ResearchPad - technical-note https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[ <b>CSA:</b> A high-throughput <b>c</b>hromosome-<b>s</b>cale <b>a</b>ssembly pipeline for vertebrate genomes]]> https://www.researchpad.co/article/elastic_article_12663 Easy-to-use and fast bioinformatics pipelines for long-read assembly that go beyond the contig level to generate highly continuous chromosome-scale genomes from raw data remain scarce.ResultChromosome-Scale Assembler (CSA) is a novel computationally highly efficient bioinformatics pipeline that fills this gap. CSA integrates information from scaffolded assemblies (e.g., Hi-C or 10X Genomics) or even from diverged reference genomes into the assembly process. As CSA performs automated assembly of chromosome-sized scaffolds, we benchmark its performance against state-of-the-art reference genomes, i.e., conventionally built in a laborious fashion using multiple separate assembly tools and manual curation. CSA increases the contig lengths using scaffolding, local re-assembly, and gap closing. On certain datasets, initial contig N50 may be increased up to 4.5-fold. For smaller vertebrate genomes, chromosome-scale assemblies can be achieved within 12 h using low-cost, high-end desktop computers. Mammalian genomes can be processed within 16 h on compute-servers. Using diverged reference genomes for fish, birds, and mammals, we demonstrate that CSA calculates chromosome-scale assemblies from long-read data and genome comparisons alone. Even contig-level draft assemblies of diverged genomes are helpful for reconstructing chromosome-scale sequences. CSA is also capable of assembling ultra-long reads.ConclusionsCSA can speed up and simplify chromosome-level assembly and significantly lower costs of large-scale family-level vertebrate genome projects. ]]> <![CDATA[Evaluation of Oxytetracycline Metabolites Cross-Reactivity with Oxytetracycline Enzyme-Linked Immunosorbent Assay (ELISA)]]> https://www.researchpad.co/article/elastic_article_11729 Antibiotics have been successfully used for the control of several plant diseases for many years. Recently, streptomycin and oxytetracycline have been approved for the treatment of Huanglongbing (HLB) in Florida. The enzyme-linked immunosorbent assay (ELISA) is the most commonly used assay for the detection of these antibiotics because it is quick, simple, and can be used to analyze many samples at the same time. However, ELISA can react with the metabolites of the parent compound and its structurally related compounds. In this study, we investigated the cross-reactivity of the oxytetracycline ACCEL ELISA kitTM with three of oxytetracycline metabolites (4-epi-oxytetracycline, α-apo-oxytetracycline, and β-apo-oxytetracycline). The α-apo-oxytetracycline and β-apo-oxytetracycline metabolite did not show any cross-reactivity in the linear range (1.5–50 ng mL−1) of the assay. Whereas 4-epi-oxytetracycline showed high cross-reactivity, and its response was similar to oxytetracycline. Our results indicated that the oxytetracycline ELISA kits estimate the level of oxytetracycline as well as its main metabolite, 4-epi-oxytetracycline.

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<![CDATA[Opportunities, Challenges and Directions in Science and Technology for Tackling COVID-19]]> https://www.researchpad.co/article/elastic_article_10718 The ongoing global crisis due to Coronavirus disease-2019 (COVID-19) pandemic has caused an enormous socioeconomic burden. A novel coronavirus causing severe acute respiratory syndrome (SARS-CoV-2) that evolved from a virus infecting bats is responsible for COVID-19, first reported in the Chinese city of Wuhan. In the absence of any specific scientifically proven and clinically tested drug or vaccine against SARS-CoV-2, the virus is wreaking havoc across the world, claiming more than 2,50,000 lives in less than 5 months, and posed a global health emergency. The scientific community is relentlessly working on the design and testing of vaccines and antiviral drugs against the novel coronavirus, several of which have reached advanced stages of testing and are undergoing clinical trials. Here we discuss the recent advances and developments in understanding the etiology and epidemiology of the COVID-19 pandemic, the factors influencing the disease transmission, and the countermeasures adopted to combat and stop further spread of the disease.

