Mastering DNA chromatogram analysis in Sanger sequencing for reliable clinical analysis

BACKGROUND

Sanger dideoxy sequencing is vital in clinical analysis due to its accuracy, ability to analyze genetic markers like SNPs and STRs, capability to generate reliable DNA profiles, and its role in resolving complex clinical cases. The precision and robustness of Sanger sequencing contribute significantly to the scientific basis of clinical investigations. Though the reading of chromatograms seems to be a routine step, many errors conducted in PCR may lead to consequent limitations in the readings of AGCT peaks. These errors are possibly associated with improper DNA amplification and its subsequent interpretation of DNA sequencing files, such as noisy peaks, artifacts, and confusion between double-peak technical errors, heterozygosity, and double infection potentials. Thus, it is not feasible to read nucleic acid sequences without giving serious attention to these technical problems. To ensure the accuracy of DNA sequencing outcomes, it is also imperative to detect and rectify technical challenges that may lead to misinterpretation of the DNA sequence, resulting in errors and incongruities in subsequent analyses.

SHORT CONCLUSION

This overview sheds light on prominent technical concerns that can emerge prior to and during the interpretation of DNA chromatograms in Sanger sequencing, along with offering strategies to address them effectively. The significance of identifying and tackling these technical limitations during the chromatogram analysis is underscored in this review. Recognizing these concerns can aid in enhancing the quality of downstream analyses for Sanger sequencing results, which holds notable improvement in accuracy, reliability, and ability to provide crucial genetic information in clinical analysis.

Tips from the shop floor: postgraduate doctors working in trauma and orthopaedics

Trauma and orthopaedics is a useful rotation for junior doctors to undertake. Experience in the specialty allows doctors to feel more confident in the diagnosis and treatment of conditions affecting the entire musculoskeletal system. Many junior doctors cover on-calls in trauma and orthopaedics departments, often with no prior specialist experience. This article provides junior doctors with up-to-date information about how to prepare for a placement in trauma and orthopaedics, as well as helpful resources for those interested in a career in trauma and orthopaedics.

Ten Traits of Great Physicians! And Tips to Help You Improve

There are certain traits that differentiate great doctors from good doctors. This article will discuss some of these traits along with tips you can incorporate to go from good to great. By applying these tips, I hope you will enhance your ability to practice medicine and improve your patients' experience.

A case of peri‑stomal ectopic variceal bleeding in a patient with decompensated cirrhosis treated with TIPS placement

Peri-stomal variceal bleeding is an underestimated complication in patients with colostomy and portal hypertension. Due to the small number of reported cases, there is currently no unified consensus on the best treatment and several options may be available. We report a case in which TIPS placement was effective.

Nailfold capillaroscopy: tips and challenges

Although nailfold capillaroscopy (NFC) appears to have a bright future in clinical practice, the lack of familiarity with the technique and how to interpret its outcomes is major barriers which have made nailfold capillaroscopy an underutilized method in standard clinical practice. Traditional methods for assessment and measurement of capillary patterns, density, and blood flow are falling behind and face some challenges. In fact, there have been calls for improvement, hence the recent publication of the standardization of NFC by the EULAR Study Group on Microcirculation in Rheumatic Diseases. Nailfold capillaroscopy has the advantage of being a non-invasive technique that provides a window into the digital microcirculation. This paved the way for a rapidly growing interest in using capillaroscopy parameters as outcome measures in research. In standard clinical practice, whilst its main application is in the identification of an underlying systemic sclerosis spectrum disorder in patients presenting with Raynaud's phenomenon, its use has expanded to include other clinical features possibly suggestive of an underlying connective tissue disease. This article presents the challenges, provides tips, and highlights the exciting potential of nailfold capillaroscopy in standard practice.

Pearls and Pitfalls of the Virtual Interview: Perspectives From Both Sides of the Camera

As the SARS-COV-2 pandemic created the need for social distancing and the implementation of nonessential travel bans, residency and fellowship programs have moved toward a web-based virtual process for applicant interviews. As part of the Society of Asian Academic Surgeons 5th Annual Meeting, an expert panel was convened to provide guidance for prospective applicants who are new to the process. This article provides perspectives from applicants who have successfully navigated the surgical subspecialty fellowship process, as well as program leadership who have held virtual interviews.

