Unveiling errors in soil microbial community sequencing: a case for reference soils and improved diagnostics for nanopore sequencing.

The sequencing platform and workflow strongly influence microbial community analyses through potential errors at each step. Effective diagnostics and experimental controls are needed to validate data and improve reproducibility. This cross-laboratory study evaluates sources of variability and error at three main steps of a standardized amplicon sequencing workflow (DNA extraction, polymerase chain reaction [PCR], and sequencing) using Oxford Nanopore MinION to analyze agricultural soils and a simple mock community. Variability in sequence results occurs at each step in the workflow with PCR errors and differences in library size greatly influencing diversity estimates. Common bioinformatic diagnostics and the mock community are ineffective at detecting PCR abnormalities. This work outlines several diagnostic checks and techniques to account for sequencing depth and ensure accuracy and reproducibility in soil community analyses. These diagnostics and the inclusion of a reference soil can help ensure data validity and facilitate the comparison of multiple sequencing runs within and between laboratories.

Growing in phosphorus-impoverished habitats in south-western Australia: How general are phosphorus-acquisition and -allocation strategies among Proteaceae, Fabaceae and Myrtaceae species?

Numerous phosphorus (P)-acquisition and -utilisation strategies have evolved in plants growing in severely P-impoverished environments. Although these strategies have been well characterised for certain taxa, like Proteaceae, P-poor habitats are characterised by a high biodiversity, and we know little about how species in other families cope with P scarcity. We compared the P-acquisition and leaf P-allocation strategies of Fabaceae and Myrtaceae with those of Proteaceae growing in the same severely P-impoverished habitat. Myrtaceae and Fabaceae exhibited multiple P-acquisition strategies: P-mining by carboxylates or phosphatases, P uptake facilitated by carboxylate-releasing neighbours, and dependence on the elevated soil P availability after fire. Surprisingly, not all species showed high photosynthetic P-use efficiency (PPUE). Highly P-efficient species showed positive correlations between PPUE and the proportion of metabolite P (enzyme substrates), and negative correlations between PPUE and phospholipids (cellular membranes) and nucleic acid P (mostly ribosomal RNA), while we found no correlations in less P-efficient species. Overall, we found that Myrtaceae and Fabaceae used a wider range of strategies than Proteaceae to cope with P scarcity, at both the rhizosphere and leaf level. This knowledge is pivotal to better understand the mechanisms underlying plant survival in severely nutrient-impoverished biodiverse ecosystems.

The Problem with Delaying Measles Elimination.

Measles is a highly infectious disease leading to high morbidity and mortality impacting people's lives and economies across the globe. The measles vaccine saves more lives than any other vaccine in the Essential Programme of Immunization and is also the most cost-effective vaccine, with an extremely high return on investment. This makes achieving measles elimination through vaccination a key child health intervention, particularly in low-income countries, where the overwhelming majority of measles deaths continue to occur. All countries and regions of the world have committed to achieving measles elimination, yet many have faced challenges securing political commitment at national and global levels and predictable, timely, and flexible support from global donors, and experienced setbacks during the COVID-19 pandemic. This has happened against a backdrop of stagnant measles vaccination coverage and declining enthusiasm for vertical programmes, culminating in a World Health Organization Strategic Advisory Group of Experts (WHO SAGE) review of the feasibility of measles eradication in 2019. Sustaining the elimination of measles long term is extremely difficult, and some countries have lost or nearly lost their measles elimination status in the face of ongoing importation of cases from neighbouring or closely connected countries in which elimination had been delayed. Thus, a widening equity gap in measles immunisation coverage creates challenges for all countries, not just those facing the greatest burden of measles morbidity and mortality. Delaying elimination of measles in some countries makes it cumulatively harder for all countries to succeed for three principal reasons: increased inequity in measles immunisation coverage makes outbreaks more likely to happen and to be larger; political will is very difficult to sustain; and immunity may wane to a point that transmission is re-established. New strategies are needed to support countries and regions in their vision for a world without measles, including ways to galvanise domestic, regional and global resources and ignite the political will that is essential to make the vision a reality.

Structural and biochemical basis for regiospecificity of the flavonoid glycosyltransferase UGT95A1.

