Mutations in potassium channel Kir2.6 cause susceptibility to thyrotoxic hypokalemic periodic paralysis.

Thyrotoxic hypokalemic periodic paralysis (TPP) is characterized by acute attacks of weakness, hypokalemia, and thyrotoxicosis of various etiologies. These transient attacks resemble those of patients with familial hypokalemic periodic paralysis (hypoKPP) and resolve with treatment of the underlying hyperthyroidism. Because of the phenotypic similarity of these conditions, we hypothesized that TPP might also be a channelopathy. While sequencing candidate genes, we identified a previously unreported gene (not present in human sequence databases) that encodes an inwardly rectifying potassium (Kir) channel, Kir2.6. This channel, nearly identical to Kir2.2, is expressed in skeletal muscle and is transcriptionally regulated by thyroid hormone. Expression of Kir2.6 in mammalian cells revealed normal Kir currents in whole-cell and single-channel recordings. Kir2.6 mutations were present in up to 33% of the unrelated TPP patients in our collection. Some of these mutations clearly alter a variety of Kir2.6 properties, all altering muscle membrane excitability leading to paralysis.

Foxd3 controls heterochromatin-mediated repression of repeat elements and 2-cell state transcription.

Repeat element transcription plays a vital role in early embryonic development. The expression of repeats such as MERVL characterises mouse embryos at the 2-cell stage and defines a 2-cell-like cell (2CLC) population in a mouse embryonic stem cell culture. Repeat element sequences contain binding sites for numerous transcription factors. We identify the forkhead domain transcription factor FOXD3 as a regulator of major satellite repeats and MERVL transcription in mouse embryonic stem cells. FOXD3 binds to and recruits the histone methyltransferase SUV39H1 to MERVL and major satellite repeats, consequentially repressing the transcription of these repeats by the establishment of the H3K9me3 heterochromatin modification. Notably, depletion of FOXD3 leads to the de-repression of MERVL and major satellite repeats as well as a subset of genes expressed in the 2-cell state, shifting the balance between the stem cell and 2-cell-like population in culture. Thus, FOXD3 acts as a negative regulator of repeat transcription, ascribing a novel function to this transcription factor.

Fact or fiction: the "5 mm Rule" in greater tuberosity fractures of the proximal humerus.

PURPOSE: The purposes of this study were 1) to assess the outcome of nonoperative management of GT fractures with > 5 mm of displacement and 2) to assess whether there is a correlation between degree of displacement and outcome. METHODS: This study was a retrospective review of consecutive low-energy GT fractures from 2011 to 2020. Radiographs from all visits were reviewed. The direction of maximal displacement was assessed. Subjects were stratified based on the amount of maximal displacement: Group 1: 0-5 mm, Group 2: 5-10 mm, Group 3: > 10 mm. Range of motion (ROM) at the time of final follow-up was assessed. The presence of persistent shoulder pain after healing was noted, as well as whether supplemental subacromial corticosteroid injection was provided as part of long-term treatment. RESULTS: A cohort of 93 fractures comprised the study group. Mean age was 62 years. Mean follow-up was 20 months. All fractures went on to union. Mean displacement was 6.2 mm. There were 43 patients in Group 1, 43 in Group 2, and 7 in Group 3. Maximal displacement was most commonly inferolateral or lateral, accounting for a combined 77% of all patients. There was no difference in final ROM between displacement groups, with at least 155 degrees of forward elevation and 45 degrees of ER in all three groups. There was no difference between Group 1 and Groups 2/3 in frequency of persistent pain or likelihood of receiving a steroid injection. CONCLUSION: Our findings do not support a discrete 5 mm displacement threshold for surgical repair of isolated greater tuberosity fractures.

Specific Factors Affecting Operating Room Efficiency: An Analysis of Case Time Estimates.

