SARS-CoV-2 NCBI consensus submission protocol: GenBank v2

This is a SARS-CoV-2 specific protocol that covers the steps needed to submit SARS-CoV-2 consensus sequence to GenBank. If you need a pipeline for frequent or large volume submissions, follow Step 1 in the SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject to get your NCBI submission environment established, then contact [email protected] to set up an account for submitting through the API. This protocol assumes (and requires) that the user has a BioProject and BioSamples(s) already registered. Complete in order:: 1. Populate your templates first. 2. SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject Step-by-step instructions for establishing a new NCBI laboratory submission account and for creating and linking a new BioProject to an existing umbrella effort. SARS-CoV-2 raw data submission to SRA (Sequence Read Archive) and metadata to BioSample. Users can modify this protocol to just create a BioSample with no linked raw data. 3. SARS-CoV-2 NCBI consensus submission protocol: GenBank (included protocol) Required: established BioProject and BioSamples Submit SARS-CoV-2 assemblies to NCBI GenBank, linking to existing BioProject, BioSamples, and raw data. Version history: V3: Direct links provided to download metadata templates (instead of hosting duplicate files). minor edits throughout the protocol.

Protective Effect of Melatonin Administration against SARS-CoV-2 Infection: A Systematic Review

Introduction: according to the World Health Organization (WHO), COVID-19 is an infectious disease caused by the SARS-CoV-2 virus, responsible for an increasing number of cases and deaths. From a preventive and therapeutic point of view, there are two concerns that affect institutions and healthcare professionals: global immunization (which is still far from being achieved) and the availability of drugs capable of preventing its consequences in the infected patient. In this sense, the role that melatonin can play is has been assessed in the recent literature. Justification and Objectives: the serious health, social and economic consequences of COVID-19 have forced an urgent search for preventive methods, such as vaccines, among others, and therapeutic methods that could be alternatives to the drugs currently used. In this sense, it must be accepted that one of the most recommended has been the administration of melatonin. The present study proposes to carry out a systematic review of its possible role in the treatment and/or prevention of COVID-19. Material and methods: a systematic review of the literature related to the prevention of COVID-19 through the administration of melatonin was carried out, following the sequence proposed by the Prisma Declaration regarding the identification and selection of documents, using the specialized health databases Trip Medical Database, Cochrane Library, PubMed, Medline Plus, BVS, Cuiden and generic databases such as Dialnet, Web of Science and Google Scholar for their retrieval. Appropriate inclusion and exclusion criteria are described for the articles assessed. The main limitation of the study has been the scarcity of works and the lack of defining a specific protocol in terms of dosage and administration schedule. Results: once the selection process was completed, and after an in-depth critical analysis, 197 papers were selected, and 40 of them were finally used. The most relevant results were: (1) melatonin prevents SARS-CoV-2 infection, (2) although much remains to be clarified, at high doses, it seems to have a coadjuvant therapeutic effect in the treatment of SARS-CoV-2 infection and (3) melatonin is effective against SARS-CoV-2 infection. Discussion: until group immunization is achieved in the population, it seems clear that we must continue to treat patients with SARS-CoV-2 infection, and, in the absence of a specific and effective antiviral therapy, it is advisable to continue researching and providing drugs that demonstrate validity based on the scientific evidence. In this regard, we believe that the available studies recommend the administration of melatonin for its anti-inflammatory, antioxidant, immunomodulatory, sleep-inducing, CD147, Mpro, p65 and MMP9 protein suppressing, nephrotoxicity-reducing and highly effective and safe effects. Conclusions: (1) melatonin has anti-inflammatory, antioxidant, immunomodulatory, and Mpro and MMP9 protein-inhibitory activity. (2) It has been shown to have a wide margin of safety. (3) The contributions reviewed make it an effective therapeutic alternative in the treatment of SARS-CoV-2 infection. (4) Further clinical trials are recommended to clearly define the administration protocol.