Glycosylation is a predominant strategy plants employ to fine-tune the properties of small molecule metabolites to affect their bioactivity, transport, and storage. It is also important in biotechnology and medicine as many glycosides are utilized in human health. Small molecule glycosylation is largely carried out by family 1 glycosyltransferases. Here, we report a structural and biochemical investigation of UGT95A1, a family 1 GT enzyme from Pilosella officinarum that exhibits a strong, unusual regiospecificity for the 3'-O position of flavonoid acceptor substrate luteolin. We obtained an apo crystal structure to help drive the analyses of a series of binding site mutants, revealing that while most residues are tolerant to mutations, key residues M145 and D464 are important for overall glycosylation activity. Interestingly, E347 is crucial for maintaining the strong preference for 3'-O glycosylation, while R462 can be mutated to increase regioselectivity. The structural determinants of regioselectivity were further confirmed in homologous enzymes. Our study also suggests that the enzyme contains large, highly dynamic, disordered regions. We showed that while most disordered regions of the protein have little to no implication in catalysis, the disordered regions conserved among investigated homologues are important to both the overall efficiency and regiospecificity of the enzyme. This report represents a comprehensive in-depth analysis of a family 1 GT enzyme with a unique substrate regiospecificity and may provide a basis for enzyme functional prediction and engineering.

Development of Desmoid Tumors After Ileorectal Anastomosis Versus Ileal Pouch-Anal Anastomosis in Familial Adenomatous Polyposis.

BACKGROUND & AIMS: Desmoid tumors (DT) are an important cause of morbidity and mortality in patients with familial adenomatous polyposis (FAP). DT development might be related to the type and approach of colectomy. We aimed to compare DT development after colectomy with ileorectal anastomosis (IRA) and proctocolectomy with ileal pouch-anal anastomosis (IPAA). METHODS: We performed an international historical cohort study in patients with FAP who underwent IRA or IPAA between 1961 and 2020. The primary outcome was the incidence of abdominal DT (either mesenteric, retroperitoneal, or abdominal wall). Patients with a DT diagnosis before or at colectomy were excluded. Time to DT was considered censored at an eventual secondary proctectomy after IRA. We used multivariable Cox regression modelling to adjust for potential confounders. RESULTS: We analyzed data from 852 patients: 514 after IRA and 338 after IPAA (median follow-up, 21 and 16 years, respectively). DTs were diagnosed in 64 IRA patients (12%) and 66 IPAA patients (20%). The cumulative DT incidence at 5 and 10 years was 7.5% and 9.3% after open IRA and 4.7% and 10.9% after laparoscopic IRA. These estimates were 13.6% and 15.4% after open IPAA and 8.4% and 10.0% after laparoscopic IPAA. The postoperative risk was significantly higher after IPAA (P < .01) in multivariable analysis, whereas approach did not significantly influence the risk. CONCLUSIONS: The risk of developing an abdominal DT was found to be significantly higher after IPAA than after IRA. Postoperative DT risk should be taken into account when choosing between IRA and IPAA in FAP.

Modeling of Valve-in-Valve Transcatheter Aortic Valve Implantation after Aortic Root Replacement Using 3-Dimensional Artificial Intelligence Algorithm.

OBJECTIVE: Aortic root replacement requires construction of a composite valve-graft and reimplantation of coronary arteries. This study assessed the feasibility of valve-in-valve transcatheter aortic valve implantation after aortic root replacement. METHODS: A retrospective review was conducted on 74 consecutive patients who received a composite valve-graft at a single institution from 2019 to 2021. Forty patients had bioprosthetic valves with adequate postoperative gated computed tomographic angiography scans. Computational simulations of balloon and self-expanding transcatheter valve deployments were performed. The modeled coronary distances were compared to traditional, manually measured valve-to-coronary distances. RESULTS: There was a statistically significant difference in the modeled versus manual measurements of valve to coronary distances were for all patients regardless of valve type or coronary artery analyzed (p <0. 05). Most patients are low risk for coronary obstruction per three-dimensional modeling including those with a valve-to-coronary distance <4 millimeters. Only one patient (2.5%) was at risk for coronary obstruction for the left coronary artery using a ballonvalve. No other valve combination was considered high risk of coronary obstruction. Five patients (12.5%) were at risk for possible valve stent deformation at the outflow, due to angulation at the graft anastomosis. CONCLUSIONS: Following aortic root replacement, all patients were candidates for Valve-in-Valve using one or both types of transcatheter heart valves. Self-expanding valves may be at higher risk for stent frame deformation at graft anastomotic lines and balloon-expandable valves may be at higher risk of coronary obstruction.

A comparative analysis of RNA-Seq and NanoString technologies in deciphering viral infection response in upper airway lung organoids.

