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Abstract Cancer transcriptional patterns reflect both unique features and shared hallmarks across diverse cancer types, but whether differences in these patterns are sufficient to characterize the full breadth of tumor phenotype heterogeneity remains an open question. We hypothesized that these shared transcriptomic signatures reflect repurposed versions of functional tasks performed by normal tissues. Starting with normal tissue transcriptomic profiles, we use non-negative matrix factorization to derive six distinct transcriptomic phenotypes, called archetypes, which combine to describe both normal tissue patterns and variations across a broad spectrum of malignancies. We show that differential enrichment of these signatures correlates with key tumor characteristics, including overall patient survival and drug sensitivity, independent of clinically actionable DNA alterations. Additionally, we show that in HR+/HER2- breast cancers, metastatic tumors adopt transcriptomic signatures consistent with the invaded tissue. Broadly, our findings suggest that cancer often arrogates normal tissue transcriptomic characteristics as a component of both malignant progression and drug response. This quantitative framework provides a strategy for connecting the diversity of cancer phenotypes and could potentially help manage individual patients.

Abstract In 1957 Abbott and Ballantine described a highly toxic activity from a dinoflagellate isolated from the English Channel in 1949 by Mary Park. From a culture maintained at Plymouth Laboratory since 1950, we have been able to isolate two toxic molecules (abbotoxin and 59-E-Chloro-abbotoxin), determine the planar structures by analysis of HRMS and 1D and 2D NMR spectra, and found them to be karlotoxin (KmTx) congeners. Both toxins kill larval zebrafish with symptoms identical to those described by Abbot and Ballantine for gobies (Gobius virescens). Using surface plasma resonance the sterol binding specificity of karlotoxins is shown to require desmethyl sterols. Our results with black lipid membranes indicate that karlotoxin forms large-conductance channels in the lipid membrane, which are characterized by large ionic conductance, poor ionic selectivity, and a complex gating behavior that exhibits strong voltage dependence and multiple gating patterns. In addition, we show that KmTx 2 pore formation is a highly targeted mechanism involving sterol-specificity. This is the first report of the functional properties of the membrane pores formed by karlotoxins and is consistent with the initial observations of Abbott and Ballantine from 1957.

Described here is the construction of a low-cost, standalone underwater camera system designed for recording processes occurring on aquatic substrates. The Submerged Microscope for Observing Substrates (SuMOS) utilizes a Raspberry Pi Zero 2 W paired with a Raspberry Pi Camera Module v3 NoIR, with IR illumination for low-light situations. It features a waterproof housing inspired by the open-source PipeCam project, with enhancements for sealing and substrate mounting. The SuMOS system operates autonomously, capturing high-resolution images at fixed intervals under various lighting conditions. Tests in the Choptank River of Maryland demonstrated the system’s robustness in capturing patterns of amphipod activity under challenging optical conditions. This versatile tool offers a scalable solution for highly time-resolved, in situ studies of processes occurring at the interface of the aquatic/solid surface boundaries. The SuMOS provides significant advantages in cost, ease of deployment, and data collection.

Abstract Translation elongation is essential for maintaining cellular proteostasis, and alterations in the translational landscape are associated with a range of diseases. Ribosome profiling allows detailed measurements of translation at the genome scale. However, it remains unclear how to disentangle biological variations from technical artifacts in these data and identify sequence determinants of translation dysregulation. Here we present Riboformer, a deep learning-based framework for modeling context-dependent changes in translation dynamics. Riboformer leverages the transformer architecture to accurately predict ribosome densities at codon resolution. When trained on an unbiased dataset, Riboformer corrects experimental artifacts in previously unseen datasets, which reveals subtle differences in synonymous codon translation and uncovers a bottleneck in translation elongation. Further, we show that Riboformer can be combined with in silico mutagenesis to identify sequence motifs that contribute to ribosome stalling across various biological contexts, including aging and viral infection. Our tool offers a context-aware and interpretable approach for standardizing ribosome profiling datasets and elucidating the regulatory basis of translation kinetics.

Abstract Melanoma response to immune-modulating therapy remains incompletely characterized at the molecular level. In this study, we assess melanoma immunotherapy response using a multi-scale network approach to identify gene modules with coordinated gene expression in response to treatment. Using gene expression data of melanoma before and after treatment with nivolumab, we modeled gene expression changes in a correlation network and measured a key network geometric property, dynamic Ollivier-Ricci curvature, to distinguish critical edges within the network and reveal multi-scale treatment-response gene communities. Analysis identified six distinct gene modules corresponding to sets of genes interacting in response to immunotherapy. One module alone, overlapping with the nuclear factor kappa-B pathway (NFkB), was associated with improved patient survival and a positive clinical response to immunotherapy. This analysis demonstrates the usefulness of dynamic Ollivier-Ricci curvature as a general method for identifying information-sharing gene modules in cancer.

Abstract Network properties account for the complex relationship between genes, making it easier to identify complex patterns in their interactions. In this work, we leveraged these network properties for dual purposes. First, we clustered pediatric sarcoma tumors using network information flow as a similarity metric, computed by the Wasserstein distance. We demonstrate that this approach yields the best concordance with histological subtypes, validated against three state-of-the-art methods. Second, to identify molecular targets that would be missed by more conventional methods of analysis, we applied a novel unsupervised method to cluster gene interactomes represented as networks in pediatric sarcoma. RNA-Seq data were mapped to protein-level interactomes to construct weighted networks that were then subjected to a non-Euclidean, multi-scale geometric approach centered on a discrete notion of curvature. This provides a measure of the functional association among genes in the context of their connectivity. In confirmation of the validity of this method, hierarchical clustering revealed the characteristic EWSR1-FLI1 fusion in Ewing sarcoma. Furthermore, assessing the effects of in silico edge perturbations and simulated gene knockouts as quantified by changes in curvature, we found non-trivial gene associations not previously identified.

Abstract As a generalization of the optimal mass transport (OMT) approach of Benamou and Brenier’s, the regularized optimal mass transport (rOMT) formulates a transport problem from an initial mass configuration to another with the optimality defined by the total kinetic energy, but subject to an advection-diffusion constraint equation. Both rOMT and the Benamou and Brenier’s formulation require the total initial and final masses to be equal; mass is preserved during the entire transport process. However, for many applications, e.g., in dynamic image tracking, this constraint is rarely if ever satisfied. Therefore, we propose to employ an unbalanced version of rOMT to remove this constraint together with a detailed numerical solution procedure and applications to analyzing fluid flows in the brain.