Inpatient Mortality Benefit with Transjugular Intrahepatic Portosystemic Shunt for Hospitalized Hepatorenal Syndrome Patients

BACKGROUND

It has been reported that transjugular intrahepatic portosystemic shunting (TIPS) might be utilized as a salvage option for hepatorenal syndrome (HRS), while randomized controlled trials are pending and real-world contemporary data on inpatient mortality is lacking.

METHODS

We conducted an observational retrospective cohort study from the National Inpatient Sample from 2005 to 2014. We included all adult patients admitted with HRS and cirrhosis, using ICD 9-CM codes. We excluded cases with variceal bleeding, Budd-Chiari, end-stage renal disease, liver transplant and transfers to acute-care facilities. TIPS' association with inpatient mortality was assessed using multivariable mixed-effects logistic regression, as well as exact-matching, thus mitigating for TIPS selection bias. The exact-matched analysis was repeated among TIPS-only versus dialysis-only patients.

RESULTS

A total of 79,354 patients were included. Nine hundred eighteen (1.2%) underwent TIPS. Between TIPS and non-TIPS groups, mean age (58 years) and gender (65% males) were similar. Overall mortality was 18% in TIPS and 48% in dialysis-only cases (n = 10,379; 13.1%). Ninety six (10.5%) TIPS patients underwent dialysis. In-hospital mortality in TIPS patients was twice less likely than in non-TIPS patients (adjusted odds ratio [aOR] = 0.43, 95% CI 0.30-0.62; p < 0.001), with similar results in matched analysis [exact-matched (em) OR = 0.39, 95% CI 0.17-0.89; p < 0.024; groups = 96; unweighted n = 463]. Head-to-head comparison showed that TIPS-only patients were 3.3 times less likely to succumb inpatient versus dialysis-only patients (contrast aOR = 0.31, 95% CI 0.20-0.46; p < 0.001), with similar findings post-matching (emOR = 0.22, 95% CI 0.15-0.33; p < 0.001; groups = 54, unweighted n = 1457).

CONCLUSIONS

Contemporary, real-world data reveal that TIPS on its own, and when compared to dialysis, is associated with decreased inpatient mortality when utilized in non-bleeders-HRS patients. Further randomized studies are needed to establish the long-term benefit of TIPS in these patients.

Dual mobility cups for total hip arthroplasty: tips and tricks

Since its creation in 1974, the Dual Mobility Cup (DMC) has been gaining in popularity, especially in the past decade. This intensive use could lead to inappropriate use and consequently to an increased complication rate. Compliance with conceptual requirements and surgical techniques will prevent the occurrence of complications that can be wrongly attributed to implants. In this context, we feel that it is essential to share our tips and tricks as well as an overview and an explanation of common errors, based on more than 45 years of clinical and research experience. From basic principles, including indications, implant choice and implant compatibility, to surgical tips, in this article orthopedic surgeons will find a practical overview of DMC in order to use it safely and with confidence.

Twelve Tips for Applicants from a Disadvantaged Background Considering a Career in Medicine

This article was migrated. The article was marked as recommended. A minority of medical school entrants draw from disadvantaged backgrounds, which remain significantly under-represented within the medical workforce. Whilst multifactorial, this may in part relate to relative lack of information about the admissions process amongst these groups. In this article, Mohammed Abdul Waduud and colleagues offer their twelve essential tips to support students from disadvantaged backgrounds who are considering applying to medical school. The authors, all of whom are from disadvantaged backgrounds, have experience in applying to medical schools within the United Kingdom. The tips within this article should support students from disadvantaged backgrounds to decide whether a career in medicine is right for them and succeed in their applications to study medicine.

Enriching analyte molecules on tips of superhydrophobic gold nanocones for trace detection with SALDI-MS