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<![CDATA[parSMURF, a high-performance computing tool for the genome-wide detection of pathogenic variants]]> https://www.researchpad.co/article/elastic_article_10165 Several prediction problems in computational biology and genomic medicine are characterized by both big data as well as a high imbalance between examples to be learned, whereby positive examples can represent a tiny minority with respect to negative examples. For instance, deleterious or pathogenic variants are overwhelmed by the sea of neutral variants in the non-coding regions of the genome: thus, the prediction of deleterious variants is a challenging, highly imbalanced classification problem, and classical prediction tools fail to detect the rare pathogenic examples among the huge amount of neutral variants or undergo severe restrictions in managing big genomic data.ResultsTo overcome these limitations we propose parSMURF, a method that adopts a hyper-ensemble approach and oversampling and undersampling techniques to deal with imbalanced data, and parallel computational techniques to both manage big genomic data and substantially speed up the computation. The synergy between Bayesian optimization techniques and the parallel nature of parSMURF enables efficient and user-friendly automatic tuning of the hyper-parameters of the algorithm, and allows specific learning problems in genomic medicine to be easily fit. Moreover, by using MPI parallel and machine learning ensemble techniques, parSMURF can manage big data by partitioning them across the nodes of a high-performance computing cluster. Results with synthetic data and with single-nucleotide variants associated with Mendelian diseases and with genome-wide association study hits in the non-coding regions of the human genome, involhing millions of examples, show that parSMURF achieves state-of-the-art results and an 80-fold speed-up with respect to the sequential version.ConclusionsparSMURF is a parallel machine learning tool that can be trained to learn different genomic problems, and its multiple levels of parallelization and high scalability allow us to efficiently fit problems characterized by big and imbalanced genomic data. The C++ OpenMP multi-core version tailored to a single workstation and the C++ MPI/OpenMP hybrid multi-core and multi-node parSMURF version tailored to a High Performance Computing cluster are both available at https://github.com/AnacletoLAB/parSMURF. ]]> <![CDATA[Functional Assessment of Lumbar Nerve Roots Using Coronal-plane Single-shot Turbo Spin-echo Diffusion Tensor Imaging]]> https://www.researchpad.co/article/elastic_article_8390 We investigated the usefulness of diffusion tensor imaging using single-shot turbo spin-echo sequence (TSE–DTI) in detecting the responsible nerve root by multipoint measurements of fractional anisotropy (FA) values. Five patients with bilateral lumbar spinal stenosis showing unilateral neurological symptoms were examined using TSE–DTI. In the spinal canal, FA values in the symptomatic side were lower than those in the asymptomatic side. TSE–DTI using multipoint measurements of FA values can differentiate the responsible lumbar nerve root.

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<![CDATA[Comparison of Silent Navigator Waveform Generation Methods]]> https://www.researchpad.co/article/elastic_article_8379 The silent navigator technique utilizes a non-selective excitation and an appropriate respiratory waveform generation method is necessary for an accurate motion detection. We compared three methods for silent navigator waveform generation. The profile generation method with coil selection (prof-selection) resulted in a high cross correlation with bellows signals and a large respiration amplitude. The prof-selection method should be used for silent navigator waveform generation.

