the graph apart from other substring indices, such as the FM-index, which are normally optimized for string pattern searching rather than for depicting the substring structure across varying lengths. However, the Prokrustean graph is expected to close this gap, as it can be built using the extended Burrows-Wheeler Transform (eBWT) in a space-efficient manner. The framework is particularly useful in pangenome and metagenome analyses, where the demand for precise multi- k approaches is increasing due to the complex and diverse nature of the information being managed. We introduce four applications implemented with the framework that extract key quantities actively utilized in modern pangenomics and metagenomics.

RETROFIT: Reference-free deconvolution of cell-type mixtures in spatial transcriptomics.

Spatial transcriptomics (ST) profiles gene expression in intact tissues. However, ST data measured at each spatial location may represent gene expression of multiple cell types, making it difficult to identify cell-type-specific transcriptional variation across spatial contexts. Existing cell-type deconvolutions of ST data often require single-cell transcriptomic references, which can be limited by availability, completeness and platform effect of such references. We present RETROFIT, a reference-free Bayesian method that produces sparse and interpretable solutions to deconvolve cell types underlying each location independent of single-cell transcriptomic references. Results from synthetic and real ST datasets acquired by Slide-seq and Visium platforms demonstrate that RETROFIT outperforms existing reference-based and reference-free methods in estimating cell-type composition and reconstructing gene expression. Applying RETROFIT to human intestinal development ST data reveals spatiotemporal patterns of cellular composition and transcriptional specificity. RETROFIT is available at https://bioconductor.org/packages/release/bioc/html/retrofit.html.

Volar Approach to the First Extensor Compartment for Surgical Treatment of DeQuervain Tenosynovitis.

Many surgical techniques have been published in regards to the operative management of DeQuervain tenosynovitis. As it has been classically described, stenosing tenosynovitis of the first extensor tendon compartment is a common tendinopathy along the radial side of the wrist causing pain and swelling in the affected area. When surgery is necessary, decompression of the abductor pollicis longus and extensor pollicis brevis tendons decreases first extensor compartment friction and has been shown to successfully alleviate symptoms. A number of varying techniques have been reported in the literature to achieve adequate decompression and minimize postoperative complications such as sensory nerve injury, incomplete decompression, and tendon subluxation. We describe a novel volar approach to the first extensor compartment, which allows direct visualization of the retinaculum and a midline retinacular release. In addition, the volar approach has an associated decreased risk of iatrogenic nerve injury by passing volar and deep to the more superficial sensory nerves that overly the retinaculum. On the basis of our experience, patients do not experience an increased risk of volar tendon subluxation with this approach.

Complication Rates after Lateral Plate Fixation of Periprosthetic Distal Femur Fractures: A Multicenter Study.

OBJECTIVE: Periprosthetic fractures of the distal femur can be challenging injuries to treat; nonunion rates of up to 22% have been reported. The purpose of this study was to determine the rate of complications and nonunion in a multicenter series, and to identify patient or surgical factors that were associated with nonunion. DESIGN: Retrospective comparative study SETTING: Three Level 1 trauma centers PATIENTS: Fifty-five patients with a periprosthetic distal femur fracture proximal to a total knee arthroplasty. Minimum follow up for inclusion was six months or until union or failure. INTERVENTION: Surgical fixation using a precontoured lateral locking plate MAIN OUTCOME MEASUREMENT: Fracture union was the primary outcome. Patient demographic and injury variables (age, comorbidities, fracture classification and characteristics) and surgical technique factors (mode of plate fixation, plate material, working length, screw density, and proximal screw type) were identified and compared between patients who developed a nonunion and those who did not. Regression analysis was performed to identify independent risk factors for nonunion. RESULTS: The overall rate of nonunion was 18% and the total complication rate was 24%. After additional surgery, 49 of 55 patients went on to heal (89%). There were no statistical differences in patient demographic or injury variables between the union and nonunion groups, and none of the variables studied were independent risk factors for nonunion in the regression analysis. CONCLUSIONS: In this series of 55 patients with periprosthetic distal femur fractures treated with precontoured lateral locking plates, 18% developed nonunion and the overall complication rate was 24%. No patient or surgical variables were identified as risk factors. Future research should seek to identify patients at high risk for complication and nonunion who could benefit from alternative fixation strategies or distal femoral replacement.

Characterization of Ti Ringspot-Associated Virus, a Novel Emaravirus Associated with an Emerging Ringspot Disease of Cordyline fruticosa.

Ti ringspot is an emerging foliar disease of the ti plant (Cordyline fruticosa) in Hawaii that is quickly spreading throughout the islands. Symptoms include small chlorotic ringspots on leaves that often coalesce to form larger lesions. Although several virus species have been discovered in symptomatic plants, none have been associated with these symptoms. Here, we report and characterize a novel virus closely associated with ti ringspot symptoms in Hawaii. The presence of double membrane bodies approximately 85 nm in diameter in symptomatic cells and sequence analyses of five genomic RNA segments obtained by high-throughput sequencing indicate that this virus is most closely related to members of the plant virus genus Emaravirus. Phylogenetic and sequence homology analyses place this virus on a distinct clade within the Emaravirus genus along with High Plains wheat mosaic emaravirus, blue palo verde broom virus, and Raspberry leaf blotch emaravirus. Sequence identity values with taxonomically relevant proteins indicate that this represents a new virus species, which we are tentatively naming ti ringspot-associated virus (TiRSaV). TiRSaV-specific reverse transcription PCR assays detected the virus in several experimental herbaceous host species following mechanical inoculation. TiRSaV was also detected in eriophyid mites collected from symptomatic ti plants, which may represent a putative arthropod vector of the virus.