The sensitivity of surface-assisted laser desorption/ionization (SALDI) mass spectrometry (MS) analysis depends on the efficiency of desorption and ionization of analyte molecules, which is usually limited by the low utilization efficiency of laser energy. Herein we demonstrate an efficient method to increase energy utilization efficiency for improving the efficiency of desorption and ionization of analyte molecules in SALDI-MS analysis. To increase the utilization efficiency of energy, a superhydrophobic gold film covered silicon nanocone array is fabricated and used as SALDI substrate. The nanocone array increases the absorption up to 99.65% at the wavelength of 355 nm, which is applied for SALDI-MS detection. The superhydrophobicity promotes the analyte molecules concentrated on the tips of nanocones where photon energy is confined, therefore, more energy can be provided for desorption and ionization of analytes. The energy efficiency is increased by using this substrate. The sensitivity of SALDI-MS analysis is greatly improved. For example, 100 amol/μL of rhodamine 6G, 100 fmol/μL of polyethyleneglycol, 100 ymol/μL of glutathione and 100 ymol/μL arginine still can be analyzed. The lake water containing malachite green was used as the real sample. The regression equation (Log I = 0.39 Log C + 6.58, R² = 0.9811) was obtained when the concentration of analyte was in the range from 10^-4 mol/L to 10^-8 mol/L. Therefore, the calculated LOD and LOQ are 1.35 × 10^-14 mol/L and 1.35 × 10^-7 mol/L, respectively. In addition, the lower relative standard deviation (0.7%, n = 10), proper recovery (113% and 91%), and low matrix effect (-1.1% and -1.1%) all demonstrate the great potential of the designed substrate in practical analysis.

Twelve tips for Applying to Clinical Academic Training in the United Kingdom

This article was migrated. The article was marked as recommended. MAW and colleagues offer their advice on applying for academic clinical training posts including the do's and don'ts. The authors all have experience of the national Integrated Academic Training (IAT) pathway in the United Kingdom. Whilst all the following top tips are not mandatory to attain a clinical academic role, we believe they would put a potential applicant in a good position to succeed, regardless of whether they were applying for an academic foundation post, academic clinical fellowship or a clinical lectureship. We have tailored our advice so that it may be considered when constructing an application as well as helping applicants for the interview.

How to approach Monteggia-like lesions in adults: A review

Monteggia-like lesions encompass a wide spectrum of fractures of the forearm and elbow associated with dislocations, subluxations and ligamentous lesions. Many attempts have been made to classify these injuries, not only to understand their pathology but also to develop optimal treatments. Unfortunately, although some of these classifications are complete, they are either complex, not immediately usable, or not exhaustive. An orthopedic surgeon who aims to rapidly treat this kind of injury needs a visual classification, and knowledge of the best surgical approach. Monteggia like lesions do not allow for mistakes during surgery, as even a minor error could be prove detrimental to performing and completing all surgical steps. In this paper, based on our extensive experience in treating these rare lesions, we suggest a practical guide to the best surgical approach for various types of Monteggia like lesions. Some technical tips and pitfalls are also described.

High-Resolution AFM-Based Force Spectroscopy

Atomic force microscopy (AFM)-based force spectroscopy is a powerful technique which has seen significant enhancements in both force and time resolution in recent years. This chapter details two AFM cantilever modification procedures that yield high force precision over different temporal bandwidths. Specifically, it explains a fairly straightforward method to achieve sub-pN force precision and stability at low frequencies (<50 Hz) by removing the metal coatings from a commercially available cantilever. A more involved procedure utilizing a focused ion beam milling machine is required to maintain high force precision at enhanced bandwidths. Both modification methods allow site-specific attachment of biomolecules onto the apex area of the tips for force spectroscopy. The chapter concludes with a comparative demonstration using the two cantilever modification methods to study a lipid-protein interaction.

Ten quick tips for machine learning in computational biology

Machine learning has become a pivotal tool for many projects in computational biology, bioinformatics, and health informatics. Nevertheless, beginners and biomedical researchers often do not have enough experience to run a data mining project effectively, and therefore can follow incorrect practices, that may lead to common mistakes or over-optimistic results. With this review, we present ten quick tips to take advantage of machine learning in any computational biology context, by avoiding some common errors that we observed hundreds of times in multiple bioinformatics projects. We believe our ten suggestions can strongly help any machine learning practitioner to carry on a successful project in computational biology and related sciences.

Outcomes in variceal hemorrhage following the use of a balloon tamponade device

BACKGROUND

Variceal hemorrhage is associated with high morbidity and mortality. A balloon tamponade device (BTD), such as the Sengstaken-Blakemore or Minnesota tube, may be used in cases of variceal hemorrhage. While these devices may be effective at controlling acute bleeding, the effect on patient outcomes remains less clear. We sought to describe the number of patients with variceal hemorrhage and a BTD who survive to discharge, survive to one-year, and develop complications related to a BTD.

METHODS

In this retrospective study, we identified patients at a single, tertiary care center who underwent placement of a BTD for upper gastrointestinal hemorrhage between 2003 and 2014. Patient characteristics and outcomes were summarized using descriptive statistics.

