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Understanding of how soil organic matter (SOM) chemistry is altered in a changing climate has advanced considerably; however, most SOM components remain unidentified, impeding the ability to characterize a major fraction of organic matter and predict what types of molecules, and from which sources, will persist in soil. We present a novel approach to better characterize SOM extracts by integrating information from three types of analyses, and we deploy this method to characterize decaying root-detritus soil microcosms subjected to either drought or normal conditions. To observe broad differences in composition, we employed direct infusion Fourier-transform ion cyclotron resonance mass spectrometry (DI-FT-ICR MS). We complemented this with liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify components by library matching. Since libraries contain only a small fraction of SOM components, we also used fragment spectral cosine similarity scores to relate unknowns and library matches through molecular networks. This integrated approach allowed us to corroborate DI-FT-ICR MS molecular formulas using library matches, which included fungal metabolites and related polyphenolic compounds. We also inferred structures of unknowns from molecular networks and improved LC-MS/MS annotation rates from â¼5 to 35% by considering DI-FT-ICR MS molecular formula assignments. Under drought conditions, we found greater relative amounts of lignin-like vs condensed aromatic polyphenol formulas and lower average nominal oxidation state of carbon, suggesting reduced decomposition of SOM and/or microbes under stress. Our integrated approach provides a framework for enhanced annotation of SOM components that is more comprehensive than performing individual data analyses in parallel.
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OBJECTIVE: As the population ages, vascular surgeons are treating progressively older, multimorbid patients at risk of peri-operative complications. An embedded physician has been shown to improve outcomes in general and orthopaedic surgery. This systematic review and meta-analysis aimed to investigate the impact of surgeon-physician co-management models on morbidity and mortality rates in vascular inpatients. DATA SOURCES: PubMed, Scopus, Embase, conference abstract listings, and clinical trial registries. REVIEW METHODS: Studies comparing adult vascular surgery inpatients under co-management with standard of care were eligible. The relative risks (RRs) of death, medical complications, and 30 day re-admission between co-management and standard care were calculated. The effect of co-management on the mean length of stay was calculated using weighted means. Risk of bias was assessed using the Methodological Index for Non-Randomised Studies, and certainty assessment with the GRADE analysis tools. RESULTS: No randomised controlled trials were identified. Eight single institution studies between 2011 and 2020 with 7 410 patients were included. All studies were observational using before-after methodology. Studies were of high to moderate risk of bias, and outcomes were of very low GRADE certainty of evidence. Co-management was associated with a statistically significant lower relative risk of death (RR 0.64, 95% confidence interval [CI] 0.44 - 0.92; p = .02), cardiac complications (RR 0.47, 95% CI 0.25 - 0.87; p = .02), and infective complications (RR 0.49, 95% CI 0.35 - 0.67; p < .001) in vascular inpatients. No statistically significant differences in length of stay (standard mean difference -0.6 days, 95% CI -1.44 - 0.24 days; p = .16) and 30 day re-admission (RR 0.96, 95% CI 0.84 - 1.08; p = .49) were noted. CONCLUSION: Early results of physician and surgeon co-management for vascular surgery inpatients showed promising results from very low certainty data. Further well designed, prospective studies are needed to determine how to maximise the impact of physicians within a vascular service to improve patient outcomes while using hospital resources effectively.
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OBJECTIVE: Resuscitative endovascular balloon occlusion of the aorta (REBOA) is used to temporise non-compressible torso haemorrhage. Recent data have suggested that vascular access complications secondary to REBOA placement are higher than initially anticipated. This updated systematic review and meta-analysis aimed to determine the pooled incidence rate of lower extremity arterial complications after REBOA. DATA SOURCES: PubMed, Scopus, Embase, conference abstract listings, and clinical trial registries. REVIEW METHODS: Studies including more than five adults undergoing emergency REBOA for exsanguinating haemorrhage that reported access site complications were eligible for inclusion. A pooled meta-analysis of vascular complications was performed using the DerSimonian-Laird weights for the random effects model, presented as a Forest plot. Further meta-analyses compared the relative risk of access complications between different sheath sizes, percutaneous access techniques, and indications for REBOA. Risk of bias was assessed using the Methodological Index for Non-Randomised Studies (MINORS) tool. RESULTS: No randomised controlled trials were identified, and the overall study quality was poor. Twenty-eight studies including 887 adults were identified. REBOA was performed for trauma in 713 cases. The pooled proportion rate of vascular access complications was 8.6% (95% confidence interval 4.97 - 12.97), with substantial heterogeneity (I2 = 67.6%). There was no significant difference in the relative risk of access complications between 7 and > 10 F sheaths (p = .54), or between ultrasound guided and landmark guided access (p = .081). However, traumatic haemorrhage was associated with a significantly higher risk of complications compared with non-traumatic haemorrhage (p = .034). CONCLUSION: This updated meta-analysis aimed to be as comprehensive as possible considering the poor quality of source data and high risk of bias. It suggested that lower extremity vascular complications were higher than originally suspected after REBOA. While the technical aspects did not appear to impact the safety profile, a cautious association could be drawn between REBOA use for traumatic haemorrhage and a higher risk of arterial complications.
