Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach

Polymorphism discovery is a routine application of next-generation sequencing technology where multiple samples are sent to a service provider for library preparation, subsequent sequencing, and bioinformatic analyses. The decreasing cost and advances in multiplexing approaches have made it possible to analyze hundreds of samples at a reasonable cost. However, because of the manual steps involved in the initial processing of samples and handling of sequencing equipment, cross-contamination remains a significant challenge. It is especially problematic in cases where polymorphism frequencies do not adhere to diploid expectation, for example, heterogeneous tumor samples, organellar genomes, as well as during bacterial and viral sequencing. In these instances, low levels of contamination may be readily mistaken for polymorphisms, leading to false results. Here we describe practical steps designed to reliably detect contamination and uncover its origin, and also provide new, Galaxy-based, readily accessible computational tools and workflows for quality control. All results described in this report can be reproduced interactively on the web as described at http://usegalaxy.org/contamination

Injectable local anaesthetic agents for dental anaesthesia

Background: Pain during dental treatment, which is a common fear of patients, can be controlled successfully by local anaesthetic. Several different local anaesthetic formulations and techniques are available to dentists. / Objectives: Our primary objectives were to compare the success of anaesthesia, the speed of onset and duration of anaesthesia, and systemic and local adverse effects amongst different local anaesthetic formulations for dental anaesthesia. We define success of anaesthesia as absence of pain during a dental procedure, or a negative response to electric pulp testing or other simulated scenario tests. We define dental anaesthesia as anaesthesia given at the time of any dental intervention. Our secondary objective was to report on patients' experience of the procedures carried out. / Search methods: We searched the Cochrane Central Register of Controlled Trials (CENTRAL; the Cochrane Library; 2018, Issue 1), MEDLINE (OVID SP), Embase, CINAHL PLUS, WEB OF SCIENCE, and other resources up to 31 January 2018. Other resources included trial registries, handsearched journals, conference proceedings, bibliographies/reference lists, and unpublished research. / Selection criteria: We included randomized controlled trials (RCTs) testing different formulations of local anaesthetic used for clinical procedures or simulated scenarios. Studies could apply a parallel or cross‐over design. / Data collection and analysis: We used standard Cochrane methodological approaches for data collection and analysis. / Main results: We included 123 studies (19,223 participants) in the review. We pooled data from 68 studies (6615 participants) for meta‐analysis, yielding 23 comparisons of local anaesthetic and 57 outcomes with 14 different formulations. Only 10 outcomes from eight comparisons involved clinical testing. We assessed the included studies as having low risk of bias in most domains. Seventy‐three studies had at least one domain with unclear risk of bias. Fifteen studies had at least one domain with high risk of bias due to inadequate sequence generation, allocation concealment, masking of local anaesthetic cartridges for administrators or outcome assessors, or participant dropout or exclusion. We reported results for the eight most important comparisons. / Success of anaesthesia: When the success of anaesthesia in posterior teeth with irreversible pulpitis requiring root canal treatment is tested, 4% articaine, 1:100,000 epinephrine, may be superior to 2% lidocaine, 1:100,000 epinephrine (31% with 2% lidocaine vs 49% with 4% articaine; risk ratio (RR) 1.60, 95% confidence interval (CI) 1.10 to 2.32; 4 parallel studies; 203 participants; low‐quality evidence). When the success of anaesthesia for teeth/dental tissues requiring surgical procedures and surgical procedures/periodontal treatment, respectively, was tested, 3% prilocaine, 0.03 IU felypressin (66% with 3% prilocaine vs 76% with 2% lidocaine; RR 0.86, 95% CI 0.79 to 0.95; 2 parallel studies; 907 participants; moderate‐quality evidence), and 4% prilocaine plain (71% with 4% prilocaine vs 83% with 2% lidocaine; RR 0.86, 95% CI 0.75 to 0.99; 2 parallel studies; 228 participants; low‐quality evidence) were inferior to 2% lidocaine, 1:100,000 epinephrine. Comparative effects of 4% articaine, 1:100,000 epinephrine and 4% articaine, 1:200,000 epinephrine on success of anaesthesia for teeth/dental tissues requiring surgical procedures are uncertain (RR 0.85, 95% CI 0.71 to 1.02; 3 parallel studies; 930 participants; very low‐quality evidence). Comparative effects of 0.5% bupivacaine, 1:200,000 epinephrine and both 4% articaine, 1:200,000 epinephrine (odds ratio (OR) 0.87, 95% CI 0.27 to 2.83; 2 cross‐over studies; 37 participants; low‐quality evidence) and 2% lidocaine, 1:100,000 epinephrine (OR 0.58, 95% CI 0.07 to 5.12; 2 cross‐over studies; 31 participants; low‐quality evidence) on success of anaesthesia for teeth requiring extraction are uncertain. Comparative effects of 2% mepivacaine, 1:100,000 epinephrine and both 4% articaine, 1:100,000 epinephrine (OR 3.82, 95% CI 0.61 to 23.82; 1 parallel and 1 cross‐over study; 110 participants; low‐quality evidence) and 2% lidocaine, 1:100,000 epinephrine (RR 1.16, 95% CI 0.25 to 5.45; 2 parallel studies; 68 participants; low‐quality evidence) on success of anaesthesia for teeth requiring extraction and teeth with irreversible pulpitis requiring endodontic access and instrumentation, respectively, are uncertain. For remaining outcomes, assessing success of dental local anaesthesia via meta‐analyses was not possible. / Onset and duration of anaesthesia: For comparisons assessing onset and duration, no clinical studies met our outcome definitions. Adverse effects (continuous pain measured on 170‐mm Heft‐Parker visual analogue scale (VAS)) Differences in post‐injection pain between 4% articaine, 1:100,000 epinephrine and 2% lidocaine, 1:100,000 epinephrine are small, as measured on a VAS (mean difference (MD) 4.74 mm, 95% CI ‐1.98 to 11.46 mm; 3 cross‐over studies; 314 interventions; moderate‐quality evidence). Lidocaine probably resulted in slightly less post‐injection pain than articaine (MD 6.41 mm, 95% CI 1.01 to 11.80 mm; 3 cross‐over studies; 309 interventions; moderate‐quality evidence) on the same VAS. For remaining comparisons assessing local and systemic adverse effects, meta‐analyses were not possible. Other adverse effects were rare and minor. / Patients' experience: Patients' experience of procedures was not assessed owing to lack of data. / Authors' conclusions: For success (absence of pain), low‐quality evidence suggests that 4% articaine, 1:100,000 epinephrine was superior to 2% lidocaine, 1:100,000 epinephrine for root treating of posterior teeth with irreversible pulpitis, and 2% lidocaine, 1:100,000 epinephrine was superior to 4% prilocaine plain when surgical procedures/periodontal treatment was provided. Moderate‐quality evidence shows that 2% lidocaine, 1:100,000 epinephrine was superior to 3% prilocaine, 0.03 IU felypressin when surgical procedures were performed. Adverse events were rare. Moderate‐quality evidence shows no difference in pain on injection when 4% articaine, 1:100,000 epinephrine and 2% lidocaine, 1:100,000 epinephrine were compared, although lidocaine resulted in slightly less pain following injection. Many outcomes tested our primary objectives in simulated scenarios, although clinical alternatives may not be possible. Further studies are needed to increase the strength of the evidence. These studies should be clearly reported, have low risk of bias with adequate sample size, and provide data in a format that will allow meta‐analysis. Once assessed, results of the 34 ‘Studies awaiting classification (full text unavailable)’ may alter the conclusions of the review

