Testing amino acid-codon affinity hypothesis using molecular docking

Genetic code refers to a set of rules that assign trinucleotides called codons to amino acids in the process of protein synthesis. Investigating the genetic code's logic and its evolutionary origin has always been both intriguing and challenging. While the correspondence rules between codons and amino acids in the genetic code are well-known, it is still unclear whether those assignments can be explained based on energetic or/and entropic arguments. As an attempt at deciphering basic thermodynamic rules governing DNA translation, we used molecular docking to investigate the ability of amino acids to bind to their corresponding anticodon compared to other codons. The total number of 1280 direct docking interactions have been performed for each amino acid-codon/anti-codon case to find whether the amino acids have a preference to bind to their cognate anticodons or codons. Based on docking scores which are expected to correlate with binding affinity, no correlation with genetic correspondence rules was observed suggesting a more subtle process, other than direct binding, to explain codon-amino-acid specificity.

Accelerometer-based prediction of skeletal mechanical loading during walking in normal weight to severely obese subjects

There is no objective way to monitor mechanical loading characteristics during exercise for bone health improvement. We developed accelerometry-based equations to predict ground reaction force (GRF) and loading rate (LR) in normal weight to severely obese subjects. Equations developed had a high and moderate accuracy for GRF and LR prediction, respectively, thereby representing an accessible way to determine mechanical loading characteristics in clinical settings.

INTRODUCTION

There is no way to objectively prescribe and monitor exercise for bone health improvement in obese patients based on mechanical loading characteristics. We aimed to develop accelerometry-based equations to predict peak ground reaction forces (pGRFs) and peak loading rate (pLR) on normal weight to severely obese subjects.

METHODS

Sixty-four subjects (45 females; 84.6 ± 21.7 kg) walked at different speeds (2-6 km·h^-1) on a force plate-equipped treadmill while wearing accelerometers at lower back and hip. Regression equations were developed to predict pGRF and pLR from accelerometry data. Leave-one-out cross-validation was used to calculate prediction accuracy and Bland-Altman plots. Actual and predicted values at different speeds were compared by repeated measures ANOVA.

RESULTS

Body mass and peak acceleration were included for pGRF prediction and body mass and peak acceleration transient rate for pLR prediction. All pGRF equation coefficients of determination were above 0.89, a good agreement between actual and predicted pGRFs, with a mean absolute percent error (MAPE) below 6.7%. No significant differences were observed between actual and predicted pGRFs at each walking speed. Accuracy indices from our equations were better than previously developed equations for normal weight subjects, namely a MAPE approximately 3 times smaller. All pLR prediction equations presented a lower accuracy compared to those developed to predict pGRF.

CONCLUSION

Walking pGRF and pLR in normal weight to severely obese subjects can be predicted with moderate to high accuracy by accelerometry-based equations, representing an easy and accessible way to determine mechanical loading characteristics in clinical settings.

Erratum to "Gastroenteropancreatic Neuroendocrine Neoplasia Characterization in Portugal: Results from the NETs Study Group of the Portuguese Society of Endocrinology, Diabetes and Metabolism"

[This corrects the article DOI: 10.1155/2019/4518742.].

Gastroenteropancreatic Neuroendocrine Neoplasia Characterization in Portugal: Results from the NETs Study Group of the Portuguese Society of Endocrinology, Diabetes and Metabolism

BACKGROUND

The incidence of gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs) has been increasing in the last five decades, but there is no large-scale data regarding these tumours in Portugal. We conducted a cross-sectional, multicentric study in main Portuguese centers to evaluate the clinical, pathological, and therapeutic profile of GEP-NENs.

METHODS

From November, 2012, to July, 2014, data from 293 patients diagnosed with GEP-NENs from 15 centers in Portugal was collected and registered in an online electronic platform.

RESULTS

Median age at diagnosis was 56.5 (range: 15-87) years with a preponderance of females (54.6%). The most frequent primary sites were the pancreas (31.1%), jejunum-ileum (24.2%), stomach (13.7%), and rectum (8.5%). Data regarding hormonal status was not available in most patients (82.3%). Stratified by the tumour grade (WHO 2010 classification), we observed 64.0% of NET G1, 24.7% of NET G2, and 11.3% of NEC. Poorly differentiated tumours occurred mainly in older patients (p = 0.017), were larger (p < 0.001), and presented more vascular (p = 0.004) and lymphatic (p = 0.001) invasion. At the time of diagnosis, 44.4% of GEP-NENs presented metastatic disease. Surgery (79.6%) and somatostatin analogues (30.7%) were the most frequently used therapies of GEP-NENs with reported grading.