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Oclusão com Balão , Doenças Cardiovasculares , Hemorragia , Hemorragia/terapia , Humanos , Extremidade Inferior/fisiopatologia , AortaRESUMO
OBJECTIVES: Persistent sciatic artery (PSA) is a rare congenital anomaly, whereby the embryonic sciatic artery remains patent with associated degrees of femoral axis hypoplasia. Aneurysmal degeneration and distal ischaemia from thromboembolic complications are common. Revascularisation strategies include embolectomy, bypass or interposition grafting and catheter-directed thrombolysis. METHODS: We describe a sedentary 88-year-old woman with right acute limb ischaemia secondary to a thrombosed PSA aneurysm and concurrent occlusive thrombus at the femoral bifurcation. RESULTS: The patient presented with a 3-day history of a cold, painful right foot. Examination revealed Rutherford IIb ischaemia. CT-angiography demonstrated no continuity between the hypoplastic superficial femoral and popliteal arteries, complete occlusion of the right PSA distal to the thrombosed aneurysm and occlusive thrombus in the right profunda. As she was too frail for femoral-distal bypass, we restored femoral axis inflow via profunda embolectomy. Her prognosis remained guarded as we deliberately did not reconstruct the PSA. However, she was discharged pain-free and mobilising with aids 2 weeks later. CONCLUSION: Limb ischaemia in frail, high-risk patients is an ever-increasing challenge for vascular surgeons and requires complex decision-making, balancing comorbidities against desired outcomes. This case illustrates that a selective approach can be sufficient to maintain function despite complex anatomy.
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Aneurisma , Doenças Vasculares Periféricas , Trombose , Humanos , Feminino , Idoso de 80 Anos ou mais , Idoso , Idoso Fragilizado , Octogenários , Isquemia/diagnóstico por imagem , Isquemia/etiologia , Isquemia/cirurgia , Artéria Poplítea/diagnóstico por imagem , Artéria Poplítea/cirurgia , Aneurisma/complicações , Aneurisma/diagnóstico por imagem , Aneurisma/cirurgia , Trombose/complicações , Trombose/diagnóstico por imagemRESUMO
BACKGROUND: Right iliac fossa (RIF) pain is a common indication for laparoscopy to diagnose and treat appendicitis. When a macroscopically normal appendix is found, there is no standard consensus regarding excision. Some surgeons remove the appendix due to the risk of microscopic inflammation and to avoid a future, repeat laparoscopy for possible appendicitis. Alternatively, others leave the appendix in situ to avoid morbidity from a potentially unnecessary procedure. We aimed to evaluate the outcomes of patients with macroscopically normal appendices left in situ. METHODS: All emergency laparoscopies without appendicectomy between January 1st 2010- December 31st 2020 were identified from theatre records. All operative notes were individually evaluated and comments on the macroscopic appearance of the appendix and any intra-operative pathology were recorded. Only patients undergoing laparoscopy for suspected appendicitis with macroscopically normal appendices were included. RESULTS: A total of 120 patients [median age 21.68 (range 9-90.8) years] were included. The cohort was predominantly female (n=105, 87.5%). Forty-eight patients (40.0%) had a positive finding during index laparoscopy. During a median duration of 94.5 (range 8-131) months' follow-up, 16 patients (13.33%) underwent a repeat laparoscopy for recurrent RIF pain. Thirteen (10.8% of total cohort) subsequently underwent an appendicectomy. Histology confirmed acute appendicitis in six cases (4.17% of entire cohort). On subanalysis of smaller cohort, index laparoscopies with no positive findings (n=72), nine patients (12.5%) underwent appendicectomy with two (2.7%) appendices demonstrating appendicitis on histological examination. CONCLUSION: 87% of the total cohort with a normal appendix at laparoscopy for RIF pain did not undergo further laparoscopy. Less than 5% of the total cohort and 2.7% of subanalysis cohort had an appendicectomy for histologically-proven appendicitis within the follow-up period. From the evidence in this study, we conclude that leaving the appendix in situ unless macroscopically inflamed is a viable alternative to excision.