Objective: The objective of this retrospective review was to evaluate whether or not pulsatile flow improves cerebral hemodynamics and clinical outcomes in pediatric congenital cardiac surgery patients. Methods: This retrospective study included 284 pediatric patients undergoing congenital cardiac surgery with cardiopulmonary bypass support utilizing nonpulsatile (n = 152) or pulsatile (n = 132) flow. Intraoperative cerebral gaseous microemboli counts, pulsatility index, and mean blood flow velocity at the right middle cerebral artery were assessed using transcranial Doppler ultrasound. Clinical outcomes were compared between groups. Results: Patient demographics and cardiopulmonary bypass characteristics between groups were similar. Although the pulsatility index during aortic crossclamping was consistently higher in the pulsatile group (P

Background: Although electronic prescription cancellation such as via CancelRx can facilitate critical communication between prescribers and pharmacy staff about discontinued medications, there is little work that explores whether CancelRx meets the needs of pharmacy staff users. Objective: This study leverages qualitative interviews with pharmacy staff to address the following question: When medication changes are made by a prescriber using CancelRx, what information is needed by pharmacy staff to make correct and effective decisions in their roles in medication management? Methods: We conducted an inductive thematic analysis of interviews with 11 pharmacy staff members (pharmacists and pharmacy technicians) across three outpatient community pharmacy sites within an academic health care system. Results: Three information needs themes were consistently identified by both pharmacists and pharmacy technicians: prescriber intent when initiating the CancelRx, clinical rationale for the medication change, and intended medication regimen. Notably, both pharmacists and pharmacy technicians often reported seeking multiple information needs not fully addressed by CancelRx in the electronic health record (EHR) to achieve the shared goals of correct dispensing of medications and supporting patient self-management. Conclusions: Our qualitative analysis reveals that outpatient community pharmacy staff in an academic health care system often seek additional information from the (EHR) following medication changes communicated by CancelRx to meet their information needs. Ideally, the prescriber would provide sufficient information through CancelRx to automatically identify all discontinued prescriptions. These limitations highlight the need for design features that support routine communication of needed information at the time of a medication change, such as structured data elements.

Abstract Background To bring evidence-based interventions (EBIs) to individuals with behavioral health needs, psychosocial interventions must be delivered at scale. Despite an increasing effort to implement effective treatments in communities, most individuals with mental health and behavioral problems do not receive EBIs. We posit that organizations that commercialize EBIs play an important role in disseminating EBIs, particularly in the USA. The behavioral health and implementation industry is growing, bringing the implementation field to an important inflection point: how to scale interventions to improve access while maintaining EBI effectiveness and minimizing inequities in access to psychosocial intervention. Main body We offer a first-hand examination of five illustrative organizations specializing in EBI implementation: Beck Institute for Cognitive Behavioral Therapy; Incredible Years, Inc.; the PAXIS Institute; PracticeWise, LLC; and Triple P International. We use the Five Stages of Small Business Growth framework to organize themes. We discuss practical structures (e.g., corporate structures, intellectual property agreements, and business models) and considerations that arise when trying to scale EBIs including balancing fidelity and reach of the intervention. Business models consider who will pay for EBI implementation and allow organizations to scale EBIs. Conclusion We propose research questions to guide scaling: understanding the level of fidelity needed to maintain efficacy, optimizing training outcomes, and researching business models to enable organizations to scale EBIs.

Dinoflagellates are one of the largest groups of marine microalgae and exhibit diverse trophic strategies. Some dinoflagellates can produce secondary metabolites that are known to be toxic, which can lead to ecologically harmful blooms. Amphidinium carterae is one species of dinoflagellate that produces toxic compounds and is used as a model for dinoflagellate studies. The impact of the microbiome on A. carterae growth and metabolite synthesis is not yet fully understood, nor is the impact of bacterial data on sequencing and assembly. An antibiotic cocktail was previously shown to eliminate 16S amplification from the dinoflagellate culture. Even with drastically reduced bacterial numbers during antibiotic treatment, bacterial sequences were still present. In this experiment, we used novel Nanopore long-read sequencing techniques on A. carterae cultures to assemble 15 full bacterial genomes ranging from 2.9 to 6.0 Mb and found that the use of antibiotics decreased the percentage of reads mapping back to bacteria. We also identified shifts in the microbiome composition and identified a potentially deleterious bacterial species arising in the absence of the antibiotic treatment. Multiple antibiotic resistance genes were identified, as well as evidence that the bacterial population does not contribute to toxic secondary metabolite synthesis.

Objective: To determine the feasibility, safety, and outcomes of an oil-based, iodinated contrast using office-based, ultrasound-imaged hysterosalpingography in women with infertility. Design: Randomized Controlled Double Blind Clinical Trial. Setting: Academic health center. Intervention(s): Tubal flushing with oil-based contrast medium (Lipiodol UF) versus saline. Main Outcome Measure(s): Ongoing pregnancy rate, pain, quality of life, and thyroid function. Result(s): Forty-eight patients (24 in each group) were analyzed. The groups were well-matched at baseline. Ongoing pregnancy was noted in 17% (4/24) of the oil-contrast group versus 37% (9/24) in the saline group. Saline group patients more frequently initiated infertility therapy in the six-month follow-up period (saline, 67% vs. oil, 33%), and no serious adverse events in either group. There were no differences in pain from the procedure between groups. There were no differences in thyroid function tests postprocedure between groups, but within the oil-contrast group, there was a slight increase in thyroid-stimulating hormone (post vs. preratio of geometric means: 1.18; 95% confidence interval [CI], 1.02–1.38) and decrease in Free T4 (postdifference vs. predifference in means: 0.08 ng/dL; 95% CI, -0.14 to -0.01). Immediately after the test, the physicians correctly guessed 79% of oil and 71% of saline randomization assignments, whereas patients correctly guessed 63% of oil and 38% of saline. Conclusion(s): This pilot study demonstrates the safety and feasibility of giving an oil-based contrast medium during ultrasound-imaged hysterosalpingography. Pregnancies were seen after oil-based administration, and this contrast is associated with minor thyroid function impairment.