PURPOSE: Operating room (OR) efficiency has an impact on surgeon productivity and patient experience. Accuracy of case duration estimation is important to optimize OR efficiency. The purpose of this study was to identify factors associated with inaccurate case time estimates in outpatient hand surgery. A better understanding of these findings may help to improve OR efficiency and scheduling. METHODS: All outpatient hand surgical cases from 2018 to 2019 were reviewed. Poorly-estimated cases (i.e., poor scheduling accuracy) were defined as those cases where the actual operative time differed from the predicted time by >50% (either quicker by >50% or slower by >50% than the predicted time). The percentages of poorly-estimated cases were analyzed, categorized, and compared by surgeon, procedure type, and scheduled case length. RESULTS: A total of 6,620 cases were identified. Of 1,107 (16.7%) cases with poorly estimated case durations, 75.2% were underestimated. There was no difference in the likelihood of poor estimation related to start time. Well-estimated cases tended to have longer scheduled case duration, but shorter realized case duration and surgical time. Our systems analysis identified specific surgeons and procedures as predictable outliers. Cases scheduled for 15-30 minutes frequently were inaccurate, whereas cases scheduled for 30-45 and 106-120 minutes had accurate estimates. CONCLUSIONS: The accuracy of case time estimations in a standard outpatient hand surgery practice is highly variable. Nearly one-fifth of outpatient hand surgery case durations are poorly estimated, and inaccurate case time estimation can be predicted based on surgeon, procedure type, and case time. CLINICAL RELEVANCE: Maximizing OR efficiency should be a priority for surgeons and hospital systems. With multiple surgeries done per day, the efficiency of the OR has an impact on surgeon productivity and patient experience.

Epigenetic alterations in longevity regulators, reduced life span, and exacerbated aging-related pathology in old father offspring mice.

Advanced age is not only a major risk factor for a range of disorders within an aging individual but may also enhance susceptibility for disease in the next generation. In humans, advanced paternal age has been associated with increased risk for a number of diseases. Experiments in rodent models have provided initial evidence that paternal age can influence behavioral traits in offspring animals, but the overall scope and extent of paternal age effects on health and disease across the life span remain underexplored. Here, we report that old father offspring mice showed a reduced life span and an exacerbated development of aging traits compared with young father offspring mice. Genome-wide epigenetic analyses of sperm from aging males and old father offspring tissue identified differentially methylated promoters, enriched for genes involved in the regulation of evolutionarily conserved longevity pathways. Gene expression analyses, biochemical experiments, and functional studies revealed evidence for an overactive mTORC1 signaling pathway in old father offspring mice. Pharmacological mTOR inhibition during the course of normal aging ameliorated many of the aging traits that were exacerbated in old father offspring mice. These findings raise the possibility that inherited alterations in longevity pathways contribute to intergenerational effects of aging in old father offspring mice.

Regional anesthesia for clavicle fracture surgery is safe and effective.

BACKGROUND: Historically, clavicle fracture repairs have been performed with patients under general anesthesia. However, in the past few years, the combination of an interscalene brachial plexus block and a modified superficial cervical plexus block has been described to provide adequate anesthesia for clavicle fracture surgery, with the added benefit of postoperative analgesia. In March 2013, members of our anesthesiology department began using this block with sedation for a subset of patients undergoing clavicle fracture fixation. METHODS: This study was a retrospective review of patients who underwent clavicle fracture repair at a single institution between June 2014 and November 2017. The decision on the type of anesthesia (regional vs. general) was made jointly by the patient, anesthesiologist, and surgeon. Demographic data, relevant perioperative times, and intraoperative pain medication consumption were recorded, and comparisons of these variables were made between the regional and general anesthesia groups. RESULTS: A total of 110 patients with 110 fractures were included. Of these patients, 52 received only regional anesthesia with the combined block whereas 58 received general anesthesia with an interscalene brachial plexus block. No major anesthetic-related complications were noted in any patients, and there were no cases in which regional anesthesia had to be converted to general anesthesia because of block failure. The anesthesia start time was significantly longer in the general anesthesia group (29 minutes vs. 20 minutes, P = .022), as was the total case time (164 minutes vs. 131 minutes, P < .001). Patients in the general anesthesia group required significantly more intraoperative fentanyl to be administered (207 µg vs. 141 µg, P = .002). CONCLUSION: Regional anesthesia using a combined brachial plexus and modified superficial cervical plexus block is a reliable, efficacious technique. The combined block appears to be a reasonable alternative to general anesthesia with an interscalene brachial plexus block, and it may have benefits regarding the anesthesia start time and total case time.

snakePipes: facilitating flexible, scalable and integrative epigenomic analysis.