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Apendicite , Apêndice , Laparoscopia , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Apendicectomia/métodos , Apendicite/diagnóstico , Apendicite/patologia , Apendicite/cirurgia , Apêndice/patologia , Apêndice/cirurgia , Criança , Feminino , Humanos , Laparoscopia/métodos , Masculino , Pessoa de Meia-Idade , Dor , Adulto JovemRESUMO
OBJECTIVES: While endovascular intervention is the recommended first option for management of common iliac artery (CIA) lesions, it lacks durable patency for Trans-Atlantic Inter-Society Consensus (TASC)-II C and D lesions involving the external iliac artery (EIA). Aorto-femoral bypass is a durable option but is unsuitable in patients with significant co-morbidities. Eversion endarterectomy provides an alternative to both endovascular and extensive open aortoiliac reconstruction for occlusive EIA disease. MATERIALS AND METHODS: A single-center, retrospective review (2000-2020) of all patients undergoing eversion endarterectomy for EIA disease was undertaken. Demographic, clinical, operative and follow-up data were recorded. RESULTS: Fifty eversion endarterectomies were performed in 47 patients. The median age was 65.0 years (range 46-82) and 66.6% were male. Sixty-eight percent (n = 34) were ASA grade 3. Indications for intervention were disabling claudication (44%) and critical limb ischaemia (56%). Angiography demonstrated 22 TASC C and 28 TASC D lesions. The median follow-up was 18.5 months (range 0-149). The technical success rate was 100%, and 84% (n = 42) experienced an immediate symptomatic improvement. Primary and primary-assisted patency at one, three and five years was 86%, 82% and 74%, and 100%, 96% and 92%, respectively. The five-year limb salvage rate was 96%. Eight limbs required reintervention to maintain patency, either by open (n = 2), endovascular (n = 3) or hybrid approach (n = 3). Thirty-day mortality was 2% (n = 1) with 10% (n = 5) experiencing a procedure-related morbidity. All-cause mortality was 38% (n = 19) during the follow-up period. CONCLUSIONS: Eversion endarterectomy is a safe, effective alternative treatment for occlusive EIA disease. This study reports durable patency at five years and low perioperative morbidity and mortality.
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Arteriopatias Oclusivas , Artéria Ilíaca , Idoso , Idoso de 80 Anos ou mais , Arteriopatias Oclusivas/diagnóstico por imagem , Arteriopatias Oclusivas/cirurgia , Endarterectomia/efeitos adversos , Feminino , Artéria Femoral/diagnóstico por imagem , Artéria Femoral/cirurgia , Humanos , Artéria Ilíaca/diagnóstico por imagem , Artéria Ilíaca/cirurgia , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos , Stents , Resultado do Tratamento , Grau de Desobstrução VascularRESUMO
OBJECTIVES: To investigate whether HE4 and CA125 could identify endometrioid adenocarcinoma patients who might most benefit from full staging surgery with lymphadenectomy. METHODS: Sequential patients with a preoperative banked serum and histology of endometrioid adenocarcinoma of endometrium who had undergone surgical staging with lymph node dissection over a 5-year period between 2011 and 2016 were included from a tertiary Gynaecological Cancer Centre, Dublin, Ireland. Preoperative serum HE4 and CA125 were measured using ELISA, with the cut-offs HE4 81 pmol/L and CA125 35 U/ml. Predictive values were estimated using AUC, sensitivity, specificity and odds ratios. RESULTS: 9.5% of the cohort had lymph node metastases. A HE4 cut-off of 81 pmol/L yielded a sensitivity of 78.6% and specificity of 53.4% for predicting lymph node metastases. Sensitivity of CA125 at 35 U/ml was 57% and specificity 91.4%. The AUC was 0.66 (0.52-0.80) for HE4 and 0.74 (0.58-0.91) for CA125. Sensitivity was 92.8% and specificity 51.1% when an elevation of either HE4 or CA125 was included, AUC was 0.72 (0.61-0.83), this combination yielded the highest NPV of 98.6%. Sensitivity was 42.9% and specificity 93.8% if both markers were elevated simultaneously, AUC was 0.68 (0.51-0.86). Preoperative clinical predictors of high-grade preoperative histology and radiology had sensitivities of 21.4% and 41.7%, respectively. Patients with a HE4 above 81 pmol/L had an odds ratio of 4.2 (1.12-15.74), p < 0.05, of lymph node metastases and CA125 had an odds ratio of 14.2 (4.16-48.31), p < 0.001. CONCLUSIONS: Serum HE4 and CA125 improved on existing methods for risk stratification of endometrioid carcinomas and warrant further investigation.