Oysters (Crassostrea virginica) were screened for 12 phycotoxins over two years in nearshore waters to collect baseline phycotoxin data and to determine prevalence of phycotoxin co-occurrence in the commercially and ecologically-relevant species. Trace to low concentrations of azaspiracid-1 and -2 (AZA1, AZA2), domoic acid (DA), okadaic acid (OA), and dinophysistoxin-1 (DTX1) were detected, orders of magnitude below seafood safety action levels. Microcystins (MCs), MC-RR and MC-YR, were also found in oysters (maximum: 7.12 μg MC-RR/kg shellfish meat wet weight), warranting consideration of developing action levels for freshwater phycotoxins in marine shellfish. Oysters contained phycotoxins that impair shellfish health: karlotoxin1-1 and 1–3 (KmTx1-1, KmTx1-3), goniodomin A (GDA), and pectenotoxin-2 (PTX2). Co-occurrence of phycotoxins in oysters was common (54%, n = 81). AZAs and DA co-occurred most frequently of the phycotoxins investigated that are a concern for human health (n = 13) and PTX2 and KmTxs co-occurred most frequently amongst the phycotoxins of concern for shellfish health (n = 9). Various harmful algal bloom (HAB) monitoring methods and tools were assessed for their effectiveness at indicating levels of phycotoxins in oysters. These included co-deployed solid phase adsorption toxin tracking (SPATT) devices, toxin levels in particulate organic matter (POM, >1.5 μm) and whole water samples and cell concentrations from water samples as determined by microscopy and quantitative real-time PCR (qPCR). The dominant phycotoxin varied between SPATTs and all other phycotoxin sample types, and out of the 11 phycotoxins detected in oysters, only four and seven were detected in POM and whole water respectively, indicating phycotoxin profile mismatch between ecosystem compartments. Nevertheless, there were correlations between DA in oysters and whole water (simple linear regression [LR]: R2 = 0.6, p

Abstract Background Compositional systems, represented as parts of some whole, are ubiquitous. They encompass the abundances of proteins in a cell, the distribution of organisms in nature, and the stoichiometry of the most basic chemical reactions. Thus, a central goal is to understand how such processes emerge from the behaviors of their components and their pairwise interactions. Such a study, however, is challenging for two key reasons. Firstly, such systems are complex and depend, often stochastically, on their constituent parts. Secondly, the data lie on a simplex which influences their correlations. Results To resolve both of these issues, we provide a general and data-driven modeling tool for compositional systems called Compositional Maximum Entropy (CME). By integrating the prior geometric structure of compositions with sample-specific information, CME infers the underlying multivariate relationships between the constituent components. We provide two proofs of principle. First, we measure the relative abundances of different bacteria and infer how they interact. Second, we show that our method outperforms a common alternative for the extraction of gene-gene interactions in triple-negative breast cancer. Conclusions CME provides novel and biologically-intuitive insights and is promising as a comprehensive quantitative framework for compositional data.

Postoperative opioid prescribing has historically lacked information critical to balancing the pain control needs of the individual patient with our professional responsibility to judiciously prescribe these high-risk medications. This data evaluates pain control, satisfaction with pain control, and opioid utilization among patients undergoing isolated mid-urethral sling (MUS) randomized to one of two different opioid prescribing regimens. This study was registered on clinicaltrials.gov (NCT04277975). Women undergoing isolated MUS by a Female Pelvic Medicine and Reconstructive Surgery physician at a Penn State Health hospital from June 1, 2020 to November 22, 2021 were offered enrollment into this prospective, randomized, open-label, non-inferiority clinical trial. Participants gave informed consent and were enrolled by a member of the study team. Allocation was concealed to patient and study personnel until randomization on the day of surgery. Preoperatively, all participants completed baseline demographic and pain surveys including CSI-9, PCS, and Likert pain score (scale 0-10). Participants were randomized to either receive a standard prescription of ten 5 mg tablets oxycodone provided preoperatively (standard) or opioid prescription provided only upon patient request postoperatively (restricted). Randomization was performed by the study team surgeon using the REDCap randomization module on the day of surgery.Following MUS, subjects completed a daily diary for 1 week, i.e., postoperative day (POD) 0 through 7. Within the dairy, subjects provided the following information: average daily pain score, opioid use and amount of opioid utilized, other forms of pain management, satisfaction with pain control, perception of the amount of opioid prescribed, and need for pain management hospital/clinic visits. The online Prescription Drug Monitoring Program (PDMP) was queried for all patients to determine if prescriptions for opioids were filled during the postoperative period. The primary outcome was average postoperative day 1 pain score and an a priori determined margin of non-inferiority was set at 2 points. Secondary outcomes included whether subject filled an opioid prescription (indicated by the online PDMP), opioid use (yes/no), satisfaction with pain control (on a scale of 1= “much worse” to 5= “much better” than expected), and how subjects felt about the amount of opioid prescribed (on a scale of 1=“prescribed far more” to 3=“prescribed the right amount” to 5=“prescribed far less” opioid than needed). 82 participants underwent isolated MUS placement and met inclusion criteria; 40 were randomized to the standard arm and 42 to the restricted group. Within this manuscript, we detail the data obtained from this randomized clinical trial and the methods utilized.

Abstract Background Oncofertility is a developing field of increasing importance, particularly in pediatric oncology, where most patients are likely to survive long‐term and have not yet had the opportunity to have children. Aims We performed a quality improvement initiative to increase our rates of fertility preservation counseling and referral through the implementation of a pediatric oncofertility team, and we report outcomes 7 years following implementation of our initiative. Methods and results We compare our baseline oncofertility survey to 44 post‐intervention survey respondents and electronic medical record documentation for 149 patients treated in 2019. Ninety‐five percent of post‐intervention survey respondents recalled fertility counseling (baseline 70%, p = .004) and 89.3% were appropriately referred for fertility preservation (baseline 50%, p = .017). Counseling was documented in 60.4% of charts; 81% of patients analyzed by chart review were appropriately referred for fertility preservation. Fertility preservation outcomes differed by sex assigned at birth. Conclusion Creation of an oncofertility team produced improvements in fertility counseling and fertility preservation referral across an extended period of time.

Abstract Network analysis methods can potentially quantify cancer aberrations in gene networks without introducing fitted parameters or variable selection. A new network curvature-based method is introduced to provide an integrated measure of variability within cancer gene networks. The method is applied to high-grade serous ovarian cancers (HGSOCs) to predict response to immune checkpoint inhibitors (ICIs) and to rank key genes associated with prognosis. Copy number alterations (CNAs) from targeted and whole-exome sequencing data were extracted for HGSOC patients (n = 45) treated with ICIs. CNAs at a gene level were represented on a protein–protein interaction network to define patient-specific networks with a fixed topology. A version of Ollivier–Ricci curvature was used to identify genes that play a potentially key role in response to immunotherapy and further to stratify patients at high risk of mortality. Overall survival (OS) was defined as the time from the start of ICI treatment to either death or last follow-up. Kaplan–Meier analysis with log-rank test was performed to assess OS between the high and low curvature classified groups. The network curvature analysis stratified patients at high risk of mortality with p = 0.00047 in Kaplan–Meier analysis in HGSOC patients receiving ICI. Genes with high curvature were in accordance with CNAs relevant to ovarian cancer. Network curvature using CNAs has the potential to be a novel predictor for OS in HGSOC patients treated with immunotherapy.

