A quick guide for student-driven community genome annotation

High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental validation over the course of many years. The majority of gene models present in biological databases today have been identified in draft genome assemblies using automated annotation pipelines that are frequently based on orthologs from distantly related model organisms. Manual curation is time consuming and often requires substantial expertise, but is instrumental in improving gene model structure and identification. Manual annotation may seem to be a daunting and cost-prohibitive task for small research communities but involving undergraduates in community genome annotation consortiums can be mutually beneficial for both education and improved genomic resources. We outline a workflow for efficient manual annotation driven by a team of primarily undergraduate annotators. This model can be scaled to large teams and includes quality control processes through incremental evaluation. Moreover, it gives students an opportunity to increase their understanding of genome biology and to participate in scientific research in collaboration with peers and senior researchers at multiple institutions

Barriers to the management of Heart Failure in Ontario Long-Term Care Homes: an Interprofessional Care perspective

Background: With population aging, the prevalence of heart failure (HF) is risingin long-term care (LTC) homes. Given this burden, there is an urgent need to establish effective HF management programs.Methods and Findings: To understand what barriers would need to be addressed to develop such a program, we conducted a series of consultations among various LTC staff, as well as residents and their family caregivers. This article uses data obtained from the consultations to describe the interprofessional (IP) barriers that exist among the various LTC staff roles. Consultation methods included a Delphi survey followed by focus group interviews of LTC staff, and then personal interviews with LTC residents with HF and their family caregivers. Data were interpreted using an IP care framework in which interpersonal relationships among LTC staff provide the most direct influence on collaborative resident-centred practice, within the broader context of conditions within the LTC home, which in turn are housed in the broader context of systemic determinants.Conclusion: Across all data sets, the most consistently mentioned determinant was communication between the resident and the healthcare team, between different healthcare providers, between shifts, between medical specialists, and between the long-term care home and the hospital

Antibody levels after BNT162b2 vaccine booster and SARS-CoV-2 Omicron infection

In the present study, immunogenicity data in 61 vaccinated healthcare workers (HCWs) either infection naïve (naïve HCWs) or with infection of Delta and/or Omicron COVID-19 (experienced HCWs) were evaluated up to 270 days after the second dose of BNT162b2 vaccine and up to 90 days after a booster dose. A decrease in antibody levels at 270 days following administration of the second dose (p = 0.0335) was observed, although values did not fall below the positivity threshold (33.8 BAU/ml). After booster vaccination, antibody levels increased after 30 days (p = 0.0486), with much higher values than after first and second vaccination. Antibody levels then decreased at 60 and 90 days after the booster dose. A comparison between mean antibody levels of naïve and experienced HCWs revealed higher values in experienced HCWs, resulting from both natural and vaccination-induced immunity. A total of 14.7% of HCWs contracted the Omicron virus variant after the vaccine booster, although none showed severe symptoms. These results support that a booster dose results in a marked increase in antibody response that subsequently decreases over time

Endovascular repair of isolated post-traumatic subclavian artery false-aneurysm (FA) using gore viabahn vbx-balloon-expandable (BE) stent-graft: case report and literature review

True and false aneurysms (FA) of the subclavian artery are at high risk of rupture due to their localization and proximity/closeness to the articular bone structures of the upper thoracic outlet and shoulders. Surgical and endovascular treatments are good options to avoid complications such as aneurysms rupture, thrombosis and distal embolism alone or in combination. Self-expandable (SE) covered stents are the most used devices for the treatment of subclavian artery aneurysms. We report on a case of post traumatic left intra-thoracic subclavian artery FA treated using endovascular technique, highlighting the usefulness of the new covered Gore Viabahn VBX-BE stent-graft that combines the advantages of a high radial strength of a BE stent with the deliverability and conformability of a SE stent

Comparison of the effects of continuous positive airway pressure, oral appliance and exercise training in obstructive sleep apnea syndrome