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Biomarcadores Tumorais/sangue , Antígeno Ca-125/sangue , Carcinoma Endometrioide/diagnóstico , Neoplasias do Endométrio/diagnóstico , Metástase Linfática/diagnóstico , Proteínas de Membrana/sangue , Proteína 2 do Domínio Central WAP de Quatro Dissulfetos/análise , Adulto , Idoso , Idoso de 80 Anos ou mais , Carcinoma Endometrioide/sangue , Carcinoma Endometrioide/patologia , Carcinoma Endometrioide/cirurgia , Neoplasias do Endométrio/sangue , Neoplasias do Endométrio/patologia , Neoplasias do Endométrio/cirurgia , Endométrio/patologia , Endométrio/cirurgia , Feminino , Humanos , Histerectomia , Excisão de Linfonodo/estatística & dados numéricos , Linfonodos/patologia , Linfonodos/cirurgia , Metástase Linfática/patologia , Pessoa de Meia-Idade , Gradação de Tumores/estatística & dados numéricos , Estadiamento de Neoplasias/estatística & dados numéricos , Valor Preditivo dos Testes , Período Pré-Operatório , Curva ROC , Valores de Referência , Estudos Retrospectivos , Medição de Risco/métodos , Salpingo-OoforectomiaRESUMO
BACKGROUND: Gastric variceal (GV) bleeding is among the most morbid sequelae of portal hypertension, with mortality ranging from 30% to 50%. Pediatric data focused on endoscopic approaches to management are needed. The present study represents the first pediatric case series of endoscopic ultrasound (EUS)-guided coil placement within feeding vessels as monotherapy for management of GV bleeding. METHODS: Using our prospectively maintained endoscopy database, we identified patients 18âyears and younger who underwent EUS-guided coil placement for management of GV bleeding from 2008 to 2018. Demographics, indication, procedural interventions/findings, and available clinical outcomes data were analyzed. RESULTS: Twelve patients (median age 15, range 11-18âyears) underwent EUS-guided coil placement for GV bleeding. All had portal hypertension, with EV in 58.3% and prior GV bleeding with attempted endoscopic management in 75%. Coil placement was accomplished using a linear echoendoscope and a 19-gauge needle. A mean of 2.75 (± 0.43) coils were placed in each patient (4, 6, 8, and 10âmm Nester Embolization Coils, Cook Medical, Bloomington, Indiana, USA). Immediate hemostasis was achieved in all patients, and 25% of patients developed recurrent gastric varices at a median of 5.5âmonths following the initial EUS-guided coil placement (range 4-6âmonths) over the median 12âmonth follow-up period. CONCLUSIONS: The present study establishes the feasibility and efficacy of EUS-guided coil placement as monotherapy for GV bleeding in children and adolescents. The technique was technically successful, with primary hemostasis achieved in all patients. EUS-guided embolization with coils may represent an alternative to current approaches for management of highly morbid GV bleeding.