Dinoflagellates are unicellular organisms that are implicated in harmful algal blooms (HABs) caused by potent toxins that are produced through polyketide synthase (PKS) pathways. However, the exact mechanisms of toxin synthesis are unknown due to a lack of genomic segregation of fat, toxins, and other PKS-based pathways. To better understand the underlying mechanisms, the actions and expression of the PKS proteins were investigated using the toxic dinoflagellate Amphidinium carterae as a model. Cerulenin, a known ketosynthase inhibitor, was shown to reduce acetate incorporation into all fat classes with the toxins amphidinol and sulpho-amphidinol. The mass spectrometry analysis of cerulenin-reacted synthetic peptides derived from ketosynthase domains of A. carterae multimodular PKS transcripts demonstrated a strong covalent bond that could be localized using collision-induced dissociation. One multi-modular PKS sequence present in all dinoflagellates surveyed to date was found to lack an AT domain in toxin-producing species, indicating trans-acting domains, and was shown by Western blotting to be post-transcriptionally processed. These results demonstrate how toxin synthesis in dinoflagellates can be differentiated from fat synthesis despite common underlying pathway.

Incorporating environmentally sustainable plant-based protein sources into aquafeeds is a priority for the aquaculture industry. Wheat gluten as a plant protein source has been successfully integrated into feeds for several fish species. However, unique nutritional requirements and the potential for intolerances necessitate the evaluation of plant-based diets by species. Previous work by our laboratory indicated that wheat gluten at less than 4% inclusion in a compound feed had a negative impact on growth and survival rate in juvenile cobia (Rachycentron canadum). In the current study, we evaluated the effects of wheat gluten inclusion in a plant-based diet in juvenile European sea bass (Dicentrarchus labrax). No major differences were observed in terms of growth rate, plasma biochemical parameters, detectable induction of plasma IgM, IgT, or factors capable of binding gliadin in response to the inclusion of 4% dietary wheat gluten. However, plasma levels of taurine doubled in the fish fed wheat gluten, and there were considerable changes to the intestinal microbiome. Despite these measurable changes, the data suggest that dietary inclusion of 4% wheat gluten is well tolerated by juvenile European sea bass in a plant-based feed formulation.

ObjectiveAdverse childhood experiences (ACEs) are linked to worsening overall health outcomes and psychological diagnoses. Routine screening, particularly in patients with postpartum depression (PPD), would identify patients who could benefit from interventions to prevent the perpetuation of ACEs and establish a system of preventative care to mitigate the risks of adverse health outcomes associated with high ACE scores. The purpose of this study is to explore the link between ACEs and PPD to advocate for the use of the ACE questionnaire as a routine screening tool in all pregnant patients diagnosed with PPD. We hypothesize that a cohort of patients with PPD will be more likely to have high-risk ACE scores than the general female population.Study DesignOur IRB approved, retrospective cohort study identified all patients diagnosed with PPD at an academic medical center between January 2015 and December 2019. The subjects were identified using retrospective chart review. Subjects were recruited via telephone and asked to complete an ACE questionnaire. Questionnaires were sent via RedCap. ACE scores were calculated, categorized as 0, 1, 2, 3, or 4 or more ACEs, and compared to the prevalence in the original Kaiser-CDC ACE study female cohort using a chi-square goodness-of-fit test.ResultsThere were 132/251 surveys completed (53% response rate). In our PPD population, 19.3% had 0 ACEs, 17.0% had 1 ACE, 13.1% had 2 ACEs, 16.5% had 3 ACEs, and 34.1% had 4 or more ACEs. These percentages were significantly different from the Kaiser-CDC ACE Study percentages of 34.5, 24.5, 15.5, 10.3, and 15.2%, respectively (p < 0.001).ConclusionOur unique study showed that women with PPD are more likely to have high-risk ACE scores than the general female population. This finding has important implications in regards to counseling, intervening to prevent perpetual ACEs, and establishing important provider-patient relationships for life-long preventative care.Non-gendered language is used when possible throughout. However, the wording from studies cited in this paper was preserved.

Cutaneous microcirculatory perfusion is commonly measured using laser Doppler flowmetry (LDF) probes, which provide a continuous, non-invasive quantification of skin blood flow (SkBF). However, inhomogeneities in the skin’s microvasculature density contribute to a decrease in reproducibility whenever an LDF probe is removed and replaced, as is the case during pre- and post-intervention or between-day measurements. Therefore, this study aimed to determine whether increasing the total number of individual LDF probes in a localized area improves the reproducibility of the measurement. Seven laser Doppler probes were secured in a custom-made acrylic holder designed to attach to the skin’s surface easily. SkBF, local skin temperature (Tsk), and blood pressure (BP) were assessed in 11 participants (6 M, 5 F, 42 ± 15 years). SkBF and Tsk were measured from the dorsal forearm (arm trial) for 5 min. Next, the multi-laser device was moved to the lateral side of the calf (leg trial), and measurements were obtained for 5 min. Each arm and leg trial was cyclically repeated three times, and all trials were separated by intermissions lasting 10–15 min. The average SkBF and the cutaneous vascular conductance (CVC) from all possible LDF probe combinations were not statistically different across the three arm and leg trials. Two-way mixed-effects models with absolute agreement were used to compute the intraclass correlation coefficient (ICC) for CVC, and the minimum ICC increased with the addition of LDF probes. The ICC of the average CVC from seven LDF probes was 0.96 between the arm trials and 0.91 between the leg trials, which suggests that there is excellent reliability and little difference between trials following the removal and replacement of the device. Moreover, all individual ICC values from ≥3 LDF probe combinations were greater than 0.70 (i.e., good reliability). These data suggest that SkBF measurements with multiple laser Doppler probes in a custom-made holder have excellent reproducibility after replacing the probes within the same participant. Therefore, this application could provide more reproducible assessments between repeated measurements (e.g., before and after exercise or clinical procedures) where the LDF probes must be removed and replaced within the same location.

Background: Optimal modalities for pain control in shoulder arthroplasty are not yet established. Although regional nerve blockade has been a well-accepted modality, complications and rebound pain have led some surgeons to seek other pain control modalities. Local injection of anesthetics has recently gained popularity in joint arthroplasty. The purpose of this study was to evaluate the effectiveness and complication rate of a low-cost local anesthetic injection mixture for use in total shoulder arthroplasty (TSA) compared with interscalene brachial plexus blockade. Methods: A total of 314 patients underwent TSA and were administered general anesthesia with either a local injection mixture (local infiltration anesthesia [LIA], n = 161) or peripheral nerve block (PNB, n = 144). Patient charts were retrospectively reviewed for postoperative pain scores, 24-hour opioid consumption, and 90-day postoperative complications. Results: Immediate postoperative pain scores were not significantly different between groups (P = .94). The LIA group demonstrated a trend toward lower pain scores at 24 hours postoperatively (P = .10). Opioid consumption during the first 24 hours following surgery was significantly reduced in the LIA group compared with the PNB group (P < .0001). There was a trend toward fewer postoperative nerve and cardiopulmonary complications in the LIA group than the PNB group (P = .22 and P = .40, respectively) Conclusion: Periarticular local injection mixtures provide comparable pain control to regional nerve blocks while reducing opioid use and postoperative complications following TSA. Local injection of a multimodal anesthetic solution is a viable option for pain management in TSA.