SUMMARY: Due to the rapidly increasing scale and diversity of epigenomic data, modular and scalable analysis workflows are of wide interest. Here we present snakePipes, a workflow package for processing and downstream analysis of data from common epigenomic assays: ChIP-seq, RNA-seq, Bisulfite-seq, ATAC-seq, Hi-C and single-cell RNA-seq. snakePipes enables users to assemble variants of each workflow and to easily install and upgrade the underlying tools, via its simple command-line wrappers and yaml files. AVAILABILITY AND IMPLEMENTATION: snakePipes can be installed via conda: `conda install -c mpi-ie -c bioconda -c conda-forge snakePipes'. Source code (https://github.com/maxplanck-ie/snakepipes) and documentation (https://snakepipes.readthedocs.io/en/latest/) are available online. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

deepTools2: a next generation web server for deep-sequencing data analysis.

We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described our deepTools Galaxy server in 2014, we have implemented new solutions for many requests from the community and our users. Here, we introduce significant enhancements and new tools to further improve data visualization and interpretation. deepTools continue to be open to all users and freely available as a web service at deeptools.ie-freiburg.mpg.de The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. A public and documented API for access to deepTools functionality is also available.

Limited effects of an eIF2αS51A allele on neurological impairments in the 5xFAD mouse model of Alzheimer's disease.

Alzheimer's disease (AD) has been associated with increased phosphorylation of the translation initiation factor 2α (eIF2α) at serine 51. Increased phosphorylation of eIF2α alters translational control and may thereby have adverse effects on synaptic plasticity, learning, and memory. To analyze if increased levels of p-eIF2α indeed promote AD-related neurocognitive impairments, we crossed 5xFAD transgenic mice with an eIF2α(S51A) knock-in line that expresses the nonphosphorylatable eIF2α variant eIF2α(S51A). Behavioral assessment of the resulting mice revealed motor and cognitive deficits in 5xFAD mice that were, with the possible exception of locomotor hyperactivity, not restored by the eIF2α(S51A) allele. Telemetric intracranial EEG recordings revealed no measurable effects of the eIF2α(S51A) allele on 5xFAD-associated epileptic activity. Microarray-based transcriptome analyses showed clear transcriptional alterations in 5xFAD hippocampus that were not corrected by the eIF2α(S51A) allele. In contrast to prior studies, our immunoblot analyses did not reveal increased levels of p-eIF2α in the hippocampus of 5xFAD mice, suggesting that elevated p-eIF2α levels are not a universal feature of AD models. Collectively, our data indicate that 5xFAD-related pathologies do not necessarily require hyperphosphorylation of eIF2α to emerge; they also show that heterozygosity for the nonphosphorylatable eIF2α(S51A) allele has limited effects on 5xFAD-related disease manifestations.

Blood transfusion in primary total shoulder arthroplasty: incidence, trends, and risk factors in the United States from 2000 to 2009.