Evolution of Explosive Strength Data in Youth Volleyball Players Before and After Pandemic

Study purpose. This study aims to verify if there are significant differences and which type of correlation is between anthropometric and jumping ability variables by testing a group (elite) of Italian volleyball players (under 16), just after a month of training, applying a specific protocol. Materials and methods. In all subjects, the following anthropometric and jumping ability parameters were assessed: height, weight, body mass index, height with a stretched arm (Reach1) and height with two extended arms (Reach2). The jumping ability was measured with the Squat jump (SJ) and Run-Up (RU) test. All data on anthropometric and jumping ability parameters were presented as mean and standard deviation (Mean ± SD). Results. The results of the jumping ability parameters (Squat Jump and Run-Up) showed significant differences between treatment initial-final: Run-Up with p = 0.000 and Squat Jump with p = 0.001; and these showed a higher correlation, especially the variables linked to the ability to jump, evident differences compared to the initial period of treatment. Conclusions. In high-level youth volleyball, the anthropometric and jumping ability profile is directly linked to the evaluation and continuous monitoring of physical qualities, and jumping ability becomes an important aspect for the control of performance.

Return to play after treating acute muscle injuries in elite football players with radial extracorporeal shock wave therapy

Background To compare lay-off times achieved by treating acute muscle injuries in elite football players with a multimodal therapy approach that includes a specific protocol of almost daily radial extracorporeal shock wave therapy (rESWT) with corresponding data reported in the literature. Methods We performed a retrospective analysis of treatments and recovery times of muscle injuries suffered by the players of an elite football team competing in the first/second German Bundesliga during one of the previous seasons. Results A total of 20 acute muscle injuries were diagnosed and treated in the aforementioned season, of which eight (40%) were diagnosed as Type 1a/muscular tightness injuries, five (25%) as Type 2b/muscle strain injuries, four (20%) as Type 3a/partial muscle tear injuries and three (15%) as contusions. All injuries were treated with the previously mentioned multimodal therapy approach. Compared with data reported by Ekstrand et al. (Br J Sports Med 47:769–774, 2013), lay-off times (median/mean) were shortened by 54% and 58%, respectively, in the case of Type 1a injuries, by 50% and 55%, respectively, in the case of Type 2b injuries as well as by 8% and 21%, respectively, in the case of Type 3a injuries. No adverse reactions were observed. Conclusions Overall, the multimodal therapy approach investigated in this study is a safe and effective treatment approach for treating Type 1a and 2b acute muscle injuries amongst elite football players and may help to prevent more severe, structural muscle injuries.

Endodontic instruments fracture in root canal: Integrative review

Introduction: Endodontic instruments fracture is related to several factors from internal dental anatomy and type, to operator inability and inexperience. Objective: To review case reports related to fracture of endodontic instruments inside the root canal. Methodology: A literature review was carried out using papers available in the PubMed and Lilacs databases. Only case reports were included, with no restriction on language and publication year Results: It was analyzed eight papers with 11 instrument fracture cases, with the highest prevalence (45.5%) of rotary instruments fracture, occurring mainly in middle-cervical and middle-apical root canals thirds. In 90.9% of cases, techniques used for removal showed successful results and in only one case (9.1%), the technique was unsuccessful and the instrument was kept inside the root canal. Final considerations: Endodontic instruments fracture is a complication can directly affect prognosis and endodontic treatment success. Several techniques and devices can be used to remove fractured fragments inside root canals, however, there is no specific protocol for their removal. Keywords: accidents; endodontics; fracture; dental instruments; prognosis.

One Session Effects of Knee Motion Visualization Using Immersive Virtual Reality in Patients with Hemophilic Arthropathy

(1) Background: Hemophilic knee arthropathy is characterized by a loss of muscle mass and decreased strength of the quadriceps muscle. The visualization of movement aims to favor the recruitment of the motor system in the same premotor and parietal areas, as would happen with the active execution of the observed action. The aim was to evaluate changes in quadriceps activation in patients with hemophilic knee arthropathy following immersive VR visualization of knee extension movements. (2) Methods: We recruited 13 patients with severe hemophilia A and knee arthropathy. Patients underwent a 15 min session of immersive VR visualization of knee extension movements. The quadriceps muscle activation was evaluated by surface electromyography. (3) Results: After the intervention, there were no changes in the muscle activation of vastus medialis, vastus lateralis, or rectus femoris muscles. There was a large effect size of changes in rectus femoris muscle activation. Age and knee joint damage did not correlate with changes in quadriceps activation. Dominance, inhibitor development, and type of treatment were not related with post-intervention muscle activation. (4) Conclusions: A session of immersive VR visualization of knee extension movement does not modify quadriceps muscle activation. A specific protocol for patients with hemophilic knee arthropathy may be effective in improving the activation of the rectus femoris muscle.