In this paper, we present a network-based clustering method, called vector Wasserstein clustering (vWCluster), based on the vector-valued Wasserstein distance derived from optimal mass transport (OMT) theory. This approach allows for the natural integration of multi-layer representations of data in a given network from which one derives clusters via a hierarchical clustering approach. In this study, we applied the methodology to multi-omics data from the two largest breast cancer studies. The resultant clusters showed significantly different survival rates in Kaplan-Meier analysis in both datasets. CIBERSORT scores were compared among the identified clusters. Out of the 22 CIBERSORT immune cell types, 9 were commonly significantly different in both datasets, suggesting the difference of tumor immune microenvironment in the clusters. vWCluster can aggregate multi-omics data represented as a vectorial form in a network with multiple layers, taking into account the concordant effect of heterogeneous data, and further identify subgroups of tumors in terms of mortality.

BACKGROUND: Psychiatric disorders, including anxiety and depression, are significantly more common in patients with inflammatory bowel disease. We established an integrated psychiatry clinic for IBD patients at our tertiary center IBD clinic to provide patients with critical, but frequently unavailable, coordinated mental health services. We undertook this study to evaluate the impact of this service on psychiatric outcomes, quality of life, and symptom experience. METHODS: We performed a longitudinal prospective study comparing patients who had been cared for at our integrated IBD-psychiatry clinic to those who had not. We abstracted demographic and clinical information as well as contemporaneous responses to validated surveys. RESULTS: Thirty-six patients cared for in the IBD-psychiatry clinic were compared to a control cohort of thirty-five IBD patients. There was a significant reduction in the HADS depression score over time in the study cohort (p=0.001), though not in the HADS anxiety score. When compared to the control group, the study cohort showed a significant reduction in the HADS depression score. No significant differences were observed in the HBI, SCCAI or SIBDQ. CONCLUSIONS: This is the first study to evaluate the impact of an integrated psychiatry clinic for IBD patients. Unlike their control counterparts, individuals treated in this clinic had a significant reduction in mean HADS depression score. Larger scale studies are necessary to verify these findings. However, this study suggests that use of an integrated psychiatry-IBD clinic model can result in improvement in mental health outcomes, even in the absence of significant changes in IBD activity.

Parkinson's disease (PD) is a neurodegenerative movement disorder that is routinely treated with levodopa. Unfortunately, long-term dopamine replacement therapy using levodopa leads to levodopa-induced dyskinesias (LID), a significant and disabling side-effect. Clinical findings indicate that LID typically only occurs following the progression of PD motor symptoms from the unilateral (Hoehn and Yahr (HY) Stage I) to the bilateral stage (HY Stage II). This suggests the presence of some compensatory interhemispheric mechanisms that delay the occurrence of LID. We therefore investigated the role of interhemispheric connections of the nigrostriatal pathway on LID expression in a rat model of PD. The striatum of one hemisphere of rats was first injected with a retrograde tracer to label the ipsi- and cross-hemispheric nigrostriatal pathways. Rats were then split into groups and unilaterally lesioned in the striatum or medial forebrain bundle of the tracer-injected hemisphere to induce varying levels of hemiparkinsonism. Finally, rats were treated with levodopa and tested for the expression of LID. Distinct subsets emerged from rats that underwent the same lesioning paradigm based on LID. Strikingly, non-dyskinetic rats had significant sparing of their cross-hemispheric nigrostriatal pathway projecting from the unlesioned hemisphere. In contrast, dyskinetic rats only had a small proportion of this cross-hemispheric nigrostriatal pathway survive lesioning. Crucially, both non-dyskinetic and dyskinetic rats had nearly identical levels of ipsi-hemispheric nigrostriatal pathway survival and parkinsonian motor deficits. Our data suggest that the survival of the cross-hemispheric nigrostriatal pathway plays a crucial role in preventing the expression of LID and represents a potentially novel target to halt the progression of this devastating side-effect of a common anti-PD therapeutic.

Abstract: Detection of minimal residual disease (MRD) pre– and post–hematopoietic cell transplantation (HCT) for pediatric acute lymphoblastic leukemia (ALL) has been associated with relapse and poor survival. Published studies have had insufficient numbers to: (1) compare the prognostic value of pre-HCT and post-HCT MRD; (2) determine clinical factors post-HCT associated with better outcomes in MRD+ patients; and (3) use MRD and other clinical factors to develop and validate a prognostic model for relapse in pediatric patients with ALL who undergo allogeneic HCT. To address these issues, we assembled an international database including sibling (n = 191), unrelated (n = 259), mismatched (n = 56), and cord blood (n = 110) grafts given after myeloablative conditioning. Although high and very high MRD pre-HCT were significant predictors in univariate analysis, with bivariate analysis using MRD pre-HCT and post-HCT, MRD pre-HCT at any level was less predictive than even low-level MRD post-HCT. Patients with MRD pre-HCT must become MRD low/negative at 1 to 2 months and negative within 3 to 6 months after HCT for successful therapy. Factors associated with improved outcome of patients with detectable MRD post-HCT included acute graft-versus-host disease. We derived a risk score with an MRD cohort from Europe, North America, and Australia using negative predictive characteristics (late disease status, non–total body irradiation regimen, and MRD [high, very high]) defining good, intermediate, and poor risk groups with 2-year cumulative incidences of relapse of 21%, 38%, and 47%, respectively. We validated the score in a second, more contemporaneous cohort and noted 2-year cumulative incidences of relapse of 13%, 26%, and 47% (P < .001) for the defined risk groups.