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<![CDATA[Transoral Mandibular Tongue-Splitting Approach in Upper Cervical Epidural Abscess: A Case Report and Review of the Literature]]> https://www.researchpad.co/article/elastic_article_7222 The transoral mandibular tongue-splitting approach is typically performed for the treatment of upper cervical tumor and instability but has not been performed for the treatment of upper cervical epidural abscess (UCEA). We report the first case of UCEA successfully treated with a transoral mandibular tongue-splitting approach. Technical Note A 62-year-old man who had medical histories of tracheotomy with intubation and dermatopathy due to radiation therapy for the treatment of nasopharyngeal carcinoma presented with neck pain and limb weakness. The imaging examination revealed bone erosion of C2-C4 vertebrae and abscess at the level of C2-C4, supporting a diagnosis of UCEA. The transcervical approach could not be used for treatment; therefore, the transoral mandibular tongue-splitting approach was used successfully to perform decompression, debridement, and iliac bone grafting. Subsequently, we reviewed the literature pertaining to the use of the transoral mandibular tongue-splitting approach. The approach can be invasive and cause some complications. However, no fatal complications have been reported, and all patients demonstrated a favorable neurological outcome with reduced neurological deficits. Conclusions This case and subsequent literature review suggest that the transoral mandibular tongue-splitting approach may be effective for the improvement of neurological outcomes without fatal complications in patients with UCEA. There may be an increasing number of patients with UCEA requiring the transoral mandibular tongue-splitting approach due to the increasing prevalence of immunocompromized status and the aging population. ]]> <![CDATA[Preliminary design of an innovative, simple, and easy-to-build portable ventilator for COVID-19 patients]]> https://www.researchpad.co/article/N6f644e2e-a85d-4c55-b627-509422858257 This technical note describes the preliminary design of a simple, easy-to-use, and easy-to-build ventilator with an unique design that can be used for COVID-19 patients in emergencies and to prevent massive loss of life in resource-poor environments. It can be assembled by a nonexpert as a homemade solution, without the need for specific equipment or technology. The proposed system is novel, inexpensive, has a reduced reliance on external power, and is very easy to maintain.

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<![CDATA[Minimally Invasive Lumbar Decompression and Removal of Symptomatic Heterotopic Bone Formation After Spinal Fusion with Recombinant Human Bone Morphogenetic Protein-2]]> https://www.researchpad.co/article/Ndf0d0ed5-7729-487f-b66f-310ddbee305f We present a case of symptomatic heterotopic bone formation following revision of posterolateral lumbar fusion/instrumentation and “off-label” use of recombinant human bone morphogenetic protein-2, treated successfully with the use of a minimally invasive tubular approach.

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<![CDATA[MaRe: Processing Big Data with application containers on Apache Spark]]> https://www.researchpad.co/article/N884e0be6-e848-49ac-9ab6-ece99e8c3667 Life science is increasingly driven by Big Data analytics, and the MapReduce programming model has been proven successful for data-intensive analyses. However, current MapReduce frameworks offer poor support for reusing existing processing tools in bioinformatics pipelines. Furthermore, these frameworks do not have native support for application containers, which are becoming popular in scientific data processing.ResultsHere we present MaRe, an open source programming library that introduces support for Docker containers in Apache Spark. Apache Spark and Docker are the MapReduce framework and container engine that have collected the largest open source community; thus, MaRe provides interoperability with the cutting-edge software ecosystem. We demonstrate MaRe on 2 data-intensive applications in life science, showing ease of use and scalability.ConclusionsMaRe enables scalable data-intensive processing in life science with Apache Spark and application containers. When compared with current best practices, which involve the use of workflow systems, MaRe has the advantage of providing data locality, ingestion from heterogeneous storage systems, and interactive processing. MaRe is generally applicable and available as open source software. ]]> <![CDATA[Open Acromioclavicular Joint Reconstruction With Semitendinosus Allograft Utilizing the Cerclage Technique]]> https://www.researchpad.co/article/N72729eb0-8130-4351-99e3-2b4f926f2c87 Acromioclavicular (AC) joint injuries most commonly occur in young males after a direct injury at the acromion. General consensus stresses nonoperative treatment for type I and II injuries and surgical treatment for types IV through VI, whereas management of type III injuries is more controversial. If surgery is indicated, there are multiple techniques including hook plate, screw fixation, coracoclavicular fixation, and anatomic and nonanatomic reconstruction. The overall complication rate is high (14%), regardless of technique. In this Technical Note, we outline a technique for open repair of a chronic AC joint separation using a semitendinosus allograft using the cerclage for enhanced fixation.