An effective mouse model for adoptive cancer immunotherapy targeting neoantigens.

The adoptive cell transfer (ACT) of T cells targeting mutated neoantigens can cause objective responses in varieties of metastatic cancers, but the development of new T cell-based treatments relies on accurate animal models. To investigate the therapeutic effect of targeting a neoantigen with ACT, we used T cells from pmel-1 T cell receptor-transgenic mice, known to recognize a WT peptide, gp100, and a mutated version of the peptide that has higher avidity. We gene-engineered B16 cells to express the WT or mutated gp100 epitopes and found that pmel-1-specific T cells targeting a neoantigen tumor target augmented recognition as measured by IFN-γ production. Neoantigen expression by B16 also enhanced the capacity of pmel-1 T cells to trigger the complete and durable regression of large, established, vascularized tumor and required less lymphodepleting conditioning. Targeting neoantigen uncovered the possibility of using enforced expression of the IL-2Rα chain (CD25) in mutation-reactive CD8+ T cells to improve their antitumor functionality. These data reveal that targeting of "mutated-self" neoantigens may lead to improved efficacy and reduced toxicities of T cell-based cellular immunotherapies for patients with cancer.

The Incidence and Outcome Differences in Severe Sepsis with and without Lactic Acidosis.

INTRODUCTION: To compare the incidence, characteristics, and outcomes of lactate expressors and nonexpressors in patients with severe sepsis and septic shock. METHODS: This is a retrospective cohort study of patients with severe sepsis and septic shock who presented over a 40-month period to an academic tertiary care center. Primary outcome of interest was in-hospital mortality. Secondary outcomes were hospital length of stay (LOS), Intensive Care Unit (ICU) LOS, and escalation of care. RESULTS: Three hundred and thirty-eight patients met inclusion criteria and were divided into a lactate expressor group (n = 197; initial lactate ≥2.5 mmol/L) and a nonexpressor group (n = 141; lactate <2.5 mmol/L). The mortality rate was 46.2% for lactate expressors and 24.8% for nonexpressors. There were no significant differences in hospital or ICU LOS. The escalation-of-care rate in the severe sepsis nonexpressor group was more than double that found in the expressor group: 16.5% versus 6.2% (P = 0.040). The two groups had baseline differences: expressor group had a higher median Acute Physiology and Chronic Health Evaluation II (APACHE II) illness severity score, and nonexpressors had an increased prevalence of comorbid conditions. APACHE II score (odds ratio [OR] 1.10 (1.07-1.14), P < 0.001) and being in the expressor group (OR 1.72 [1.03-2.89], P = 0.039) increased the odds of mortality. CONCLUSIONS: In patients with severe sepsis and septic shock, lactate nonexpressors are common. Although the mortality in this cohort is less than its counterparts who present with lactate elevation, it is still significant which warrants vigilance in their care.

Outcomes of severe sepsis and septic shock patients after stratification by initial lactate value.

BACKGROUND: In the setting of severe sepsis and septic shock, mortality increases when lactate levels are ≥ 4 mmol/L. However, the consequences of lower lactate levels in this population are not well understood. The study aimed to determine the in-hospital mortality associated with severe sepsis and septic shock when initial lactate levels are < 4 mmol/L. METHODS: This is a retrospective cohort study of septic patients admitted over a 40-month period. Totally 338 patients were divided into three groups based on initial lactate values. Group 1 had lactate levels < 2 mmol/L; group 2: 2-4 mmol/L; and group 3: ≥ 4 mmol/L. The primary outcome was in-hospital mortality. RESULTS: There were 111 patients in group 1, 96 patients in group 2, and 131 in group 3. The mortality rates were 21.6%, 35.4%, and 51.9% respectively. Univariate analysis revealed the mortality differences to be statistically significant. Multivariate logistic regression demonstrated higher odds of death with higher lactate tier group, however the findings did not reach statistical significance. CONCLUSION: This study found that only assignment to group 3, initial lactic acid level of ≥ 4 mmol/L, was independently associated with increased mortality after correcting for underlying severity of illness and organ dysfunction. However, rising lactate levels in the other two groups were associated with increased severity of illness and were inversely proportional to prognosis.

A homogeneous enzyme fragment complementation-based beta-arrestin translocation assay for high-throughput screening of G-protein-coupled receptors.

G-protein-coupled receptors (GPCRs) represent one of the largest gene families in the human genome and have long been regarded as valuable targets for small-molecule drugs. The authors describe a new functional assay that directly monitors GPCR activation. It is based on the interaction between beta-arrestin and ligand-activated GPCRs and uses enzyme fragment complementation technology. In this format, a GPCR of interest is fused to a small (approximately 4 kDa), optimized alpha fragment peptide (termed ProLink) derived from beta-galactosidase, and beta-arrestin is fused to an N-terminal deletion mutant of beta-galactosidase (termed the enzyme acceptor [EA]). Upon activation of the receptor, the beta-arrestin-EA fusion protein binds the activated GPCR. This interaction drives enzyme fragment complementation, resulting in an active beta-galactosidase enzyme, and thus GPCR activation can be determined by quantifying beta-galactosidase activity. In this report, the authors demonstrate the utility of this technology to monitor GPCR activation and validate the approach using a Galphai-coupled GPCR, somatostatin receptor 2. Potential application to high-throughput screens in both agonist and antagonist screening modes is exemplified.