BACKGROUND: Total shoulder arthroplasty (TSA) may be associated with substantial blood loss, and some patients require perioperative blood transfusion. Possible blood transfusion methods include predonated autologous blood transfusion, perioperative autologous blood transfusion, and allogeneic blood transfusion (ALBT). The purposes of the present study were to assess the incidence and recent trends over time of blood transfusion in TSA and analyze patient and hospital characteristics that affect the risk of ALBT. METHODS: This study used national hospital discharge data from the National Inpatient Sample between 2000 and 2009. The data were used to generate the overall blood transfusion rate, and linear regression was used to assess trends in transfusion patterns over time. Logistic regression analysis was performed to analyze which patient and hospital characteristics independently influence the likelihood that a given patient undergoes ALBT. RESULTS: The overall blood transfusion rate (ie, the proportion of patients who received at least 1 transfusion of any kind) was 6.7%. This rate increased over time, from 4.9% in 2000 to 7.1% in 2009 (P < .001). Risk factors associated with ALBT included age, gender, race, insurance status, hospital region, and hospital annual caseload. CONCLUSIONS: The increase in overall blood transfusion rate in TSA found in the present study may be related to factors specific to TSA, such as the introduction of reverse total shoulder arthroplasty during the study period. A variety of patient and hospital characteristics contribute to the risk of undergoing ALBT.

Bison: bisulfite alignment on nodes of a cluster.

BACKGROUND: DNA methylation changes are associated with a wide array of biological processes. Bisulfite conversion of DNA followed by high-throughput sequencing is increasingly being used to assess genome-wide methylation at single-base resolution. The relative slowness of most commonly used aligners for processing such data introduces an unnecessarily long delay between receipt of raw data and statistical analysis. While this process can be sped-up by using computer clusters, current tools are not designed with them in mind and end-users must create such implementations themselves. RESULTS: Here, we present a novel BS-seq aligner, Bison, which exploits multiple nodes of a computer cluster to speed up this process and also has increased accuracy. Bison is accompanied by a variety of helper programs and scripts to ease, as much as possible, the process of quality control and preparing results for statistical analysis by a variety of popular R packages. Bison is also accompanied by bison_herd, a variant of Bison with the same output but that can scale to a semi-arbitrary number of nodes, with concomitant increased demands on the underlying message passing interface implementation. CONCLUSIONS: Bison is a new bisulfite-converted short-read aligner providing end users easier scalability for performance gains, more accurate alignments, and a convenient pathway for quality controlling alignments and converting methylation calls into a form appropriate for statistical analysis. Bison and the more scalable bison_herd are natively able to utilize multiple nodes of a computer cluster simultaneously and serve to simplify to the process of creating analysis pipelines.

Adult-onset fluoxetine treatment does not improve behavioral impairments and may have adverse effects on the Ts65Dn mouse model of Down syndrome.

Down syndrome is caused by triplication of chromosome 21 and is associated with neurocognitive phenotypes ranging from severe intellectual disability to various patterns of more selective neuropsychological deficits, including memory impairments. In the Ts65Dn mouse model of Down syndrome, excessive GABAergic neurotransmission results in local over-inhibition of hippocampal circuits, which dampens hippocampal synaptic plasticity and contributes to cognitive impairments. Treatments with several GABA(A) receptor antagonists result in increased plasticity and improved memory deficits in Ts65Dn mice. These GABA(A) receptor antagonists are, however, not suitable for clinical applications. The selective serotonin reuptake inhibitor fluoxetine, in contrast, is a widely prescribed antidepressant that can also enhance plasticity in the adult rodent brain by lowering GABAergic inhibition. For these reasons, we wondered if an adult-onset 4-week oral fluoxetine treatment restores spatial learning and memory impairments in Ts65Dn mice. Fluoxetine did not measurably improve behavioral impairments of Ts65Dn mice. On the contrary, we observed seizures and mortality in fluoxetine-treated Ts65Dn mice, raising the possibility of a drug × genotype interaction with respect to these adverse treatment outcomes. Future studies should re-address this in larger animal cohorts and determine if fluoxetine treatment is associated with adverse treatment effects in individuals with Down syndrome.

Targeted Muscle Reinnervation (TMR) and Other Considerations in Upper Extremity Amputation.