Patients with end-stage renal disease treated with dialysis are often prescribed complex medication regimens, placing them at risk for drug-drug interactions and other medication-related problems. Particularly in the context of a broader interest in more patient-centered value-based care, improving medication management is an increasingly important focus area. However, current medication management metrics, designed for the broader patient population, may not be well suited to the specific needs of patients with kidney disease, especially given the complexity of medication regimens used by dialysis patients. We propose a kidney pharmacy-focused quality pyramid that is intended to provide a framework to guide dialysis organizations, health care providers, and/or clinicians with respect to an optimal medication management approach for dialysis patients. Incorporation of core programs in medication management, including medication reconciliation, safety programs, and medication therapy management for patients at high risk for medication-related problems, may result in improved outcomes. Although a growing body of evidence supports the concept that active medication management can improve medication adherence and reduce medication-related problems, these strategies are viewed as costly and are not widely deployed. However, if done effectively, pharmacy-led medication management has the potential to be one of the more cost-effective disease management strategies and may greatly improve outcomes for these complex patients. Index Words: end-stage renal disease, medication management, pharmacy

Intraocular injection of silicone oil as a tamponade agent is a commonly used technique for the treatment of retinal detachment. An incompletely understood phenomenon which can occur after injection is the migration of silicone oil from the vitreous chamber to the intracranial space. Because the appearance of silicone oil can mimic hemorrhage or other pathologies on CT and MRI, careful comparison with prior studies is necessary to avoid unnecessary follow-up studies. We report a case of intracranial migration of intraocular silicone oil following repetitive head trauma. Keywords: Silicone oil, Intracranial hemorrhage, Trauma, Retinal detachment

Normal development of the patella typically involves fusion of secondary ossification centers into a single bone during adolescence, with failure of fusion resulting in bipartite and tripartite patellae. In such variants, injury to incomplete ossification center fusion, though uncommon, has been reported to occur in the setting of traumatic quadriceps tendon rupture. The authors present a rare and complex case of traumatic bipartite fragment separation, patellar avulsion, and a complex partial quadriceps tendon tear confirmed surgically in a 36-year-old male. In this case, a tear in the lateral aspect of the quadriceps tendon attached to the nonfused patellar ossification center resulted in retraction of the band containing the bipartite fragment and separation of the patellar fragments, with superior displacement of the smaller bony avulsion likely due to complex attachments from the medial aspect of the quadriceps tendon. Knowledge of the classical locations of a bipartite and tripartite patella can aid in the differentiation of the anatomic variant versus patellar avulsion. Additionally, knowledge of the variable and complex nature of the quadriceps tendon aids in understanding the process of patellar avulsions and various tears, leading to the appropriate orthopedic management. Keywords: Bipartite patella, Quadriceps rupture, Trauma

Purpose The aim of this article is to investigate the impact of a 1-minute video describing resident training with a cataract surgical simulator on patients' perceptions regarding resident involvement in cataract surgery and to identify factors associated with patient willingness to have cataract surgery performed by a resident. Design Cross-sectional survey. Methods An anonymous Likert-style survey was conducted among 430 consecutive adult patients who presented for eye examination at the Penn State Health Eye Center. The survey included questions regarding demographics, understanding of the medical training hierarchy, and patient willingness to have a resident perform their cataract surgery. There were six questions regarding patient willingness to have residents perform their cataract surgery and the second question in this set informs the patient that residents are supervised by an experienced cataract surgeon. Patients were randomly assigned to one of two groups: patients in Group 1 completed the survey only, while patients in Group 2 watched a 1-minute video describing resident training with a cataract surgical simulator prior to completing the survey. Results Four hundred fourteen of the 430 patients (96.3%) completed the survey. Overall, 24.7% (n = 102) of respondents expressed willingness to allow an ophthalmology resident to perform their cataract surgery, and that proportion increased to 54.0% (n = 223) if the patient was informed that the resident would be supervised by an experienced cataract surgeon. Patients in Group 2 were twice as likely compared with patients in Group 1 to express willingness to allow an ophthalmology resident to perform their cataract surgery (odds ratio 1.92 [1.18–3.11], p = 0.009). Conclusions A thorough informed consent process including information regarding attending supervision and a brief video detailing resident training with a cataract surgery simulator may increase patient willingness to allow resident participation in cataract surgery.

Thymoma can cause several autoimmune conditions in a number of patients. Nephrotic syndrome is considered to be a rare systemic manifestation from thymic lesions. The most common renal pathology associated with thymoma is minimal change disease (MCD). Herein, we reported a case of 58-year-old man with type B3 thymoma, who developed nephrotic syndrome after the tumor recurrence. The renal biopsy showed the morphologic features of membranous nephropathy (MN). Both immunofluorescent study and serum level for phospholipase A2 receptor (PLA2R) antibody were negative, suggesting a secondary type. Literature review suggests that there is a correlation between thymoma subtype and renal pathology, i.e. lymphocyte predominant thymoma (type B1, B2) is associated with MCD, while type B3 thymoma is associated with MN.

In recent years it has become possible to collect GPS data from drivers and to incorporate these data into automobile insurance pricing for the driver. These data are continuously collected and processed nightly into metadata consisting of mileage and time summaries of each discrete trip taken, and a set of behavioral scores describing attributes of the trip (e.g, driver fatigue or driver distraction), so we examine whether it can be used to identify periods of increased risk by successfully classifying trips that occur immediately before a trip in which there was an incident leading to a claim for that driver. Identification of periods of increased risk for a driver is valuable because it creates an opportunity for intervention and, potentially, avoidance of a claim. We examine metadata for each trip a driver takes and train a classifier to predict whether the following trip is one in which a claim occurs for that driver. By achieving an area under the receiver–operator characteristic above 0.6, we show that it is possible to predict claims in advance. Additionally, we compare the predictive power, as measured by the area under the receiver–operator characteristic of XGBoost classifiers trained to predict whether a driver will have a claim using exposure features such as driven miles, and those trained using behavioral features such as a computed speed score.

The present study investigates the response of the marine fish cobia, Rachycentron canadum, to stressors as measured by phosphorylation of the α-subunit of the translational initiation factor, eIF2. eIF2α is the target of phosphorylation by a family of kinases that respond to a range of physiological stressors. Phosphorylation of eIF2α inhibits overall protein synthesis, but also facilitates the reprogramming of gene expression to adapt to, and recover from, stress. The deduced coding sequence of cobia eIF2α has 94% identity to both zebrafish (Danio rerio) and human eIF2α sequences with identical phosphorylation and kinase docking sites. Here we use cobia larvae and a cobia cell line derived from muscle (Cm cells) to investigate the response of cobia eIF2α to various stressors. In Cm cells, phosphorylation of eIF2α is increased by nutrient deficiency and endoplasmic reticulum stress (ER stress), consistent with the activation of the eIF2 kinases, GCN2, and PERK. In cobia juveniles, diet and water temperature affect the phosphorylation state of eIF2α. We conclude that evaluation of eIF2α phosphorylation could function as an early marker to evaluate diet, environmental stressors, and disease in cobia and may be of particular use in optimizing conditions for rearing cobia larvae and juveniles.