TP7.2.1 Outcomes of Modified Karydakis flap in the surgical management of sacrococcygeal pilonidal disease: A single surgeon’s experience

Aim To determine the incidence of post-operative complications of patients with sacrococcygeal pilonidal disease who were treated with the Modified Karydakis flap with a specific management bundle. Primary outcomes assessed included the post-operative incidence of seroma, haematoma, SSI, deep SSI, wound dehiscence, re-admissions, return to theatre and flap necrosis. Secondary outcome evaluated was recurrence at 6 month follow up. Method It was a retrospective analysis of a single surgeon’s (FA’s) practice results of Modified Karydakis flaps on patients with sacrococcygeal pilonidal disease who were managed according to a specific protocol. Data was collected between June 2017 and June 2020. 96 patients were analysed, of which 9 were excluded as they had excision without closure. Pre, per and post-operative management for the remaining 87 patients was according to a standardised protocol. Data was collected from patient’s notes and from prospectively and retrospectively maintained patient data bases (Theatre System, Medway). Results Primary outcomes: • Seroma: 8/87 (9.2%) • Haematoma: 1/87 (1.2%) • SSI: 10/87 (11.5%) • Deep SSI: 4/87 (4.6%) • Superficial dehiscence: 7/87 (8.0%) • Re-admission: 4/87 (4.6%) • Return to theatre: 0 (0%) • Flap necrosis: 0 (0%) Secondary outcome: • Recurrence at 6 months: 2/87 (2.3%) Conclusions Good surgical results can be obtained with Modified Karadakis flap, provided meticulous surgical technique is applied. Placement of a suction drain for a minimum of 72 hours reduces incidence of post-operative haematoma and seroma formation. Three post-operative doses of broad spectrum intravenous antibiotics followed by 5 days of oral antibiotics helps reduce post-operative infections.

Carcinosarcoma del cuello uterino: reporte de un caso y revisión de la literatura

Cervical carcinosarcomas are extremely rare, accounting for less than 0.5% of cervical tumors. Due to its low incidence there is no specific protocol of action, which is associated with a poor prognosis. It is frequently diagnosed in postmenopausal women and in advanced stage, with large tumors with vaginal and parametrial metastases. Surgery is considered the treatment of choice, requiring in some cases adjuvant radio-chemotherapy. The prognosis will depend fundamentally on the stage at the time of diagnosis. Since there is little published evidence on this type of tumors we see the need for the publication of cases and reviews of the literature in this regard, to develop unified protocols for the management of this rare pathology. We present the case of a 51-yearold woman who consulted for postmenopausal metrorrhagia, observing a cervical mass with vaginal involvement, corresponding to a carcinosarcoma of the cervix; receiving treatment with radio-chemotherapy, with few side effects and good response. Keywords: Carcinosarcoma, uterine cervix, chemotherapy, radiotherapy, surgery.

Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018

Background: Virus genome sequencing is increasingly utilized in epidemiological surveillance. Genomic data allows comprehensive evaluation of underlying viral diversity and epidemiology to inform control. For human rhinovirus (HRV), genomic amplification and sequencing is challenging due to numerous types, high genetic diversity and inadequate reference sequences. Methods: We developed a tiled amplicon type-specific protocol for genome amplification and sequencing on the Illumina MiSeq platform of two HRV types, A15 and A101. We then assessed added value in analyzing whole genomes relative to the VP4/2 region only in the investigation of HRV molecular epidemiology within the community in Kilifi, coastal Kenya. Results: We processed 73 nasopharyngeal swabs collected between 2016-2018, and 48 yielded at least 70% HRV genome coverage. These included all A101 samples (n=10) and 38 (60.3%) A15 samples. Phylogenetic analysis revealed that the Kilifi A101 sequences interspersed with global A101 genomes available in GenBank collected between 1999-2016. On the other hand, our A15 sequences formed a monophyletic group separate from the global genomes collected in 2008 and 2019. An improved phylogenetic resolution was observed with the genome phylogenies compared to the VP4/2 phylogenies. Conclusions: We present a type-specific full genome sequencing approach for obtaining HRV genomic data and characterizing infections.