In this study, we delved into the comparative analysis of gene expression data across RNA-Seq and NanoString platforms. While RNA-Seq covered 19,671 genes and NanoString targeted 773 genes associated with immune responses to viruses, our primary focus was on the 754 genes found in both platforms. Our experiment involved 16 different infection conditions, with samples derived from 3D airway organ-tissue equivalents subjected to three virus types, influenza A virus (IAV), human metapneumovirus (MPV), and parainfluenza virus 3 (PIV3). Post-infection measurements, after UV (inactive virus) and Non-UV (active virus) treatments, were recorded at 24-h and 72-h intervals. Including untreated and Mock-infected OTEs as control groups enabled differentiating changes induced by the virus from those arising due to procedural elements. Through a series of methodological approaches (including Spearman correlation, Distance correlation, Bland-Altman analysis, Generalized Linear Models Huber regression, the Magnitude-Altitude Score (MAS) algorithm and Gene Ontology analysis) the study meticulously contrasted RNA-Seq and NanoString datasets. The Magnitude-Altitude Score algorithm, which integrates both the amplitude of gene expression changes (magnitude) and their statistical relevance (altitude), offers a comprehensive tool for prioritizing genes based on their differential expression profiles in specific viral infection conditions. We observed a strong congruence between the platforms, especially in identifying key antiviral defense genes. Both platforms consistently highlighted genes including ISG15, MX1, RSAD2, and members of the OAS family (OAS1, OAS2, OAS3). The IFIT proteins (IFIT1, IFIT2, IFIT3) were emphasized for their crucial role in counteracting viral replication by both platforms. Additionally, CXCL10 and CXCL11 were pinpointed, shedding light on the organ tissue equivalent's innate immune response to viral infections. While both platforms provided invaluable insights into the genetic landscape of organoids under viral infection, the NanoString platform often presented a more detailed picture in situations where RNA-Seq signals were more subtle. The combined data from both platforms emphasize their joint value in advancing our understanding of viral impacts on lung organoids.

Criteria for distinguishing heterogeneous from homogeneous conditions for aromatic diisocyanates in water.

Environmental fate and toxicity testing typically requires knowledge of the water solubility of the test substances. Determining the solubility of aromatic diisocyanates in water poses great challenges because of their hydrophobic nature and water-reactivity. The reactive dissolution process is dynamic and the establishment of a steady-state equilibrium cannot readily be observed. In preparation of experimental work, computer simulation was used to derive and evaluate criteria that enable distinguishing homogeneous (i.e., substances would be fully dissolved in water) from heterogeneous (i.e., a separate organic phase would be present) conditions. The simulation utilized available kinetic information and models representing the main physical and chemical processes taking place. It was found that the transition to heterogeneous conditions (i.e., the exceedance of the solubility limit with increasing loading) can be identified by observing either a rapid decline in ultimate yield of the diamine hydrolysis product from near-stoichiometric to much lower values, or a decrease in rate of formation of the diamine hydrolysis product relative to its ultimate yield. The latter criterion is expected to be the more powerful indicator. These criteria can be used in future work to define and interpret an experimental program for determining solubility limits for aromatic diisocyanates or other poorly-soluble, water-reactive substances.

Partnered dance evokes greater intrinsic motivation than home exercise as therapeutic activity for chemotherapy-induced deficits: secondary results of a randomized, controlled clinical trial.

Introduction: Dance has been proposed to support superior intrinsic motivation over non-dance forms of therapeutic physical activity. However, this hypothesis has yet to be evaluated empirically, particularly among populations living with neuropathology such as survivors of cancer with neurologic complications from chemotherapy treatment. Questions about motivation are relevant to clinical outcomes because motivation mediates neuroplasticity. We conducted this secondary analysis of a randomized-controlled study to begin to investigate the relationships between personal motivation and neurophysiologic effects of dance-based intervention for healthy aging among populations with neurologic complications of cancer. Methods: We measured motivation using the Intrinsic Motivation Inventory, a validated patient-reported outcome from the psychological approach of Self Determination Theory. We assessed intrinsic motivation, extrinsic motivation, and satisfaction with intervention within a randomized controlled trial of dance versus exercise designed to alleviate symptoms of chemotherapy-induced impairment. Fifty-two survivors of breast cancer with chemotherapy-induced neuropathy diagnosis and associated sensorimotor functional deficits were randomized (1:1) to 8 weeks of partnered dance or home exercise, performed biweekly (NCT05114005; R21-AG068831). Results: While satisfaction did not differ between interventions, intrinsic motivation was higher among participants randomized to dance than those randomized to exercise (p < 0.0001 at all timepoints: 2 weeks, 4 weeks, 6 weeks, and 8 weeks of intervention), as was extrinsic motivation at 2 weeks (p = 0.04) and 8 weeks (p = 0.01). Discussion: These data provide evidence that social dance is more motivating than the type of home exercise generally recommended as therapeutic physical activity. The results inform directions for future study of the effect of dance-based therapeutics on embodied agency, neuroplastic changes, and clinically-relevant neuropathic improvement.

