LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants.

BACKGROUND: Short tandem repeats (STRs) are widely distributed across the human genome and are associated with numerous neurological disorders. However, the extent that STRs contribute to disease is likely under-estimated because of the challenges calling these variants in short read next generation sequencing data. Several computational tools have been developed for STR variant calling, but none fully address all of the complexities associated with this variant class. RESULTS: Here we introduce LUSTR which is designed to address some of the challenges associated with STR variant calling by enabling more flexibility in defining STR loci, allowing for customizable modules to tailor analyses, and expanding the capability to call somatic and multiallelic STR variants. LUSTR is a user-friendly and easily customizable tool for targeted or unbiased genome-wide STR variant screening that can use either predefined or novel genome builds. Using both simulated and real data sets, we demonstrated that LUSTR accurately infers germline and somatic STR expansions in individuals with and without diseases. CONCLUSIONS: LUSTR offers a powerful and user-friendly approach that allows for the identification of STR variants and can facilitate more comprehensive studies evaluating the role of pathogenic STR variants across human diseases.

Health care access, psychosocial outcomes and mental health in adults living with epilepsy during the COVID-19 pandemic.

PURPOSE: People living with epilepsy (PLWE) have a higher prevalence of mental health comorbidities and poorer psychosocial outcomes compared to the general population. The aim of this study was to examine psychosocial outcomes, mental health, healthcare accessibility, and seizure burden in PLWE during the COVID-19 pandemic. METHODS: We conducted a cross-sectional study of adults with epilepsy treated in an urban multicenter health system from 2021 to 2022. A standardized questionnaire assessed for COVID-19 history, comorbidities, access to antiseizure medications (ASMs) and neurological care, seizure burden, and psychosocial outcomes (e.g., employment, social and financial support). The Patient Health Questionnaire-9 (PHQ-9) and Generalized Anxiety Disorder-7 (GAD-7) were administered to evaluate for depression and anxiety. Frequency and proportions for categorical variables and median and interquartile ranges for continuous variables were calculated. RESULTS: Fifty-five PLWE participated (95 % response rate). Median age was 40 years (IQR 31.5-66.5), 61.8 % were women, 47.3 % had a bachelor's degree or higher and 29.1 % each had Medicaid and Medicare insurance. Race (from highest to lowest %) was: 32.7 % White, 20 % Black, 20 % Latinx, 14.5 % Asian, and 12.7 % selected "other" or "prefer not to say." COVID-19 had been diagnosed in 21.8 % of participants. Symptoms of anxiety and depression were self-reported by 43.6 % and 34.5 % of patients, respectively, with many describing this symptom as new post-pandemic (37.5 % and 31.6 %, respectively). Using validated scales, 52.7 % had depression (PHQ-9 score ≥ 5) with 30.9 % having moderate/severe depression (PHQ-9 score ≥ 10), while 29.1 % had probable generalized anxiety disorder (GAD-7 score ≥ 8). Seizure burden increased in 21.8 % of participants, while 20 % reported fewer seizures and 29.1 % were seizure free since the COVID-19 pandemic. Economic impacts of the pandemic included job loss (25 % amongst those employed at onset of pandemic), new or worsened financial difficulties (40 %), and new or worsened social support issues (30.9 %). Of all participants, 18.2 % reported difficulties accessing ASMs and 25.5 % cancelled visits, but of those with cancelled visits, 78.6 % had their appointments rescheduled as a telehealth visit. CONCLUSION: Our cohort of PLWE experienced some challenges during the COVID-19 pandemic including poorer mental health and financial and employment-related stressors. Encouragingly, healthcare access was relatively spared during the COVID-19 crisis, with some patients even reporting a reduction in seizure burden. However, PLWE require ongoing psychosocial support with particular attention to decompensation of mental health and social stressors that may be exacerbated by the COVID-19 pandemic.

Sequential bilateral total ankle replacements: No difference in patient-reported outcomes between the first and second ankle.