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Varizes Esofágicas e Gástricas , Hemostase Endoscópica , Adolescente , Criança , Cianoacrilatos , Varizes Esofágicas e Gástricas/terapia , Hemorragia Gastrointestinal/etiologia , Hemorragia Gastrointestinal/terapia , Hemostasia , Humanos , Resultado do Tratamento , Ultrassonografia de IntervençãoRESUMO
AIM: Patients with locally advanced and locally recurrent rectal cancer (LARC/LRRC) experience higher rates of local recurrence (LR) and poorer overall survival than patients with primary rectal cancer restricted to the mesorectum despite improved neoadjuvant treatment regimens and radical surgical procedures. Intraoperative radiotherapy (IORT) has been suggested as an adjunctive tool in the surgical management of these challenging cases. However, clear evidence regarding the oncological benefit of IORT is sparse. The aim of this review was to update this evidence in the era of standardized neoadjuvant radiotherapy administration. METHOD: A systematic review of patients who received IORT as part of multimodal treatment for advanced rectal cancer from 2000 to 2020 and an analysis of IORT and surgery/external beam radiotherapy (EBRT) groups was performed. The primary endpoint was the rate of LR between the two groups. RESULTS: Seven papers met the predefined criteria. LR was reduced by the addition of IORT when compared with the surgery/EBRT alone group (14.7% vs. 21.4%; OR 0.55, 95% CI 0.27-1.14; p = 0.11). There was no increase in reported genitourinary morbidity, wound issues, pelvic collections or anastomotic leak in those patients who received IORT. Notably, there was no survival difference between the two groups. CONCLUSION: The addition of IORT to current treatment strategies in the management of patients with LARC/LRRC is associated with a lower rate of locoregional recurrence without increased morbidity. However, this marks a highly selective group of patients, with heterogeneity regarding indications, prior neoadjuvant treatments and/or IORT dosing.
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Recidiva Local de Neoplasia , Neoplasias Retais , Terapia Combinada , Humanos , Terapia Neoadjuvante , Neoplasias Retais/radioterapia , Neoplasias Retais/cirurgiaRESUMO
Research over the past decade has identified several of the key limiting features of multidrug resistance (MDR) in cancer therapy applications, such as evolving glycoprotein receptors at the surface of the cell that limit therapeutic uptake, metabolic changes that lead to protection from multidrug resistant mediators which enhance degradation or efflux of therapeutics, and difficulty ensuring retention of intact and functional drugs once endocytosed. Nanoparticles have been demonstrated to be effective delivery vehicles for a plethora of therapeutic agents, and in the case of nucleic acid based agents, they provide protective advantages. Functionalizing cell penetrating peptides, also known as protein transduction domains, onto the surface of fluorescent quantum dots creates a labeled delivery package to investigate the nuances and difficulties of drug transport in MDR cancer cells for potential future clinical applications of diverse nanoparticle-based therapeutic delivery strategies. In this study, eight distinct cell penetrating peptides were used (CAAKA, HSV1-VP22, HIV-TAT, HIV-gp41, Ku-70, hCT(9-32), integrin-ß3, and K-FGF) to examine the different cellular uptake profiles in cancer versus drug resistant melanoma (A375 & A375-R), mesothelioma (MSTO & MSTO-R), and glioma (rat 9L and 9L-R, and human U87 & LN18) cell lines. The results of this study demonstrate that cell penetrating peptide uptake varies with drug resistance status and cell type, likely due to changes in cell surface markers. This study provides insight into developing functional nanoplatform delivery systems in drug resistant cancer models.
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Antineoplásicos/administração & dosagem , Peptídeos Penetradores de Células/química , Portadores de Fármacos , Resistência a Múltiplos Medicamentos , Resistencia a Medicamentos Antineoplásicos , Sequência de Aminoácidos , Animais , Antineoplásicos/metabolismo , Linhagem Celular Tumoral , Endocitose , Corantes Fluorescentes/química , Humanos , Microscopia de Fluorescência , Pontos Quânticos , RatosAssuntos
Carcinoma de Células Escamosas , Neoplasias de Cabeça e Pescoço , Transplante de Rim , Neoplasias Cutâneas , Humanos , Carcinoma de Células Escamosas/cirurgia , Carcinoma de Células Escamosas/patologia , Neoplasias Cutâneas/cirurgia , Neoplasias Cutâneas/patologia , Carcinoma de Células Escamosas de Cabeça e Pescoço , Prognóstico , Invasividade Neoplásica/patologiaRESUMO
As massively parallel sequencing is implemented in forensic genetics, an understanding of sequence data must accompany these advancements, that is, accurate modeling of data for proper statistical analysis. Allelic drop-out, a common stochastic effect seen in genetic data, is often modeled in statistical analysis of STR results. This proof-of-concept study sequenced several serial dilutions of a standard sample ranging from 4 ng to 7.82 pg to evaluate allelic drop-out trends on a select panel of autosomal STRs using the ForenSeq™ DNA Signature Prep Kit, Primer Set A on the Illumina MiSeq FGx. Parameters assessed included locus, profile, and run specific information. A majority of the allelic drop-out occurred in DNA concentrations less than 31.25 pg. Statistical results indicated a need for locus-specific modeling based on STR descriptors, like simple versus compound repeat patterns. No correlation was seen between average read count of scored alleles and allelic drop-out at a locus. A statistical correlation was observed between the amount of allelic drop-out and the starting amount of DNA in a sample, average read count of a sample, and total read count generated on a flow cell. This study supports using common allelic drop-out factors used in fragment length analysis on sequenced STRs while including additional locus, sample, and run specific information. Results demonstrate multiple factors that can be considered when developing probability of allelic drop-out models for sequenced autosomal STRs including locus-specific analysis, total read count of a profile, and total read count sequenced on a flow cell.