Evolving Concepts of Pain Management in Elderly Patients.

PURPOSE OF REVIEW: The elderly population typically suffer from a variety of diseases that mostly reflect the degenerative changes linked with the aging process. These diseases may be exacerbated by acute pain or by an abrupt aggravation of previously stable chronic pain. RECENT FINDINGS: Physical and psychological changes associated with aging may influence one's experience of pain and, as a result, the severity of pain. Pain treatment in the elderly can be complex and is often a budgetary burden on the nation's health care system. These difficulties arise, in part, because of unanticipated pharmacodynamics, changed pharmacokinetics, and polypharmacy interactions. Therefore, it is critical to integrate a multidisciplinary team to develop a management strategy that incorporates medical, psychological, and surgical methods to control persistent pain conditions. It is in this critical process that pain prediction models can be of great use. The purpose of pain prediction models for the elderly is the use of mathematical models to predict the occurrence and intensity of pain and pain-related conditions. These mathematical models employ a vast quantity of data to ascertain the many risk factors for the development of pain problems in the elderly, whether said risks are adjustable or not. These models will pave the way for more informed medical decision making that are based on the findings of thousands of patients who have previously experienced the same illness and related pain conditions. However, future additional research needs to be undertaken to build prediction models that are not constrained by substantial legal or methodological limitations.

Tomivosertib reduces ectopic activity in dorsal root ganglion neurons from patients with radiculopathy.

Spontaneous activity in dorsal root ganglion (DRG) neurons is a key driver of neuropathic pain in patients suffering from this largely untreated disease. While many intracellular signalling mechanisms have been examined in preclinical models that drive spontaneous activity, none have been tested directly on spontaneously active human nociceptors. Using cultured DRG neurons recovered during thoracic vertebrectomy surgeries, we showed that inhibition of mitogen-activated protein kinase interacting kinase (MNK) with tomivosertib (eFT508, 25 nM) reversibly suppresses spontaneous activity in human sensory neurons that are likely nociceptors based on size and action potential characteristics associated with painful dermatomes within minutes of treatment. Tomivosertib treatment also decreased action potential amplitude and produced alterations in the magnitude of after hyperpolarizing currents, suggesting modification of Na+ and K+ channel activity as a consequence of drug treatment. Parallel to the effects on electrophysiology, eFT508 treatment led to a profound loss of eIF4E serine 209 phosphorylation in primary sensory neurons, a specific substrate of MNK, within 2 min of drug treatment. Our results create a compelling case for the future testing of MNK inhibitors in clinical trials for neuropathic pain.

A single-cell atlas deconstructs heterogeneity across multiple models in murine traumatic brain injury and identifies novel cell-specific targets.

Traumatic brain injury (TBI) heterogeneity remains a critical barrier to translating therapies. Identifying final common pathways/molecular signatures that integrate this heterogeneity informs biomarker and therapeutic-target development. We present the first large-scale murine single-cell atlas of the transcriptomic response to TBI (334,376 cells) across clinically relevant models, sex, brain region, and time as a foundational step in molecularly deconstructing TBI heterogeneity. Results were unique to cell populations, injury models, sex, brain regions, and time, highlighting the importance of cell-level resolution. We identify cell-specific targets and previously unrecognized roles for microglial and ependymal subtypes. Ependymal-4 was a hub of neuroinflammatory signaling. A distinct microglial lineage shared features with disease-associated microglia at 24 h, with persistent gene-expression changes in microglia-4 even 6 months after contusional TBI, contrasting all other cell types that mostly returned to naive levels. Regional and sexual dimorphism were noted. CEREBRI, our searchable atlas (https://shiny.crc.pitt.edu/cerebri/), identifies previously unrecognized cell subtypes/molecular targets and is a leverageable platform for future efforts in TBI and other diseases with overlapping pathophysiology.

Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life.

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1 Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.

Evaluation of adherence to STARD for Abstracts in a diverse sample of diagnostic accuracy abstracts published in 2012 and 2019 reveals suboptimal reporting practices.