Targeted muscle reinnervation (TMR) is a procedure in which amputated nerves are transferred to motor branches of functionally expendable muscles, which can then serve as "biological amplifiers" of neurologic information. It is a technique that was developed with the primary intent of improving myoelectric prosthesis control in high level upper extremity amputees. Over time, TMR has been shown to confer significant benefits in terms of both residual and phantom limb pain and as such has become a powerful tool in neuroma management in amputees and non-amputees. This review first discusses general principles of amputation management in the upper extremity, including the different types of prosthetics that are available for these patients. The history, rationale, and evolution of TMR will then be outlined, followed by several relevant surgical principles. Finally, the current evidence for and against TMR will be reviewed. Robust data on the functional benefits are still needed, and future studies will continue to clarify its role in both upper and lower extremity amputees.

Proximal Hamate Autograft for Proximal Scaphoid Pole Reconstruction A Case Report.

Avascular necrosis (AVN) and subsequent fragmentation of the proximal pole of the scaphoid following fracture is a challenging problem to treat. Multiple treatment methods have been described, although they have been shown to have varying degrees of success and are associated with donor site morbidities. This case report demonstrates a technique and the excellent radiographic and clinical outcome at 8 months postoperatively for reconstruction of the proximal pole of the scaphoid using an ipsilateral proximal pole of the hamate autograft.

Complete loss of H3K9 methylation dissolves mouse heterochromatin organization.

Histone H3 lysine 9 (H3K9) methylation is a central epigenetic modification that defines heterochromatin from unicellular to multicellular organisms. In mammalian cells, H3K9 methylation can be catalyzed by at least six distinct SET domain enzymes: Suv39h1/Suv39h2, Eset1/Eset2 and G9a/Glp. We used mouse embryonic fibroblasts (MEFs) with a conditional mutation for Eset1 and introduced progressive deletions for the other SET domain genes by CRISPR/Cas9 technology. Compound mutant MEFs for all six SET domain lysine methyltransferase (KMT) genes lack all H3K9 methylation states, derepress nearly all families of repeat elements and display genomic instabilities. Strikingly, the 6KO H3K9 KMT MEF cells no longer maintain heterochromatin organization and have lost electron-dense heterochromatin. This is a compelling analysis of H3K9 methylation-deficient mammalian chromatin and reveals a definitive function for H3K9 methylation in protecting heterochromatin organization and genome integrity.

Clinical photographs in the assessment of adult spinal deformity: a comparison to radiographic parameters.

OBJECTIVE: The goal of this study was to reliably predict sagittal and coronal spinal alignment with clinical photographs by using markers placed at easily localized anatomical landmarks. METHODS: A consecutive series of patients with adult spinal deformity were enrolled from a single center. Full-length standing radiographs were obtained at the baseline visit. Clinical photographs were taken with reflective markers placed overlying C2, S1, the greater trochanter, and each posterior-superior iliac spine. Sagittal radiographic parameters were C2 pelvic angle (CPA), T1 pelvic angle (TPA), and pelvic tilt. Coronal radiographic parameters were pelvic obliquity and T1 coronal tilt. Linear regressions were performed to evaluate the relationship between radiographic parameters and their photographic "equivalents." The data were reanalyzed after stratifying the cohort into low-body mass index (BMI) (< 30) and high-BMI (≥ 30) groups. Interobserver and intraobserver reliability was assessed for clinical measures via intraclass correlation coefficients (ICCs). RESULTS: A total of 38 patients were enrolled (mean age 61 years, mean BMI 27.4 kg/m2, 63% female). All regression models were significant, but sagittal parameters were more closely correlated to photographic parameters than coronal measurements. TPA and CPA had the strongest associations with their photographic equivalents (both r2 = 0.59, p < 0.001). Radiographic and clinical parameters tended to be more strongly correlated in the low-BMI group. Clinical measures of TPA and CPA had high intraobserver reliability (all ICC > 0.99, p < 0.001) and interobserver reliability (both ICC > 0.99, p < 0.001). CONCLUSIONS: The photographic measures of spinal deformity developed in this study were highly correlated with their radiographic counterparts and had high inter- and intraobserver reliability. Clinical photography can not only reduce radiation exposure in patients with adult spinal deformity, but also be used to assess deformity when full-spine radiographs are unavailable.