BACKGROUND: Total ankle replacement is an established treatment for end-stage arthritis. However, there is little data examining outcomes in sequential bilateral replacements. This study aimed to compare outcomes between first and second ankles in sequential replacement. METHODS: Patients were retrospectively contacted to complete a follow-up questionnaire including the Manchester-Oxford Foot Questionnaire (MOXFQ), EQ-5D-3 L, and a question assessing satisfaction. Electronic records identified demographics, procedural details, and complications. RESULTS: Twenty patients underwent sequential bilateral ankle replacement over the study period. At a mean follow-up of four years, 18 patients completed the follow-up questionnaire. There was no statistically significant difference between first and second ankles in terms of MOXFQ score, EQ-5D-3 L or satisfaction. Eleven complications were noted. CONCLUSIONS: We report excellent outcomes after sequential bilateral ankle replacement with no difference in outcomes between first and second ankles. These results can be used to counsel patients in the future and manage expectations. LEVEL OF EVIDENCE: IV.

Aberrant Ventricular Conduction: Revisiting an Old Concept.

The well-defined concept of aberrant ventricular conduction was introduced over 100 years ago and, despite advances in cardiac physiology and electrophysiologic testing, it is still widely misunderstood. Aberrant ventricular conduction is due to physiologic refractoriness of the His-Purkinje system and in most cases does not reflect underlying conduction system disease. Electrophysiologically, aberrant ventricular conduction can manifest with premature atrial ectopics, the Ashman phenomenon with atrial tachyarrhythmias, concealed conduction, echo beats and with the sinus mechanism including rate dependent bundle branch block, bradycardia dependent bundle branch block and early sinus beats. It is important to recognise aberrant ventricular conduction in the context of a broad complex tachycardia, as the differentiation between supraventricular tachyarrhythmias with aberrant ventricular conduction and ventricular tachyarrhythmias carry different therapeutic and prognostic implications. This review will define the ECG footprints of aberrant ventricular conduction to allow accurate ECG interpretation.

Serrated Polyposis Syndrome in a Young Adolescent Patient.

Serrated polyps are pathological neoplastic lesions in the colon with subtle gross morphology leading to underreporting during colonoscopy. While detection rates are increasing in average-risk adult screening colonoscopy, the rate of detection during pediatric colonoscopy is unknown. Serrated polyposis syndrome is characterized by the presence of multiple serrated polyps in the colon and an increased risk of developing colorectal cancer. Cancer prevention relies on early recognition, endoscopic clearance of all polyps > 5 mm, and continued interval surveillance or prophylactic colectomy. We report the diagnosis and management of serrated polyposis syndrome in a young adolescent patient and highlight the subtle features of serrated polyps that may go unrecognized leading to underreporting in childhood.

Predicting Swallowing Outcomes from Objective Videofluoroscopic Timing and Displacement Measures in Head and Neck Cancer Patients.

Radiation therapy with or without chemotherapy compromises swallowing efficiency and safety in patients with head and neck cancer (HNC). The resulting dysphagia leads to overall morbidity, with altered diets, reduced nutritional intake, reduced quality of life, and potential interruption of curative cancer treatment. Despite well-documented radiation-related changes in swallowing physiology, scarce research exists on the potential clinical value for measurements of swallowing timing and displacement in this population. This study investigated the discriminatory value of quantitative timing and displacement parameters for the Functional Oral Intake Scale and Penetration Aspiration Scale scores using pre- and post-radiation videofluoroscopy data. Swallowtail Software Version 1 (Belldev Medical, Arlington Heights, IL) was used to obtain objective timing and displacement measurements from the pre- and post-radiation videofluoroscopy data for 31 patients who underwent radiation therapy, with or without chemotherapy, for head and neck cancer. The total pharyngeal transit time (BP2) (p < 0.000, r = 0.43) in pudding bolus trials and the maximal upper esophageal sphincter opening (PESMax/cm) (p = 0.001, r = 0.31) in thin bolus trials were discriminatory for Functional Oral Intake Scale (FOIS). Findings suggest that measurement of post-radiation changes using objective and quantitative parameters may offer some discriminatory value regarding future dysphagia risk and prognosis based on total pharyngeal transit time and degree of UES opening. In addition, the results suggest that different bolus types may offer different discriminatory values in HNC population, and that some timing and displacement variables may have discriminatory value for patients' diet levels independent from any aspiration risk.