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Alelos , Impressões Digitais de DNA , Sequenciamento de Nucleotídeos em Larga Escala , Repetições de Microssatélites , Análise de Sequência de DNA , Humanos , Estudo de Prova de Conceito , Reação em Cadeia da PolimeraseRESUMO
OBJECTIVE: Endovenous ablation has revolutionized treatment of varicose vein surgery but is associated with a risk of venous thromboembolism. There is no consensus regarding anticoagulation protocols for these patients. This network meta-analysis (NMA) aims to identify which anticoagulant is optimal in this cohort for clot prevention with minimal risk of adverse bleeding events. METHODS: Library databases were searched for studies where patients were treated with one or more anticoagulants following endovenous ablation for varicose veins. The methodological quality of included studies was quantified using the Risk of Bias (ROB) assessment tools. Findings were reported using the meta-analysis of observational studies in epidemiology (MOOSE) checklist. Statistical analysis was carried out using metainsight (rpackage). RESULTS: Observational data on just under 1500 patients prescribed post ablation anticoagulation (Rivaroxaban, Enoxaparin, Fondaparinux) were analyzed. Patient characteristics were comparable across the cohorts. 81 thrombotic and 40 minor bleeding events occurred in total. Overall rivaroxaban is found to be superior to the other agents. CONCLUSIONS: This NMA indicates that prophylactic rivaroxaban is the highest ranked anticoagulant for thromboprophylaxis in patients post endovenous ablation for varicose veins, with a low risk of adverse bleeding. The choice whether to anticoagulate these patients is likely to remain at the discretion of the treating clinician.
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Anticoagulantes , Procedimentos Endovasculares , Metanálise em Rede , Varizes , Tromboembolia Venosa , Adulto , Idoso , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Técnicas de Ablação/efeitos adversos , Anticoagulantes/efeitos adversos , Anticoagulantes/administração & dosagem , Procedimentos Endovasculares/efeitos adversos , Inibidores do Fator Xa/administração & dosagem , Inibidores do Fator Xa/efeitos adversos , Hemorragia/induzido quimicamente , Medição de Risco , Fatores de Risco , Rivaroxabana/administração & dosagem , Rivaroxabana/efeitos adversos , Resultado do Tratamento , Varizes/cirurgia , Tromboembolia Venosa/prevenção & controle , Tromboembolia Venosa/etiologia , Tromboembolia Venosa/diagnósticoRESUMO
The PrepFiler™ Forensic DNA Extraction Kits allow for optimal genomic DNA isolation and purification from forensic samples through a bind-wash-elute-based technique that can be performed manually or robotically using the Applied Biosystems AutoMate Express™ Forensic DNA Extraction System. The extraction kits come in two formats: the standard kit used for common case type samples, like bodily fluid swabs or stains, and a BTA kit for more challenging evidence sample types that can be submitted for analysis, like bones, teeth, and adhesive-type samples. Both forms of extraction, manual and semi-automated, require an initial manual incubation step using a lysis buffer to release the DNA into solution. If following the semi-automated protocol, the lysate can be purified and eluted on the AutoMate Express™. After lysis, the DNA binds to magnetic beads in the presence of a chaotropic salt and is washed multiple times with an ethanol-based wash buffer to purify the sample and remove potential PCR inhibitors. After removing the wash liquid, elution buffer is added to the tube containing the DNA-bound magnetic beads and heated, which disrupts the bonding between the DNA and beads. The DNA is then concentrated in the final tube and can be moved forward through the DNA analysis workflow. This chapter describes a manual DNA isolation method and the extraction procedures following both manual and robotic methods using the PrepFiler™ chemistries in conjunction with the AutoMate Express™ Forensic DNA Extraction System.