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<![CDATA[Nanoscopic Single-Incision Anterior Labrum Repair]]> https://www.researchpad.co/article/N21d01ce9-046d-42b4-8b35-bfde335c9fe5

Arthroscopy frequently has been used to treat a variety of shoulder conditions, including anterior labrum tears. Anterior labrum repair techniques have progressed from multiple incision techniques to most recently a single anterior working portal with a posterior viewing portal. With the development of the NanoScope (Arthrex, Naples, FL), we do not need to make a standard portal for viewing purposes. In this article, we describe the single-incision anterior labrum repair bypassing the need for a posterior skin incision. The removal of this incision and portal should result in less fluid needed and less swelling. We hope this leads to less pain and improved patient outcomes.

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<![CDATA[Two-Stage Anterior Cruciate Ligament Reconstruction Revision Surgery for Severe Bone Defects With Anterolateral Ligament Reconstruction Technique]]> https://www.researchpad.co/article/N074074a8-a4b1-4f71-a7a0-1e022ef87b2a

Anterior cruciate ligament revision surgery poses a number of specific difficulties. These include the lack of bone mass to enable effective fixation of the reconstruction, morbidity of the donor area when bone autograft is used to fill the tunnels, and absence of the semitendinosus and gracilis homolateral tendons in cases in which they have already been used in the primary surgical procedure. To address all these problems, we describe a 2-stage revision technique that uses bone allograft for tunnel filling and Achilles allograft for ligament reconstruction. In addition, the intervention includes an extra-articular phase in which the anterolateral ligament is reinforced to increase the rotational stability of the knee, thus improving the prognosis of operation.

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<![CDATA[The Outside-In, Percutaneous Release of the Medial Collateral Ligament for Knee Arthroscopy]]> https://www.researchpad.co/article/Nc5f038db-6da6-4abd-af21-7b75994142b4

The outside-in, percutaneous release of the medial collateral ligament (MCL) is a technique used to increase the medial tibiofemoral joint space during arthroscopy to facilitate the use of instrumentation and improve visualization without causing iatrogenic cartilage damage. A recent systematic review of the literature has shown this technique to be efficacious and safe, with no evidence of associated short- or long-term complications. This technique has been used for this indication by the senior author without requiring any deviation from our institution’s standard protocol for knee arthroscopy. In an attempt to standardize this technique’s utilization and allow for further evaluation in the literature, the senior author’s method for this percutaneous, outside-in approach of “pie crusting” the MCL is described.

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<![CDATA[Anconeus-Sparing Minimally Invasive Approach for Lateral Ulnar Collateral Ligament Reconstruction in Posterolateral Elbow Instability]]> https://www.researchpad.co/article/N65a4c264-81be-4d0d-9670-7ce538cbe160

Posterolateral elbow instability with an insufficiency of the lateral ulnar collateral ligament commonly results from elbow trauma. However, other etiologies such as iatrogenic injuries after primary surgical treatment for lateral epicondylitis or repetitive corticosteroid injections also may lead to a lateral ulnar collateral ligament insufficiency. In these cases, surgical treatment can help to restore posterolateral stability of the elbow. Besides the stabilizing effect of the ligamentous structures, the anconeus muscle is the most import active stabilizer against posterolateral elbow instability. Therefore, the aim of the present technique is to present an anconeus-sparing, minimally invasive approach to restore posterolateral stability. This technique may serve as an alternative for typically used all open access.