RESULTS

34 patients with a BTD were identified. Median age was 57.5 (IQR 47-63) and 76% (26/34) were male. Approximately 59% (20/34) of patients survived to discharge, and 41% (13/32) were alive after one year. Two patients were lost to follow-up. Of those surviving to discharge, 95% (19/20) had undergone transjugular intrahepatic portosystemic shunt (TIPS), while 36% (5/14) of patients who did not survive to discharge had TIPS (p<0.01). One complication, an esophageal perforation, was identified and managed conservatively.

CONCLUSION

In this cohort of patients undergoing BTD placement for variceal hemorrhage, approximately 59% of patients were alive at discharge and 41% were alive after one year. Placement of a BTD as a temporizing measure in the management of acute variceal hemorrhage may be helpful, particularly when utilized as a bridge to more definitive therapy.

Ten Immunization-Related Tips in Outpatient Practice

Keeping up with immunization recommendations and implementing them can be an ongoing challenge for clinicians. Ten tips related to various immunizations given in the outpatient setting are presented, as well as resources useful to the clinician in his or her daily practice.

Endoscopic retrograde cholangiopancreatography in periampullary diverticulum: The challenge of cannulation

Periampullary diverticulum (PAD) is duodenal outpunching defined as herniation of the mucosa or submucosa that occurs via a defect in the muscle layer within an area of 2 to 3 cm around the papilla. Although PAD is usually asymptomatic and discovered incidentally during endoscopic retrograde cholangiopancreatography (ERCP), it is associated with different pathological conditions such as common bile duct obstruction, pancreatitis, perforation, bleeding, and rarely carcinoma. ERCP has a low rate of success in patients with PAD, suggesting that this condition may complicate the technical application of the ERCP procedure. Moreover, cannulation of PAD can be challenging, time consuming, and require the higher level of skill of more experienced endoscopists. A large portion of the failures of cannulation in patients with PAD can be attributed to inability of the endoscopist to detect the papilla. In cases where the papilla is identified but does not point in a suitable direction for cannulation, different techniques have been described. Endoscopists must be aware of papilla identification in the presence of PAD and of different cannulation techniques, including their technical feasibility and safety, to allow for an informed decision and ensure the best outcome. Herein, we review the literature on this practical topic and propose an algorithm to increase the success rate of biliary cannulation.

Endoscopic septoplasty: Tips and pearls

This article is designed to provide a step-by-step description of our endoscopic septoplasty technique and discuss its difficulties and technical tips. Endoscopic septoplasty comprises 10 steps: diagnostic endoscopy, subperichondral infiltration, left mucosal incision, dissection of the left subperichondral flap, cartilage incision (0.5 centimetre posterior to the mucosal incision), dissection of the right subperichondral flap, anterior cartilage resection, perpendicular plate dissection, dissection and resection of the maxillary crest, endoscopic revision, mucosal suture and Silastic stents. A satisfactory postoperative result was observed at 3 months in 97% of cases in this series. The main contraindication to endoscopic septoplasty is anterior columellar deviation of the nasal septum requiring a conventional procedure.

Are you Scared Yet?: Evaluating Fear Appeal Messages in Tweets about the Tips Campaign

In March 2012, the CDC launched "Tips from Former Smokers," a $54 million national campaign featuring individuals experiencing long-term health consequences of smoking. The campaign approach was based on strong evidence that anti-tobacco ads portraying fear, graphic images, and personal testimonials are associated with attitudinal and behavior change. Yet it was also controversial; critics cited the danger that viewers might reject such intensely graphic messages. Tasked with informing this debate, our study analyzes the corpus of Tips campaign-related tweets obtained via the Twitter Firehose. We provide a novel and rigorous method for media campaign evaluation within the framework of the Extended Parallel Process Model. Among the relevant Tweets, 87% showed evidence of message acceptance, while 7% exhibited message rejection.