OBJECTIVE: To evaluate the completeness of reporting in a sample of abstracts on diagnostic accuracy studies before and after the release of STARD for Abstracts in 2017. METHODS: We included 278 diagnostic accuracy abstracts published in 2012 (N=138) and 2019 (N=140) and indexed in EMBASE. We analyzed their adherence to 10 items of the 11-item STARD for Abstracts checklist and explored variability in reporting across abstract characteristics using multivariable Poisson modeling. RESULTS: Most of the 278 abstracts (75%) were published in discipline-specific journals, with a median impact factor of 2.9 (IQR: 1.9-3.7). The majority (41%) of abstracts reported on imaging tests. Overall, a mean of 5.4/10 (SD: 1.4) STARD for Abstracts items was reported (range: 1.2-9.7). Items reported in less than one-third of abstracts included 'eligible patient demographics' (24%), 'setting of recruitment' (30%), 'method of enrolment' (18%), 'estimates of precision for accuracy measures' (26%), and 'protocol registration details' (4%). We observed substantial variability in reporting across several abstract characteristics, with higher adherence associated with the use of a structured abstract, no journal limit for abstract word count, abstract word count above the median, one-gate enrolment design, and prospective data collection. There was no evidence of an increase in the number of reported items between 2012 and 2019 (5.2 vs. 5.5 items; adjusted reporting ratio 1.04 [95%CI: 0.98-1.10]). CONCLUSION: This sample of diagnostic accuracy abstracts revealed suboptimal reporting practices, without improvement between 2012 and 2019. The test evaluation field could benefit from targeted knowledge translation strategies to improve completeness of reporting in abstracts.

Evaluating Lab-Based Eligibility Criteria by Race/Ethnicity in Clinical Trials of Diffuse Large B-Cell Lymphoma.

Underrepresentation of racial and ethnic subgroups in cancer clinical trials remains a persistent challenge. Restrictive clinical trial eligibility criteria have been shown to exacerbate this problem. We previously identified that up to 24% of patients treated with standard immunochemotherapy (IC) would have been excluded from recent first-line trials in diffuse large B-cell lymphoma (DLBCL) based on 5 lab-based criteria. These ineligible patients had worse clinical outcomes and increased deaths related to lymphoma progression suggesting the potential exclusion of patients who could have benefited most from the novel therapies being evaluated. Utilizing data from the prospectively enrolled Lymphoma Epidemiology Outcomes (LEO) Cohort study, with demographics broadly similar to the U.S. patients diagnosed with lymphoma, we evaluated the impact of laboratory eligibility criteria from recent first-line DLBCL trials across various racial and ethnic backgrounds. There were significant differences in the baseline lab values by race/ethnicity with Black/African American (AA) patients having the lowest mean hemoglobin and highest creatinine clearance. Based on recent clinical trial eligibility criteria, AA and Hispanic patients had higher rates of lab-based ineligibility compared to Non-Hispanic Whites. The largest gap in the clinical outcomes between eligible (ref) and non-eligible patients was noted within AA patients with an overall survival hazard ratio based on POLARIX clinical trial criteria of 4.09, 95% CI: 1.83-9.14. A thoughtful approach to the utility of each criterion and cut offs for eligibility needs to be evaluated in the context of its differential impact across various racial/ethnic groups.

Treatment Outcomes Among Patients With a Positive Candida Culture Close to Randomization Receiving Rezafungin or Caspofungin in the ReSTORE Study.

BACKGROUND: Rezafungin, a novel, once-weekly echinocandin for the treatment of candidemia and/or invasive candidiasis (IC) was non-inferior to caspofungin for Day 30 all-cause mortality (ACM) and Day 14 global cure in the Phase 3 ReSTORE trial (NCT03667690). We conducted pre-planned subgroup analyses for patients with a positive culture close to randomization in ReSTORE. METHODS: ReSTORE was a multicenter, double-blind, double-dummy, randomized trial in patients aged ≥18 years with candidemia and/or IC treated with once-weekly intravenous rezafungin (400 mg/200 mg) or once-daily intravenous caspofungin (70 mg/50 mg). This analysis comprised patients with a positive blood culture drawn between 12 hours before and 72 hours after randomization, or a positive culture from another normally sterile site sampled between 48 hours before and 72 hours after randomization. Efficacy endpoints included Day 30 ACM, Day 14 global cure rate, and Day 5 and 14 mycological response. Adverse events were evaluated. RESULTS: This analysis included 38 patients randomized to rezafungin and 46 to caspofungin. In the rezafungin and caspofungin groups, respectively: Day 30 ACM was 26.3% and 21.7% (between-group difference [95% confidence interval] 4.6% [-13.7, 23.5]); Day 14 global response was 55.3% and 50.0% (between-group difference 5.3% [-16.1, 26.0]); and Day 5 mycological eradication was 71.1% and 50.0% (between-group difference 21.1% [-0.2, 40.2]). Safety was comparable between treatments. CONCLUSIONS: These findings support the efficacy and safety of rezafungin compared with caspofungin for the treatment of candidemia and/or IC in patients with a positive culture close to randomization, with potential early treatment benefits for rezafungin.