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Impressões Digitais de DNA , Dente , Impressões Digitais de DNA/métodos , Repetições de Microssatélites , Osso e Ossos , DNA/genéticaRESUMO
LRmix Studio performs statistical analyses on forensic casework samples by calculating a likelihood ratio (LR) following a semi-continuous, unrestricted approach. The software utilizes a basic probabilistic model allowing the comparison of two alternative hypotheses regarding the evidence profile to include known and/or unknown contributors, for a maximum of a 4-person mixture. Other statistical factors that are included in this model are the incorporation of multiple probability of drop-out values, probability of drop-in, a correction factor for population substructure, assumed contributor inclusion, and inclusion of an unknown relative in the defense hypothesis. A range of plausible probability of drop-out values can be calculated for various contributors and hypotheses based on a Monte Carlo probability method and included in the likelihood ratio calculation. The software also includes several ways to test the validity and robustness of the probabilistic model. A sensitivity analysis can be performed by calculating likelihood ratios for the given profile against a range of drop-out values. Additionally, a non-contributor test can be performed on the crime scene sample and the chosen LR parameters to test the robustness of the model. This can give a point of comparison of the likelihood ratio generated for the person of interest (POI) compared to "random man" profiles generated from uploaded allelic frequencies. Finally, the analysis can be printed in a well-structured and user-friendly report that includes all analysis parameters. Within this chapter, the reader will learn the steps to calculate a likelihood ratio using the semi-continuous software, LRmix Studio. Additional tools supplied through the software will also be explained and demonstrated.
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Impressões Digitais de DNA , DNA , Masculino , Humanos , Funções Verossimilhança , Impressões Digitais de DNA/métodos , DNA/análise , Repetições de Microssatélites , Modelos Estatísticos , SoftwareRESUMO
The RapidHIT™ ID System by Applied Biosystems allows the generation of a CODIS compatible STR profile in 90 min. The preloaded cartridges, fully automated workflow, and user-friendly computer interface allow for quick and simple single sample processing both in the laboratory and outside by non-laboratory personnel, like law enforcement officers. DNA processing utilizes a direct amplification workflow to generate an STR profile targeting the CODIS or ESS core loci. In conjunction with the RapidLINK™ Software, the system performs an initial analysis, flagging any profiles that do not meet single-source full profile parameters. Additionally, the RapidLINK™ allows for users to manage a multi-instrument/multi-location Rapid DNA system and view results in real-time. This gives users off-site the ability to track and even analyze results. The system allows for rapid reference sample analysis in locations like booking stations and national or border security agencies to obtain quick feedback of database hits for investigative leads while the subject is still in custody. RapidHIT™ ID DNA systems can also be set up at sites to aid in victim identification during mass disasters. The following chapter describes the process of generating a forensic DNA profile using the RapidHIT™ ID instrumentation from start to finish. Additionally, basic use and analysis using the RapidLINK™ and GeneMarker™ HID software is included.
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Impressões Digitais de DNA , Repetições de Microssatélites , Impressões Digitais de DNA/métodos , Reação em Cadeia da Polimerase , Reprodutibilidade dos Testes , DNA/genéticaRESUMO
Sequencing forensic DNA samples that are amplified and prepared with the ForenSeq™ DNA Signature Prep Kit allows for the simultaneous targeting of forensically relevant STR and SNP markers. The MiSeq™ FGx system allows massively parallel sequencing of these markers in a single analysis. The library preparation targets autosomal, Y-, and X-STRs, as well as identity SNPs. The kit can also be used to generate investigative information regarding the DNA contributor by analyzing phenotypic SNPs to predict hair color, eye color, and ancestry SNPs.Through two rounds of amplification, all loci are amplified and tagged with individualizing barcodes for sequencing capture and identification. Using bead-based technology, the libraries are purified by the removal of left-over amplification reagents and then normalized to ensure equal representation of all samples during sequencing. The individual libraries are then pooled for insertion into the MiSeq FGx. The pooled libraries are then added to a pre-packaged cartridge that contains all reagents necessary for optimal sequencing. Libraries are captured on a flow cell and undergo bridge amplification for the generation of individual clusters. Sequencing of each cluster is performed using a Sequence-By-Synthesis technology. The following chapter describes the methodology and process of library preparation of samples using the ForenSeq™ DNA Signature Prep Kit Primer Set A and B. Once completed, the chapter then focuses on the setup of a sequencing run on the MiSeq FGx and the sequencing methodology employed by the instrument.