OBJECTIVE: There are several treatments for obstructive sleep apnea syndrome, such as weight loss, use of an oral appliance and continuous positive airway pressure, that can be used to reduce the signs and symptoms of obstructive sleep apnea syndrome. Few studies have evaluated the effectiveness of a physical training program compared with other treatments. The aim of this study was to assess the effects of physical exercise on subjective and objective sleep parameters, quality of life and mood in obstructive sleep apnea patients and to compare these effects with the effects of continuous positive airway pressure and oral appliance treatments. METHODS: Male patients with moderate to severe obstructive sleep apnea and body mass indices less than 30 kg/m2 were randomly assigned to three groups: continuous positive airway pressure (n = 9), oral appliance (n = 9) and physical exercise (n = 7). Polysomnographic recordings, blood samples and daytime sleepiness measurements were obtained prior to and after two months of physical exercise or treatment with continuous positive airway pressure or an oral appliance. Clinicaltrials.gov: NCT01289392 RESULTS: After treatment with continuous positive airway pressure or an oral appliance, the patients presented with a significant reduction in the apnea-hypopnea index. We did not observe changes in the sleep parameters studied in the physical exercise group. However, this group presented reductions in the following parameters: T leukocytes, very-low-density lipoprotein and triglycerides. Two months of exercise training also had a positive impact on subjective daytime sleepiness. CONCLUSIONS: Our results suggest that isolated physical exercise training was able to modify only subjective daytime sleepiness and some blood measures. Continuous positive airway pressure and oral appliances modified the apnea-hypopnea index.AFIPCEPECEMSACNPqFAPESPUniversidade Federal de São Paulo (UNIFESP) Departamento de PsicobiologiaUNIFESP, Depto. de Psicobiologia2009/01031-1 e 98/14303-3SciEL

Sleep characteristics and inflammatory markers in women with post-traumatic stress disorder

Introduction: Sexual violence is one of the most severe traumatic events. It is associated with a higher risk for post-traumatic stress disorder (PTSD) development. Sleep disturbances such as insomnia are frequently reported by PTSD patients and play a key role in the development and course of the disorder. Sleep disturbances are associated with higher levels of pro-inflammatory cytokines emphasizing the importance of sleep studies in individuals with PTSD. Objectives: To investigate the association between subjective and objective sleep measurements and PTSD symptoms with inflammatory markers in women with PTSD following sexual assault. Methods: In this longitudinal study fifty-seven women with PTSD were evaluated for sleep measurements and inflammatory markers. Participants completed the Clinician-Administered PTSD Scale, the Beck Depression Inventory, the Pittsburgh Sleep Quality Index (PSQI), and the Insomnia Severity Index. In addition, patients underwent full in-lab polysomnography and serum levels of interleukin (IL)-1β, IL-6, tumor necrosis factor (TNF)-α, and C-reactive protein (CRP) measurement. All assessments were performed at baseline and after one year. Patients received pharmacological and/or psychological interventions between baseline and one-year follow-up. Results: Despite improving PTSD symptoms severity and sleep quality (expressed in PSQI), we found an increase in the inflammatory markers IL-1β, TNF-α, IL-6 and CRP after one year of follow-up. These findings suggest that neurobiological processes may advance independently of PTSD symptoms. We found a significant increase in the levels of IL-1β and TNF-α associated with decreased slow-wave sleep (p = 0.019 and p = 0.018 respectively), IL-6 associated with arousal index (p = 0.024), and CRP associated with insomnia severity (p = 0.012), and sleep duration longer than 6 h per night (p < 0.001). Conclusions: Sleep impairments in PTSD may be associated with a gradual and persistent alteration in the immune system, resulting in a progressive inflammatory process. Our results suggest that sleep mechanisms are involved in this incident inflammatory process in young women with PTSD

CT Perfusion in the Characterisation of Renal Lesions: An Added Value to Multiphasic CT

Objective. To prospectively evaluate if computed tomography perfusion (CTp) could be a useful tool in addition to multiphasic CT in renal lesion characterisation. Materials and Methods. Fifty-eight patients that were scheduled for surgical resection of a renal mass with a suspicion of renal cell carcinoma (RCC) were enrolled. Forty-one out of 58 patients underwent total or partial nephrectomy after CTp examination, and a pathological analysis was obtained for a total of 49 renal lesions. Perfusion parameters and attenuation values at multiphasic CT for both lesion and normal cortex were analysed. All the results were compared with the histological data obtained following surgery. Results. PS and MTT values were significantly lower in malignant lesions than in the normal cortex (P < 0.001 and P = 0.011, resp.); PS, MTT, and BF values were also statistically different between oncocytomas and malignant lesions. According to ROC analysis, the accuracy, sensitivity, and specificity to predict RCC were 95.92%, 100%, and 66.7%, respectively, for CTp whereas they were 89.80%, 93.35%, and 50%, respectively, for multiphasic CT. Conclusion. A significant difference between renal cortex and tumour CTp parameter values may suggest a malignant renal lesion. CTp could represent an added value to multiphasic CT in differentiating renal cells carcinoma from oncocytoma

Supplement: "Localization and broadband follow-up of the gravitational-wave transient GW150914" (2016, ApJL, 826, L13)