Dinoflagellates are unicellular protists that display unusual nuclear features such as large genomes, condensed chromosomes and multiple gene copies organized as tandem gene arrays. Genetic regulation is believed to be controlled at the translational rather than transcriptional level. An important player in this process is initiation factor eIF4E which binds the 7-methylguanosine cap structure (m7G) at the 5′-end of mRNA. Transcriptome analysis of eleven dinoflagellate species has established that each species encodes between eight to fifteen eIF4E family members. Determining the role of eIF4E family members in gene expression requires a method of knocking down their expression. In other eukaryotes this can be accomplished using translational blocking morpholinos that bind to complementary strands of RNA, therefore inhibiting the mRNA processing. Previously, unmodified morpholinos lacked the ability to pass through cell membranes, however peptide-based reagents have been used to deliver substances into the cytosol of cells by an endocytosis-mediated process without damaging the cell membrane. We have successfully delivered fluorescently-tagged morpholinos to the cytosol of Amphidinium carterae by using a specific cell penetrating peptide with the goal to target an eIF4e-1a sequence to inhibit translation. Specific eIF4e knockdown success (up to 42%) has been characterized via microscopy and western blot analysis.

Bile cast nephropathy (BCN) is seen in patients who have acute kidney injury and severe hyperbilirubinemia due to a wide range of hepatobiliary system diseases. Findings seen by renal biopsy include acute tubular injury with necrotic and sloughed epithelial cells, yellow-green pigment within tubular epithelial cells, and pigmented granular casts. Hall’s special stain for bile turns these casts green. In recent years, BCN has been described in a small number of case reports and clinical studies primarily in the setting of severe liver dysfunction. We present 2 diverse cases of BCN. The first involves an adult with hepatorenal syndrome secondary to alcoholic steatohepatitis and early cirrhosis. Second, we describe the first reported case of BCN in a child with fulminant hepatic failure due to Wilson’s disease. Our cases expand the spectrum of causative diseases, and they provide further evidence that BCN is a distinct pathologic entity which may be found in both adult and pediatric patients with a variety of severe liver diseases.

With the popularity of synthetic cannabinoid street drugs such as “K2 and Spice,” a number of serious neurologic adverse events are coming to light. This case is a 36-year-old African American man, with no significant medical history, who presented with extensive left cervical and intracranial internal carotid artery occlusion and subsequent ischemic stroke. The patient endorsed smoking K2—a synthetic cannabinoid (SC) with structural similarity to cannabis. The mechanism by which SC abuse induces a prothrombotic state leading to ischemic neurovascular sequelae is currently unclear, although a temporal association in the absence of other stroke risk factors suggests a causal relationship. Our case highlights the need for emergent neuroimaging upon suspected SC overdose. Practitioners should be vigilant in recognizing that ischemic stroke and unexplained neurologic deficit can arise after SC abuse, especially in younger populations with few stroke risk factors and who are prone to chronic cannabis use. Keywords: Synthetic cannabinoid, K2, Thrombosis, Stroke, CVA

Proliferative glomerulonephritis with monoclonal immunoglobulin G deposits (PGNMID) is a recently described, uncommon renal disorder which is considered a monoclonal gammopathy of renal significance. Although some patients will have a detectable monoclonal spike, overt hematologic malignancy is found in only a minority. Most patients with PGNMID are over the age of 50 years, and to our knowledge no cases have been reported in children or adolescents. Renal biopsy shows variable histologic patterns by light microscopy, with membranoproliferative and membranous patterns being most common. Immunofluorescence microscopy demonstrates restriction to a single immunoglobulin G heavy chain isotype and a single light chain subtype. Electron microscopy reveals granular, unorganized deposits. We report a rare pediatric case which occurred in a 17-year-old female. The rarity of this entity in the adult population has not permitted a standard treatment regimen to be established. Our adolescent patient was treated with multiple treatment regimens including prednisone, mycophenolate mofetil, rituximab, bortezomib, and daratumumab. Our case demonstrates that awareness of this disorder by pediatric nephrologists and pathologists is vital to guide accurate disease classification, prognosis, and treatment.

Abstract Background Giant cell arteritis (GCA) is an immune mediated inflammatory disease of medium and large arteries which afflicts older people. The classical presentation features include: headache, visual disturbances, and jaw claudication. Patients diagnosed with GCA have also been observed to be at higher risk for the subsequent development of strokes. Case presentation We describe a case of an 84-year old right-handed man who presented to hospital with dysarthria, dysphagia, right-sided facial drop, a history of generalized weakness and multiple falls. He was admitted to geriatric medicine with the working diagnosis of a posterior circulation stroke syndrome. He was also started on antibiotic treatment for a possible community-acquired pneumonia because of the presence of a low-grade fever and a chest radiograph showing ill-defined left lower lobe airspace disease. Initial lab results were remarkable for an erythrocyte sedimentation rate (ESR) of 112 mm/h and a C-reactive protein (CRP) level of 110 mg/L consistent with an active inflammatory state. Neurovascular imaging showed mild atherosclerotic changes of the aortic arch and proximal great vessels without significant stenosis. The patient was started on daily high-dose prednisone because of the possibility of a cerebral vasculitis. Bilateral biopsy of temporal arteries showed giant cell arteritis. The patient’s neurologic status and inflammatory markers significantly improved (ESR 52 mm/h, CRP 7.0 mg/L) and he was eventually discharged to a seniors home with services. Conclusion The initial presentation of giant cell arteritis as a stroke syndrome, especially in the posterior circulation territory, is exceedingly rare. Other atypical presenting symptoms may include chronic cough and fever of unknown origin. The elevated ESR and CRP levels were clues to the diagnosis and clinical decision-making should be driven by a high index of suspicion since no single test (ESR, CRP, temporal artery biopsy) has perfect sensitivity. Elevated CRP may have a role in increasing stroke risk. This case report illustrates that in older people clinicians must consider atypical presentations of disease more often since timely diagnosis and initiation of treatment can result in optimal outcomes.

Esophageal pneumatosis is a rare condition with diverse potential etiologies including traumatic, mechanical, ischemic, obstructive respiratory, autoimmune, immunodeficient, and infectious causes. Here, we present a case of esophageal pneumatosis in the setting of upper gastrointestinal and small bowel ileus, diagnosed on computed tomography (CT), with acute resolution after nasogastric tube decompression. A patient presented to the emergency department with epigastric discomfort. CT of the abdomen/pelvis demonstrated intramural air in the mid-to-distal esophagus, consistent with esophageal pneumatosis, and diffuse dilatation of the visualized esophagus, stomach, and small bowel, consistent with an ileus. Patient was managed with nasogastric tube decompression and bowel rest. Subsequent esophagram did not demonstrate any evidence of perforation and a repeat CT of the abdomen/pelvis, performed 11 hours after initial diagnostic CT, demonstrated interval resolution of patient's esophageal pneumatosis, and improvement of patient's ileus.

Dabigatran etexilate is a relatively new anticoagulant from the class of direct thrombin inhibitors which is administered orally and does not require routine blood work monitoring. Dabigatran may be attractive to both clinicians and patients because of both its convenience and efficacy; however, clinical complications are still being elucidated. Here, we present a previously unreported case of spinal subarachnoid and subdural hematoma presenting as a Brown-Séquard-like myelopathy in a patient after minor trauma in the setting of Dabigatran anticoagulation.