SLIM microscopy allows for visualization of DNA-containing liposomes designed for sperm-mediated gene transfer in cattle.

Naked DNA has been shown to bind naturally to the sperm, a method called sperm-mediated gene transfer (SMGT). Based on these observations, we examined the efficiency of exogenous DNA binding to sperm using liposomes. In this experiment, we analyzed methods to select frozen-thawed bovine sperm, and evaluated the binding of exogenous DNA to those sperm. To determine the optimal selection method, we used Computer-Assisted Sperm Analysis (CASA). Percoll or Swim-Up were used to select sperm, followed by incubation up to 3 h with the liposome-DNA complexes. The samples were collected after 1 h and after 3 h. We used enhanced green fluorescent protein (eGFP) in combination with the liposomes as a marker for exogenous DNA binding. Five treatments per selection method were analyzed: (1) no incubation, no liposomes and no DNA, (2) incubation with no liposomes and no DNA, (3) incubation with liposomes and no DNA, (4) incubation with liposomes and 1 µg of DNA and (5) incubation with liposomes and 10 µg of DNA. The CASA results for total motility and rapid motility were statistically significant (P < 0.01) between the control and the other treatments in the Percoll group as opposed to Swim-Up. Swim-Up was therefore chosen as the optimal selection method. In order to determine if the liposome-DNA complex had bound to sperm, real time PCR was used to detect GFP DNA and images of the sperm were analyzed using the Spatial Light Interference Microscopy (SLIM). SLIM confirmed the presence of liposomes on the sperm head and tail.

Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods.

While the collective impact of marine viruses has become more apparent over the last decade, a deeper understanding of virus-host dynamics and the role of viruses in nutrient cycling would benefit from direct observations at the single-virus level. We describe two new complementary approaches - stable isotope probing coupled with nanoscale secondary ion mass spectrometry (nanoSIMS) and fluorescence-based biorthogonal non-canonical amino acid tagging (BONCAT) - for studying the activity and biogeochemical influence of marine viruses. These tools were developed and tested using several ecologically relevant model systems (Emiliania huxleyi/EhV207, Synechococcus sp. WH8101/Syn1 and Escherichia coli/T7). By resolving carbon and nitrogen enrichment in viral particles, we demonstrate the power of nanoSIMS tracer experiments in obtaining quantitative estimates for the total number of viruses produced directly from a particular production pathway (by isotopically labelling host substrates). Additionally, we show through laboratory experiments and a pilot field study that BONCAT can be used to directly quantify viral production (via epifluorescence microscopy) with minor sample manipulation and no dependency on conversion factors. This technique can also be used to detect newly synthesized viral proteins. Together these tools will help fill critical gaps in our understanding of the biogeochemical impact of viruses in the ocean.

Assessing Infant Carriage Systems: Ground Reaction Force Implications for Gait of the Caregiver.

Objective To assess the acute alterations of anterior infant carriage systems on the ground reaction force experienced during over-ground walking. Background Previous research has identified the alterations in posture and gait associated with an increased anterior load (external or internal); however, the forces applied to the system due to the altered posture during over-ground walking have not been established. Method Thirteen mixed gender participants completed 45 over-ground walking trials at a self-selected pace under three loaded conditions (unloaded, semi-structured carrier 9.9 kg, and structured carrier 9.9 kg). Each trial consisted of a 15-m walkway, centered around a piezoelectric force platform sampling at 1,200 Hz. Differences were assessed between loaded and unloaded conditions and across carriers using paired samples t tests and repeated measures ANOVA. Results Additional load increased all ground reaction force parameters; however, the magnitude of force changes was influenced by carrier structure. The structured carrier displayed increased force magnitudes, a reduction in the time to vertical maximum heel contact, and an increased duration of the flat foot phase in walking gait. Conclusion Evidence suggests that the acute application of anterior infant carriers alters both kinetic and temporal measures of walking gait. Importantly, these changes appear to be governed not solely by the additional mass but also by the structure of the carrier. Application These findings indicate carrier structure should be considered by the wearer and may be used to inform policy in the recommendation of anterior infant carriage systems use by caregivers.