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<![CDATA[The Chinese Knot Stitch Technique Using a Footprint Ultrasuture Anchor for Rotator Cuff Repair]]> https://www.researchpad.co/article/N58e8335e-007e-4058-8ae4-bb525e81d438

Management of the rotator cuff presents specific challenges to orthopaedic surgeons. Several locking suture methods have been reported but often fail for a number of reasons. We describe a different technique that is easy to perform and inspired by the Chinese knot, an arthroscopic double-locking suture using a footprint ultrasuture anchor. This technique is similar to the suture-bridge structure on the bursal side of the tendon in that it increases tissue grip and stabilizes initial tendon-to-bone fixation. This technique is especially suitable for the patients who have bursal-side partial-thickness or degenerative small- and medium-sized rotator cuff tears.

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<![CDATA[Achieving a Perfectly Spherical Femoroplasty: Pearls, Pitfalls, and Optimal Surgical Technique]]> https://www.researchpad.co/article/Nfaaeb9f1-c667-41ca-a846-a421a148ff09

Femoroacetabular impingement describes a pathologic interaction between the bony femoral head/neck junction and acetabulum. Cam-type femoroacetabular impingement results from an aspherical femoral head architecture, which increases early contact along the acetabular surface during hip range of motion. Errant arthroscopic femoroplasty recently has been discussed within the literature to describe a preventable etiology of failed hip arthroscopy, most notably cam over- and under-resection. We present an arthroscopic surgical technique for achieving the perfectly spherical femoroplasty, meant to minimize complications and improve postoperative outcomes.

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<![CDATA[Arthroscopic Primary Repair of the Anterior Cruciate Ligament With Single-Bundle Graft Augmentation]]> https://www.researchpad.co/article/N42d7ceec-1107-475f-af94-100253c0bd0f

Recently, there has been a resurgence of interest in ligament preservation of the anterior cruciate ligament (ACL) that has the advantage of preserving the native tissue and maintaining proprioceptive function. Studies reporting outcomes of remnant-preserving ACL surgery have shown encouraging results with a higher potential for early healing and better functional outcomes compared with remnant-resecting surgery. Over the past decade, several surgical techniques for remnant preservation of the ACL have been proposed. In this technical note, the technique of primary ACL repair with graft augmentation is described. The goal of this technique is to preserve and tension the native tissue, thereby restoring the anatomy as much as possible while avoiding cyclops lesions, whereas the additional graft provides strength to the repaired ligament.

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<![CDATA[Outerbridge-Kashiwagi Procedure for the Treatment of a Supracondylar Humerus Fracture Malunion (O-K Procedure)]]> https://www.researchpad.co/article/Nb26feeb1-d6ca-4764-aac7-042944ab8c35

The Outerbridge-Kashiwagi (O-K) procedure has conventionally been used for the treatment of osteoarthritis of the elbow and to treat posttraumatic sequelae including posttraumatic arthritis, stiffness, contracture, and ulnar neuritis. The procedure involves exposure of the posterior elbow joint as well creating a window posteriorly through the olecranon fossa to target anterior aspects of the elbow. Several case series have shown the O-K procedure to have good functional outcomes with minimal complications. Used mostly for the surgical treatment of adult osteoarthritis, the O-K procedure has not been previously described for the treatment of a pediatric supracondylar humerus fracture malunion. This article and accompanying video will present the pearls and discuss the technique of the O-K procedure used to treat the loss of elbow flexion as a sequelae of supracondylar humerus fracture malunion.

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<![CDATA[Combined Anterior Cruciate Ligament Primary Repair With an Autograft Reconstruction]]> https://www.researchpad.co/article/Nac407062-42dc-490f-916c-0aa95d0ed451

Anterior cruciate ligament (ACL) reconstruction using an autograft gives good results that could provide improved failure rates. ACL augmentation saving the remnant has demonstrated advantages, such as saving vascular supply and nerve receptors, which could be useful for healing. Conversely, isolated repair techniques are gaining interest but do not give good results because structural augmentation is necessary to reinforce the repair and expect healing. We describe a technique combining the advantages of both techniques with an autograft using the semitendinosus and repair of the remnant. This combined technique allows protection and redirection of the remnant, improves graft incorporation, and covers more graft by suturing the remnant around an autologous graft.

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