Tubuloreticular inclusions (TRIs) are subcellular structures located within the cisternae of endoplasmic reticulum. Formation of TRIs has been linked to the exposure of excess interferon (IFN), either from endogenous or exogenous sources. In renal disease, TRIs have been most commonly associated with systemic lupus erythematosus (SLE), and human immunodeficiency virus-associated nephropathy (HIVAN). Case reports of patients with renal biopsies showing TRIs without underlying SLE or HIV are infrequent in adults, and to our knowledge none have been reported in children. We report 3 pediatric cases in which the renal biopsy showed TRIs on electron microscopy without underlying SLE or HIV infection. The first patient presented at 2 years of age with nephrotic syndrome and renal failure. His renal biopsy revealed focal segmental glomerulosclerosis and TRIs. The second patient presented at 6 months of age with infantile nephrotic syndrome, and his renal biopsy revealed membranous glomerulopathy and TRIs. The last patient presented at 4 years of age with acute kidney injury of unclear etiology leading to chronic kidney disease. Her biopsy revealed acute and chronic tubulointerstitial nephritis with TRIs. Despite extensive evaluation in all 3 patients, including testing for HIV infection and SLE, we could not identify an underlying etiology to explain the presence of TRIs. In conclusion, renal biopsy with TRIs in the absence of underling SLE and HIV remains obscure. We propose a possible role for excess IFN triggered by an abnormal immune response to common viral infections in the formation of TRIs and renal injury.

ABSTRACT Small proteins consisting of 50 or fewer amino acids have been identified as regulators of larger proteins in bacteria and eukaryotes. Despite the importance of these molecules, the total number of small proteins remains unknown because conventional annotation pipelines usually exclude small open reading frames (smORFs). We previously identified several dozen small proteins in the model organism Escherichia coli using theoretical bioinformatic approaches based on sequence conservation and matches to canonical ribosome binding sites. Here, we present an empirical approach for discovering new proteins, taking advantage of recent advances in ribosome profiling in which antibiotics are used to trap newly initiated 70S ribosomes at start codons. This approach led to the identification of many novel initiation sites in intergenic regions in E. coli. We tagged 41 smORFs on the chromosome and detected protein synthesis for all but three. Not only are the corresponding genes intergenic but they are also found antisense to other genes, in operons, and overlapping other open reading frames (ORFs), some impacting the translation of larger downstream genes. These results demonstrate the utility of this method for identifying new genes, regardless of their genomic context. IMPORTANCE Proteins comprised of 50 or fewer amino acids have been shown to interact with and modulate the functions of larger proteins in a range of organisms. Despite the possible importance of small proteins, the true prevalence and capabilities of these regulators remain unknown as the small size of the proteins places serious limitations on their identification, purification, and characterization. Here, we present a ribosome profiling approach with stalled initiation complexes that led to the identification of 38 new small proteins.

Microbial sharing between humans and animals has been demonstrated in a variety of settings. However, the extent of microbial sharing that occurs within the healthcare setting during animal-assisted intervention programs is unknown. Understanding microbial transmission between patients and therapy dogs can provide important insights into potential health benefits for patients, in addition to addressing concerns regarding potential pathogen transmission that limits program utilization. This study evaluated for potential microbial sharing between pediatric patients and therapy dogs and tested whether patient–dog contact level and a dog decolonization protocol modified this sharing. Patients, therapy dogs, and the hospital environment were sampled before and after every group therapy session and samples underwent 16S rRNA sequencing to characterize microbial communities. Both patients and dogs experienced changes in the relative abundance and overall diversity of their nasal microbiome, suggesting that the exchange of microorganisms had occurred. Increased contact was associated with greater sharing between patients and therapy dogs, as well as between patients. A topical chlorhexidine-based dog decolonization was associated with decreased microbial sharing between therapy dogs and patients but did not significantly affect sharing between patients. These data suggest that the therapy dog is both a potential source of and a vehicle for the transfer of microorganisms to patients but not necessarily the only source. The relative contribution of other potential sources (e.g., other patients, the hospital environment) should be further explored to determine their relative importance.

The rate of protein synthesis varies according to the mRNA sequence in ways that affect gene expression. Global analysis of translational pausing is now possible with ribosome profiling. Here, we revisit an earlier report that Shine-Dalgarno sequences are the major determinant of translational pausing in bacteria. Using refinements in the profiling method as well as biochemical assays, we find that SD motifs have little (if any) effect on elongation rates. We argue that earlier evidence of pausing arose from two factors. First, in previous analyses, pauses at Gly codons were difficult to distinguish from pauses at SD motifs. Second, and more importantly, the initial study preferentially isolated long ribosome-protected mRNA fragments that are enriched in SD motifs. These findings clarify the landscape of translational pausing in bacteria as observed by ribosome profiling.

Many detection methods for phycotoxins, bioactive compounds produced by harmful algae, focus on one compound or a class of related compounds. Multiple harmful algal species often co-occur in the environment, however, emphasizing the need to analyze for the presence of multiple groups of marine and freshwater phycotoxins in environmental samples, e.g., extracts from solid phase adsorption toxin tracking (SPATT). Two methods were developed to screen for 13 phycotoxins (microcystin-RR, -LR, -YR, azaspiracid-1, -2, karlotoxin 3, goniodomin A, brevetoxin-2, yessotoxin, pectenotoxin-2, dinophysistoxin-1, -2, and okadaic acid) in organic SPATT extracts using ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) equipped with a trapping dimension (trap) and at-column dilution (ACD). The performance of each compound under 36 combinations of chromatographic conditions was characterized, and two final methods, acidic and basic, were selected based on peak shapes, signal intensities, resolution, and the separation in time of positive and negative MS ionization modes. Injection volumes of up to 1 mL were possible through trap/ACD technology, resulting in limits of detection between 0.001 and 0.05 µg/L across the analytes. Benefits highlighted in this study, beyond the improved detection limits and co-detection of multiple toxin groups, include the ability to inject samples of 100% organic solvent, ensuring analyte stability and streamlining workflow through the elimination of laborious sample preparation steps.

Ribosome profiling is a powerful method for globally assessing the activity of ribosomes in a cell. Despite its application in many organisms, ribosome profiling studies in bacteria have struggled to obtain the resolution necessary to precisely define translational pauses. Here, we report improvements that yield much higher resolution in E. coli profiling data, enabling us to more accurately assess ribosome pausing and refine earlier studies of the impact of polyproline motifs on elongation. We comprehensively characterize pausing at proline-rich motifs in the absence of elongation factor EFP. We find that only a small fraction of genes with strong pausing motifs have reduced ribosome density downstream, and we identify features that explain this phenomenon. These features allow us to predict which proteins likely have reduced output in the efp-knockout strain.