Characterization of five unclassified orthobunyaviruses (Bunyaviridae) from Africa and the Americas.

The Bunyaviridae family is made up of a diverse range of viruses, some of which cause disease and are a cause for concern in human and veterinary health. Here, we report the genomic and antigenic characterization of five previously uncharacterized bunyaviruses. Based on their ultrastructure, antigenic relationships and phylogenomic relationships, the five viruses are classified as members of the Orthobunyavirus genus. Three are viruses in the California encephalitis virus serogroup and are related to Trivittatus virus; the two others are most similar to the Mermet virus in the Simbu serogroup, and to the Tataguine virus, which is not currently assigned to a serogroup. Each of these five viruses was pathogenic to newborn mice, indicating their potential to cause illness in humans and other animals.

The degree of astrocyte activation in multiple system atrophy is inversely proportional to the distance to α-synuclein inclusions.

Multiple system atrophy (MSA) exhibits widespread astrogliosis together with α-synuclein (α-syn) glial cytoplasmic inclusions (GCIs) in mature oligodendrocytes. We quantified astrocyte activation by morphometric analysis of MSA cases, and investigated the correlation to GCI proximity. Using Imaris software, we obtained "skinned" three-dimensional models of GFAP-positive astrocytes in MSA and control tissue (n=75) from confocal z-stacks and measured the astrocyte process length and thickness and radial distance to the GCI. Astrocytes proximal to GCI-containing oligodendrocytes (r<25µm) had significantly (p, 0.05) longer and thicker processes characteristic of activation than distal astrocytes (r>25µm), with a reciprocal linear correlation (m, 90µm(2)) between mean process length and radial distance to the nearest GCI (R(2), 0.7). In primary cell culture studies, α-syn addition caused ERK-dependent activation of rat astrocytes and perinuclear α-syn inclusions in mature (MOSP-positive) rat oligodendrocytes. Activated astrocytes were also observed in close proximity to α-syn deposits in a unilateral rotenone-lesion mouse model. Moreover, unilateral injection of MSA tissue-derived α-syn into the mouse medial forebrain bundle resulted in widespread neuroinflammation in the α-syn-injected, but not sham-injected hemisphere. Taken together, our data suggests that the action of localized concentrations of α-syn may underlie both astrocyte and oligodendrocyte MSA pathological features.

Aromatherapy for the treatment of PONV in children: a pilot RCT.

BACKGROUND: Postoperative nausea and vomiting (PONV) is one of the most common postoperative complications of general anesthesia in pediatrics. Aromatherapy has been shown to be effective in treating PONV in adults. Given the encouraging results of the adult studies, we planned to determine feasibility of doing a large-scale study in the pediatric population. METHODS: Our group conducted a pilot randomized controlled trial examining the effect of aromatherapy on post-operative nausea and vomiting in patients 4-16 undergoing ambulatory surgery at a single center. Nausea was defined as a score of 4/10 on the Baxter Retching Faces Scale (BARF scale). A clinically significant reduction was defined as a two-point reduction in Nausea. Post operatively children were administered the BARF scale in 15 min internals until discharge home or until nausea score of 4/10 or greater. Children with nausea were randomized to saline placebo group or aromatherapy QueaseEase™ (Soothing Scents, Inc, Enterprise, AL: blend of ginger, lavender, mint and spearmint). Nausea scores were recorded post intervention. RESULTS: A total of 162 subjects were screened for inclusion in the study. Randomization occurred in 41 subjects of which 39 were included in the final analysis. For the primary outcome, 14/18 (78 %) of controls reached primary outcome compared to 19/21 (90 %) in the aromatherapy group (p = 0.39, Eta 0.175). Other outcomes included use of antiemetic in PACU (control 44 %, aromatherapy 52 % P = 0.75, Eta 0.08), emesis (Control 11 %, 9 % aromatherapy, P = 0.87, Eta = 0.03). There was a statistically significant difference in whether subjects continued to use the intervention (control 28 %, aromatherapy 66 %, p-value 0.048, Eta 0.33). CONCLUSION: Aromatherapy had a small non-significant effect size in treating postoperative nausea and vomiting compared with control. A large-scale randomized control trial would not be feasible at our institution and would be of doubtful utility. TRIAL REGISTRATION: ClinicalTrials.gov NCT02663154 .

Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition.

BACKGROUND: Due to the large amount of data produced by advanced microscopy, automated image analysis is crucial in modern biology. Most applications require reliable cell nuclei segmentation. However, in many biological specimens cell nuclei are densely packed and appear to touch one another in the images. Therefore, a major difficulty of three-dimensional cell nuclei segmentation is the decomposition of cell nuclei that apparently touch each other. Current methods are highly adapted to a certain biological specimen or a specific microscope. They do not ensure similarly accurate segmentation performance, i.e. their robustness for different datasets is not guaranteed. Hence, these methods require elaborate adjustments to each dataset. RESULTS: We present an advanced three-dimensional cell nuclei segmentation algorithm that is accurate and robust. Our approach combines local adaptive pre-processing with decomposition based on Lines-of-Sight (LoS) to separate apparently touching cell nuclei into approximately convex parts. We demonstrate the superior performance of our algorithm using data from different specimens recorded with different microscopes. The three-dimensional images were recorded with confocal and light sheet-based fluorescence microscopes. The specimens are an early mouse embryo and two different cellular spheroids. We compared the segmentation accuracy of our algorithm with ground truth data for the test images and results from state-of-the-art methods. The analysis shows that our method is accurate throughout all test datasets (mean F-measure: 91%) whereas the other methods each failed for at least one dataset (F-measure≤69%). Furthermore, nuclei volume measurements are improved for LoS decomposition. The state-of-the-art methods required laborious adjustments of parameter values to achieve these results. Our LoS algorithm did not require parameter value adjustments. The accurate performance was achieved with one fixed set of parameter values. CONCLUSION: We developed a novel and fully automated three-dimensional cell nuclei segmentation method incorporating LoS decomposition. LoS are easily accessible features that ensure correct splitting of apparently touching cell nuclei independent of their shape, size or intensity. Our method showed superior performance compared to state-of-the-art methods, performing accurately for a variety of test images. Hence, our LoS approach can be readily applied to quantitative evaluation in drug testing, developmental and cell biology.

Aspirin in the perioperative period: a review of the recent literature.

PURPOSE OF REVIEW: The indications for aspirin (ASA) for both primary and secondary prevention of thrombotic events continue to evolve. We review some of these indications and the recent literature regarding the perioperative administration of ASA. RECENT FINDINGS: ASA for primary prevention of cardiac ischemia, stroke, cancer, and death remains controversial. When used for primary prevention, ASA may be safely discontinued perioperatively. Patients with coronary or carotid artery stents should continue to receive ASA perioperatively. For patients with ischemic heart disease currently receiving ASA for secondary prevention of cardiac ischemia and stroke undergoing general surgery, orthopedic surgery, ophthalmological surgery, cardiovascular surgery, major vascular surgery, or a urological procedure, continuation of ASA is probably well tolerated, but further study is required. There is no indication to initiate ASA perioperatively in patients with stable ischemic heart disease as the risks outweigh the benefits. Until further data become available, decisions regarding the perioperative continuation of ASA should be made on a case-by-case risk-benefit analysis. SUMMARY: The continuation or discontinuation of ASA perioperatively remains a complicated issue. Further, well designed trials are needed for additional clarification.