Frequency of depression among patients with neurocysticercosis Depressão em pacientes portadores de neurocisticercose

Neurocysticercosis (NCC) is a common central nervous system infection caused by Taenia solium metacestodes. OBJECTIVE: To investigate the occurrence of depression in patients with calcified NCC form. The study group consisted of 114 patients subdivided in four groups: NCC with epilepsy, NCC without epilepsy, epilepsy without NCC and chronic headache. METHOD: Depression was evaluated and quantified by the Hamilton Rating Scale for Depression (HRSD-21). RESULTS: Percentage of patients with depression was as follows: group 1 (83%); group 2 (88%); group 3 (92%); group 4 (100%). The majority of patients had moderate depression. CONCLUSION: Incidence of depression in all groups was higher than in the general population. It is possible that, in a general way, patients with chronic diseases would have depression with similar intensity. NCC is associated with the presence of depression.<br>Neurocysticercose (NCC) é uma infecção do sistema nervoso central comum causada por metacestodes da Taenia solium. OBJETIVO: investigar a ocorrência de depressão nos pacientes com NCC forma calcificada. O grupo de estudo é formado por 114 pacientes subdivididos em quatro grupos: NCC com epilepsia, NCC sem epilepsia, epilepsia sem NCC e cefaléia crônica. MÉTODO: A presença de depressão foi determinada e quantificada pela Escala de Depressão de Hamilton (HRSD-21). RESULTADOS: A porcentagem de pacientes com depressão foi: grupo 1 (83%); grupo 2 (88%); grupo 3 (92%); grupo 4 (100%). A maioria dos pacientes apresentou depressão moderada. CONCLUSÃO: A incidência da depressão em todos os grupos foi mais elevada do que na população geral, contudo não houve diferença entre os grupos estudados. É possível que, de uma maneira geral, os pacientes portadores de doença crônica apresentarem a depressão em intensidade similar. NCC está associada com a presença de depressão