This Supplement provides supporting material for Abbott et al. (2016a). We briefly summarize past electromagnetic (EM) follow-up efforts as well as the organization and policy of the current EM follow-up program. We compare the four probability sky maps produced for the gravitational-wave transient GW150914, and provide additional details of the EM follow-up observations that were performed in the different bands

Inflammatory markers in women with PTSD due to sexual abuse

Introdução: A violência sexual é um dos eventos traumáticos com maior risco para o desenvolvimento de transtorno de estresse pós-traumático (TEPT), que é caracterizado por uma resposta biológica disfuncional ao estresse marcada pelo desequilíbrio do eixo Hipotálamo-Hipófise-Adrenal (HPA), atividade imune alterada e mudanças na estrutura e no funcionamento cerebral. O TEPT está altamente relacionado a níveis aumentados de marcadores inflamatórios, maior comorbidade com doenças clínicas e prejuízo funcional importante. Objetivo: A presente tese objetiva investigar anormalidades em níveis de marcadores inflamatórios e hormônios do eixo HPA em mulheres que sofreram violência sexual e desenvolveram TEPT em dois momentos, no início do quadro e um ano depois. Além de comparar se há diferença em relação aos níveis hormonais e marcadores inflamatórios entre dois grupos de pacientes com TEPT que receberam tratamento com sertralina ou psicoterapia. Método: 58 mulheres com TEPT em decorrência de violência sexual com intervalo máximo para inclusão de seis meses após o trauma, foram comparadas a 44 controles saudáveis. No momento de triagem para entrada das pacientes no estudo (momento 1), foi aplicado um questionário sociodemográfico e foram aplicados os seguintes instrumentos: Entrevista Neuropsiquiátrica internacional (MINI), Questionário sobre Traumas na Infância (QUESI), Inventário de Depressão de Beck (BDI), Inventário de Ansiedade de Beck (BAI) e Escala de TEPT Administrada pelo Clínico (Clinician Administered PTSD Scale-CAPS-5), além da dosagem sérica de ACTH, IL-1β, IL-6, TNF-α, MCP-1, PCR e cortisol salivar. As pacientes foram randomizadas para receber tratamento com sertralina ou psicoterapia interpessoal (IPT) por 14 semanas, quando foram reaplicados o BDI, BAI e CAPS-5 (momento 2). O seguimento se deu por um ano, com o tratamento usual, conforme a necessidade. Os instrumentos BDI, BAI e CAPS-5 foram reaplicados e os mesmos exames foram coletados ao final de um ano (momento 3). Este estudo visou avaliar os momentos 1 e 3. Resultados: Cinquenta e seis pacientes apresentaram TEPT e episódio depressivo, segundo a MINI. No momento 1, os níveis de ACTH no grupo com TEPT foram maiores quando comparados ao grupo controle. Essa diferença foi proporcional à viii gravidade do TEPT, avaliada pela CAPS-5 (p=0,026) e também pela subescala D, que avalia sintomas negativos do humor (p=0,045), e proporcional à gravidade dos sintomas depressivos avaliados pela BDI (p<0,0001). Os níveis de cortisol medidos às 22 horas foram maiores para o grupo TEPT comparado ao grupo controle (p=0,037). Na avaliação inicial, não houve diferença significativa entre os marcadores inflamatórios das pacientes comparadas às do grupo controle. Ao final de um ano, houve aumento significativo dos níveis dos marcadores inflamatórios no grupo de pacientes comparadas ao grupo controle, IL-1β (p<0,0001), MCP-1 (p<0,0001), TNF-α (p<0,0001) e PCR (p<0,0001) e níveis de cortisol (p=0,046). Houve melhora significativa dos sintomas depressivos (p<0,001) e de TEPT (p<0,001), independentemente do grupo de tratamento após um ano. Conclusão: A maioria da amostra com TEPT apresentou sintomas depressivos concomitantes aos sintomas de TEPT, o que pode ser considerado parte de uma psicopatologia relacionada a trauma, especificamente ao trauma de violência sexual, sugerindo uma variabilidade fenotípica inter-indivíduo. A essa especificidade psicopatológica pode-se implicar um funcionamento peculiar do eixo HPA, que se apresenta hiperestimulado e com funcionamento mais semelhante ao modelo de transtorno depressivo maior, com maiores níveis de cortisol, observado principalmente após um ano. O aumento dos marcadores inflamatórios após um ano, mesmo com a melhora dos sintomas, pode indicar que o TEPT em decorrência de violência sexual em mulheres evolui com alterações inflamatórias persistentes, que expõem essas mulheres a um maior risco de doenças crônicas e inflamatórias, muitas vezes relacionadas a um pior prognóstico clínico e mortalidade precoce. Este estudo traz novas perspectivas para o conhecimento atual da neurobiologia do TEPT e contribui para o estímulo de desenvolvimento de novas abordagens que possam atuar nesse desfecho.Introduction: Sexual violence is one of the traumatic events with greater risk of developing post-traumatic stress disorder (PTSD). PTSD is characterized by a biological response marked by the hypothalamic-pituitary-adrenal (HPA) axis, altered immune activity and changes on the cerebral structure and functioning. Besides that, PTSD is also highly related to increased levels of inflammatory markers, greater comorbidity with clinical diseases and relevant functional loss. Objective: This thesis aims at evaluating abnormalities in the inflammatory markers levels and HPA axis hormones in women who suffered sexual violence and developed PTSD in two moments, at the baseline, and one year later. To compare whether there is a difference in hormone and inflammatory markers levels between the two groups of PTSD patients who received treatment with sertraline or psychotherapy. Methods: Fifty-eight women with PTSD due to sexual violence with a maximum inclusion interval of six months were compared to forty-four healthy controls. At the time of screening for patients to enter the study (time 1) a socio-demographic questionnaire as well as the following instruments were applied: InternationalNeuropsychiatric Interview (MINI), Childhood Trauma Questionnaire (CTQ), Beck Depression Inventory (BDI), Beck Anxiety Inventory (BAI) and Clinician Administered PTSD Scale-CAPS-5 in addition to serum ACTH, IL-1β, IL-6, TNF-α, MCP-1, PCR and salivary cortisol. The patients were randomized to receive either sertraline treatment or interpersonal psychotherapy (IPT) for 14 weeks (time 2) when the BDI, BAI and CAPS-5 instruments were reapplied and the same exams were collected at the end of one year (time 3). This study aimed to evaluate moments 1 and 3. Results: Fifty-six patients presented PTSD and depressive episode, according to the MINI. At time 1, ACTH levels on the PTSD group were higher when compared to the control group. This difference was proportional to PTSD severity, assessed by CAPS- 5 (p=0.026) and also by the CAPS-5 subscale D, which assesses negative mood symptoms (p=0.045) and proportional to the severity of depressive symptoms assessed by BDI (p<0.0001). The cortisol levels measured at 10 pm were higher for the PTSD group compared to the control group (p=0.037). On the initial evaluation, x there was not any significant difference among the patients’ inflammatory markers compared to the controls. By the end of one year there was a significant increase on the level of inflammatory markers on the patient group compared to the controls IL-1β (p = <0,0001), MCP-1 (p <0,0001), TNF-α (p<0,0001) and PCR (p<0,0001) and cortisol levels (p=0.046). There was significant improvement on the depressive symptoms (p<0.0001) and PTSD (p<0,001), regardless the group after one year. Discussion: Most of the PTSD sample presented depressive symptoms concomitant with the PTSD, which can be considered part of a trauma-related psychopathology, specifically the trauma of sexual violence, suggesting an inter-individual phenotypic variability. This psychopathological specificity may imply a peculiar functioning of the HPA axis, which is hyperstimulated and functioning more similarly to the model of major depressive disorder, with higher levels of cortisol, observed mainly after one year. The increase in inflammatory markers after one year, even with the improvement of symptoms, may indicate that PTSD in women due to sexual violence evolves with persistent inflammatory changes, which expose these women to a greater risk of chronic and inflammatory diseases, often related to a worse clinical prognosis and early mortality. This study brings new perspectives to the current knowledge of the neurobiology of PTSD and contributes to stimulating the development of new approaches that can act on this outcome.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)2014/12559-

Diagnostic utility of FGF-23 in mineral bone disorder during chronic kidney disease

Our data confirm that intact fibroblast growth factor 23 (iFGF-23) concentration is increased in patients with chronic kidney disease (CKD) and that it increases with disease progression (stages I-V). Therefore, iFGF-23 could be considered an early biomarker in the course of chronic kidney disease-mineral bone disorder (CKD-MBD), which has several aspects that make it potentially useful in clinical practice. The availability of an automated method for iFGF-23 assay may represent an added value in the management of the patient with CKD-MBD already from the early stages of the disease, before the increase of the routinely used laboratory parameters, 1-84 parathyroid hormone (PTH) and 25-OH-vitamin D (25-OH-vitD), which occur in more advanced stages of the disease