Surgical Site Infection After Open Upper Extremity Fracture and the Effect of Urgent Operative Intervention.

OBJECTIVES: To identify which factors are predictive of surgical site infection in upper extremity fractures, and to assess whether the timing of operative debridement influences infection risk. DESIGN: Retrospective database review. SETTING: Hospitals participating in the American College of Surgeons National Surgical Quality Improvement Program (NSQIP) database. PATIENTS: Patients in the NSQIP database with fractures involving the upper extremity. INTERVENTION: Surgical management of upper extremity fracture, including operative debridement for open injuries. MAIN OUTCOME MEASUREMENTS: Surgical site infection, including both superficial and deep infections. RESULTS: A total of 22,578 patients were identified, including 1298 patients with open injuries (5.7% of total). The overall wound infection rate was 0.79%. Patients with open injuries were found to have a higher incidence of infection compared with those with closed injuries (1.7% vs. 0.7%, P < 0.001). Independent risk factors for 30-day infection included open fracture diagnosis, obesity, smoking, and American Society of Anesthesiolgists class >2 (all P < 0.05). Of patients with open fractures, 79.7% were taken expediently to the operating room. The rate of infection did not differ based on whether surgery was performed expediently or not (1.8% vs. 1.1%, P = 0.431). CONCLUSIONS: Based on an analysis of the NSQIP database, the overall risk of surgical site infection following intervention for open or closed upper extremity fractures remains low. Risk factors for infection include open injury, obesity, and cigarette smoking. There was no difference in the infection rate based on the urgency of operative debridement. LEVEL OF EVIDENCE: Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.

Surgical Management of Scaphotrapeziotrapezoid Arthritis.

Scaphotrapeziotrapezoid (STT) arthritis occurs commonly with basal joint arthritis, but can also occur in isolation or in conjunction with other patterns of wrist arthritis, such as scapholunate advanced collapse. Surgical options depend on the specific clinical scenario encountered. Isolated STT arthritis was classically managed with arthrodesis, but is now often addressed with distal scaphoid resection (open or arthroscopic), trapeziectomy (partial or complete) and partial trapezoid resection, or implant arthroplasty. Development of postoperative dorsal intercalary segment instability is a notable concern with any of these techniques. STT arthritis in conjunction with basal joint arthritis can be managed effectively with trapeziectomy and either partial trapezoid excision or distal scaphoid excision. STT arthritis with scapholunate advanced collapse is uncommon, but can be managed with proximal row carpectomy or scaphoidectomy and four-corner fusion. If basal joint arthritis is also present, trapeziectomy can additionally be performed, but grip strength is likely to be substantially diminished.

RELACS nuclei barcoding enables high-throughput ChIP-seq.

Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is an invaluable tool for mapping chromatin-associated proteins. Current barcoding strategies aim to improve assay throughput and scalability but intense sample handling and lack of standardization over cell types, cell numbers and epitopes hinder wide-spread use in the field. Here, we present a barcoding method to enable high-throughput ChIP-seq using common molecular biology techniques. The method, called RELACS (restriction enzyme-based labeling of chromatin in situ) relies on standardized nuclei extraction from any source and employs chromatin cutting and barcoding within intact nuclei. Barcoded nuclei are pooled and processed within the same ChIP reaction, for maximal comparability and workload reduction. The innovative barcoding concept is particularly user-friendly and suitable for implementation to standardized large-scale clinical studies and scarce samples. Aiming to maximize universality and scalability, RELACS can generate ChIP-seq libraries for transcription factors and histone modifications from hundreds of samples within three days.

Community-Driven Data Analysis Training for Biology.

The primary problem with the explosion of biomedical datasets is not the data, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences. This project is accessible at https://training.galaxyproject.org.