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Impressões Digitais de DNA , Repetições de Microssatélites , Impressões Digitais de DNA/métodos , Repetições de Microssatélites/genética , Reprodutibilidade dos Testes , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Polimorfismo de Nucleotídeo Único , Primers do DNA , Análise de Sequência de DNARESUMO
The future of forensic DNA testing is being shaped by the research and usage of next-generation systems, which have increased the multiplexing capabilities of the field and the type and amount of genetic data that can be utilized for investigations. The NGS adoption for casework has been slow, albeit the plethora of data that has been published. This study evaluated the current opinions on sequencing in forensics. A 20-question online-survey focusing on NGS knowledge, training, and usage was distributed to 6001 forensic DNA researchers and practitioners worldwide. A total of 367 responses were obtained from all continents (North/South America (69.8%), Europe (21.2%), Asia (5.5%), Oceania (2.5%), and Africa (1%)). The respondents consisted of 50% practitioners, 31% researchers, and 19% both. Of these, 38% already own a next-gen sequencing instrument, and 13% are planning to purchase one. Overall, there exists an extensive knowledge on next-gen sequencing within the forensic community, including among laboratories that have not yet implemented this high-throughput technology in their workflows. Current usage focuses primarily on SNP analysis for investigative leads and mitochondrial DNA analysis while future applications included both STR and SNP testing applied to general casework. The major overall concerns respondents have for implementing a sequencing instrument include limited funding, staffing, lack of time, and the cost-effectiveness of providing this service. Specific technical concerns that the respondents had are the lack of training, statistical applications, bioinformatics support, and of rigorous guidelines and recommendations. Most of the respondents do believe there will be a technology shift from using CE only to the use of NGS on casework in 5-10 years. In addition, around 66% of respondents believe that it is moderately to very likely that the court will accept sequencing analysis. Sixteen percent fell in the middle, and the remaining 15% believe it is more unlikely, with 3% of respondents believing it is very unlikely. In conclusion, this work outlines current analytical challenges experienced by the global forensic DNA community and addresses different strategies for the implementation of next-gen sequencing technologies in casework.
Assuntos
DNA Mitocondrial , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , DNA Mitocondrial/genética , Análise de Sequência de DNA , Impressões Digitais de DNA , Genética ForenseRESUMO
INTRODUCTION: Mondor's disease of the penis, or superficial thrombophlebitis affecting penile veins, is a rare condition. Common causes include prothombotic states, venous stasis or excessive manipulation. The literature includes one case report of Mondor's Disease after endovenous laser ablation and foam sclerotherapy and a case series after open saphenofemoral junction ligation. However, there have been no noted cases of this rare complication after mechanochemical ablation of the GSV. CASE DETAILS: A 50-year-old man with bilateral great saphenous venous incompetence had truncal mechanochemical ablation of both above-knee GSV segments with the ClariveinTM device with adjunctive 1% Fibrovein foam to varicose tributaries. Day three post-operatively he began experiencing suprapubic pain and noted tender "cord-like" veins along the penile shaft. Duplex investigation of the penis demonstrated occlusive thrombus in the superficial veins draining into the dorsal vein of the penis. The patient was treated with 75 mg oral Clopidogrel for four weeks and his symptoms resolved without functional impairment. CONCLUSIONS: Vascular surgeons should be aware that this rare albeit self-limiting thrombotic complication can occur after endovenous mechanochemical ablation of the great saphenous vein with adjunct foam sclerotherapy, particularly as this procedure is performed very frequently. Interestingly, the majority of reported cases have occurred after bilateral interventions. The patients can be reassured that their symptoms will likely settle and the use of anti-thrombotic therapy is largely at the surgeon's discretion.