Common genetic variants in the plasminogen activation pathway are not associated with multiple sclerosis.

Matrix metalloproteinase 9 (MMP9) is involved in multiple sclerosis (MS) aetiology. Previously, we identified differential gene expression of plasminogen activation cascade genes in MS patients. Based on our gene expression results, we wanted to identify whether polymorphisms in the genes associated with the plasminogen pathway could predict MS risk. We genotyped 1153 trio families, 727 MS cases and 604 healthy controls for 17 polymorphisms in MMP9, plasminogen activator urokinase (PLAU), PLAU receptor (PLAUR) and serpin peptidase inhibitor/clade 2/member B2 (SERPINB2) genes. No associations were found between the 17 polymorphisms and MS. Also, gene expression levels were analysed according to genotype: no associations were observed. In conclusion despite the consistent evidence for the role of MMP9 and the plasminogen activation cascade in MS, we found no associations between genotype nor gene expression. This suggested there are other potentially modifiable factors influencing gene expression in MS.

Contribution of Trunk Rotation and Abdominal Muscles to Sprint Kayak Performance.

Over the past two decades the importance of trunk contribution to sporting performance has been highlighted through the expanse of literature concerning core stability and strength. However, the role of trunk motion and the abdominal muscles are yet to be established during sprint kayak performance. The purpose of this study was to determine the associations among trunk rotation, kayak velocity, and abdominal muscle activity during on-water sprint kayaking. Eight international paddlers completed five 150 m sprint trials. During each trial peak muscle activation (peak root-mean-squared electromyogram) of the latissimus dorsi, rectus abdominus, external obliques and rectus femoris for ipsilateral (stroke side) and contralateral (opposite side) were recorded as the paddler passed through a 5-m calibrated volume, in conjunction with upper and lower trunk rotation and kayak velocity. Results indicated a significant strong negative relationship between lower trunk rotation and peak velocity (r = -0.684, p < 0.05). Furthermore, a significant strong positive relationship (p < 0.05) with mean velocity was identified for the contralateral rectus abdominus and multiple significant associations between the rectus femoris, rectus abdominus and external obliques during the paddle stroke. Findings indicate that limiting the rotation of the lower trunk will increase both the peak and the mean velocity, with the rectus abdominus, external oblique and rectus femoris combining to assist in this process. Training should therefore focus on developing the strength of these muscle groups to enhance performance.

Discriminative Ability of Dye Injected Into a Meat Model to Determine Accuracy of Ultrasound-Guided Injection.

INTRODUCTION: The utility of using meat models for ultrasound-guided regional anesthesia simulation training has been well established. Feedback is considered the most important element of successful simulation-based education, and simulation offers an opportunity for evaluation. The objective of this study was to establish the discriminative ability of dye injected into a meat model to determine whether injectate is properly placed in the perineural (PN) space, thus providing an additional tool for learner feedback and evaluation. METHODS: Meat models containing a beef tendon (simulating a nerve) were injected with dye in one of 3 locations: PN, intraneural, and intramuscular. Blinded assessors then independently interpreted the dye staining on the models, marked the interpreted injection location, ease of interpretation, and whether staining was present on the beef tendon. RESULTS: Thirty meat models were injected with dye and independently assessed. Determining the location of injection was deemed to be easy or very easy in 72% of the models. Assessors correctly identified PN, intraneural, and intramuscular injections 100%, 95%, and 85% of the time, respectively. Assessor agreement was 87%. CONCLUSIONS: The location of dye injected into a meat model, simulating a peripheral nerve blockade, can be accurately and reliably scored to provide feedback to learners. This technique offers a novel means of providing feedback to trainees and assessing block success in ultrasound-guided regional anesthesia simulation.

Long-term outcomes after terminalization for acute fingertip injuries.

The primary aim of this study was to report outcomes after fingertip terminalization in 90 patients over a 19-year period. We report excellent functional outcomes and satisfaction, but a 33% incidence of neuropathic pain.