Aroma potential of Brancellao grapes from different cluster positions

In this study the presence of aroma compounds in grapes of Brancellao (Vitis vinifera L.) was investigated in order to obtain its aroma potential fingerprint. It is well known that differences exist in aromatic compounds amongst grapevine varieties at ripening stages. Within the framework of an increasingly competitive market, the chance of obtaining different wines from vines of the same variety grown at the same vineyard is becoming of increasing importance. This can be done through the managing of the vineyard, but also some wineries have assayed the separation of the tip and shoulder berries of the clusters of a specific variety with this objective. In this work it is evaluated that, in the final stages of maturation, differences exist in the probable alcoholic degree, total acidity of the must, as well as in the aromatic composition of skin and flesh of berries coming from the tips and shoulders of the clusters. Gas chromatography coupled to mass spectrometry (GC-MS) was used to determine the aromatic composition, in the skin and flesh of each sample, either tip or shoulder berries from the clusters. The obtained results showed that there was not variability for the probable alcoholic degree and total acidity between the shoulders and tips, whereas there was variability for their aromatic composition. For the berries from the tips of the clusters most of volatiles were found in the flesh (except aldehydes) and spicy and floral nuances (with the only exception of β-ionone) were in higher proportions. For the berries from the shoulders of the clusters, most of volatiles were found in the skin (monoterpenes, norisoprenoids, aldehydes, and C6 alcohols), where the flesh was slightly richer in aromatic alcohols, volatile phenols and pantolactone; β-ionone and herbaceous nuances were in higher proportions. These results are promising for those wineries that are considering the chance of separating berries from tips and shoulders of the clusters for the elaboration of different quality wines.

Bacteremia and "Endotipsitis" following transjugular intrahepatic portosystemic shunting

AIM

To identify all cases of bacteremia and suspected endotipsitis after Transjugular intrahepatic portosystemic shunting (TIPS) at our institution and to determine risk factors for their occurrence.

METHODS

We retrospectively reviewed records of all patients who underwent TIPS in our institution between 1996 and 2009. Data included: indications for TIPS, underlying liver disease, demographics, positive blood cultures after TIPS, microbiological characteristics, treatment and outcome.

RESULTS

49 men and 47 women were included with a mean age of 55.8 years (range 15-84). Indications for TIPS included variceal bleeding, refractory ascites, hydrothorax and hepatorenal syndrome. Positive blood cultures after TIPS were found in 39/96 (40%) patients at various time intervals following the procedure. Seven patients had persistent bacteremia fitting the definition of endotipsitis. Staphylococcus species grew in 66% of the positive cultures, Candida and enterococci species in 15% each of the isolates, and 3% cultures grew other species. Multi-variate regression analysis identified 4 variables: hypothyroidism, HCV, prophylactic use of antibiotics and the procedure duration as independent risk factors for positive blood cultures following TIPS (P < 0.0006, 0.005, 0.001, 0.0003, respectively). Prophylactic use of antibiotics before the procedure was associated with a decreased risk for bacteremia, preventing mainly early infections, occurring within 120 d of the procedure.

CONCLUSION

Bacteremia is common following TIPS. Risk factors associated with bacteremia include failure to use prophylactic antibiotics, hypothyroidism, HCV and a long procedure. Our results strongly support the use of prophylaxis as a means to decrease early post TIPS infections.

Is color-Doppler US a reliable method in the follow-up of transjugular intrahepatic portosystemic shunt (TIPS)?

Transjugular intrahepatic portosystemic shunt (TIPS) has become a widely accepted treatment for complications of portal hypertension. Shunt or hepatic vein stenoses or occlusions are common short- and mid-term complications of the procedure, with a one-year primary patency ranging from 25% to 66%. When promptly identified, shunt stenosis or occlusion may be treated before the recurrence of gastrointestinal bleeding or ascites. The revision is usually successful and the primary-assisted patency of TIPS is approximately 85% at one year.Doppler sonography is a widely accepted screening modality for TIPS patients, both as a routine follow-up in asymptomatic patients and in those cases with clinically suspected TIPS malfunction.In a routine US follow-up, a TIPS patient is scheduled for a control 24 h after the procedure, and then after one week, 1 month, 3 months, and at 3-month intervals thereafter. Venography is at present performed solely on the basis of a suspected shunt dysfunction during the sonographic examination.Color-Doppler sonography is the most reliable method for monitoring the shunt function after TIPS implantation. Several studies have shown that Doppler sonography is a sensitive and relatively specific way to detect shunt malfunction, particularly when multiple parameters are examined. Achieving high sensitivity is optimal so that malfunctioning shunts can be identified and shunt revision can be performed before symptomatic deterioration. Venous angiography is at present indicated only on the basis of US suspicion of shunt compromise. Power-Doppler US and US contrast media can be useful in particular conditions, but are not really fundamental.