CONCLUSION

In general, Portuguese patients with GEP-NENs presented similar characteristics to other populations described in the literature. This cross-sectional study represents the first step to establish a national database of GEP-NENs that may aid in understanding the clinical and epidemiological features of these tumours in Portugal.

Assessment of bariatric surgery efficacy on Obstructive Sleep Apnea (OSA)

A worldwide rise in weight and obesity is taking place, associated with an increase in several comorbid conditions, such as Obstructive Sleep Apnea (OSA). Bariatric surgery is an effective treatment approach for obesity, with resultant improvement in obesity-related comorbidities. However, the relationship between this type of treatment and OSA is not well established. This systematic review aims to assess and characterize the impact that different types of bariatric surgery have on obese OSA patients. 22 articles with stated preoperative apnea-hypopnea index (AHI), apnea index (AI) or respiratory disturbance index (RDI) were analyzed in this review. A significant improvement in AHI/AI/RDI occurred after surgery, in addition to the foreseeable reduction in body mass index (BMI). Moreover, almost every study stated a postoperative reduction of the AHI to < 20/h and/or a >50% postoperative reduction of AHI, with few exceptions. The interventions with a combined malabsorptive and restrictive mechanism, like roux-en-Y gastric bypass (RYGB), were more efficacious in resolving and improving OSA than purely restrictive ones, like laparoscopic adjustable gastric banding (LAGB). In conclusion, bariatric surgery has a significant effect on OSA, leading to its resolution or improvement, in the majority of cases, at least in the short/medium term (1-2 years). However, the different results must be interpreted with caution as there are many potential biases resulting from heterogeneous inclusion criteria, duration of follow-up, diagnostic methodology and assessed variables.

Beyond central adiposity: liver fat and visceral fat area are associated with metabolic syndrome in morbidly obese patients

BACKGROUND

Despite its widespread clinical use, both body mass index (BMI) and waist circumference have been reported as inaccurate methods to measure abdominal obesity. The main objective of this study was to determine the relation between visceral fat area and fatty liver infiltration with the expression of metabolic syndrome (MS) in morbidly obese patients.

METHODS

We recruited a random selection of 100 morbidly obese patients on pre-operative evaluation for bariatric surgery. A pre-operative CT slice at L4-L5 level, was performed to measure visceral fat and at T12 level to measure hepatic attenuation.

RESULTS

Patients with MS had lower hepatic attenuation values (median 49.9 vs 55.5HU; p = .018) and had more VAT (242 vs 172 cm(2);p = .001). Conventional measures (BMI: p = .729 and waist circumference: p = .356), were not useful in discriminating morbidly obese patients with MS. By multivariable logistic regression, fatty liver infiltration (OR = 5.3; p = .03) and age (OR = 1.08; p = .04) were the only factors independently related to the presence of MS. MS prevalence was 100%, 71% and 55%, respectively for patients with both fatty liver and visceral adiposity; one; or none of this findings (AUC - .715; p = .016).

CONCLUSION

CT scan seems to measure 2 important markers of MS: visceral adiposity and hepatic fatty infiltration. In morbidly obese patients, both visceral adiposity and hepatic fatty infiltration increase the risk for the presence of MS.

Petersen's space hernia: A rare but expanding diagnosis

BACKGROUND

Petersen's space hernia is caused by the herniation of intestinal loops through the defect between the small bowel limbs, the transverse mesocolon and the retroperitoneum, after any type of gastrojejunostomy. The laparoscopic approach facilitates the occurrence of this type of hernia, due to the lack of post-operative adhesions which prevent bowel motility and hence, herniation.

CASE REPORT

We report the case of a 46 year-old male submitted to an open antrectomy and vagotomy with a Roux-en-Y reconstruction six-years before, for the treatment of bleeding gastric ulcer.He presented with epigastric abdominal pain radiating to the back and alimentary vomiting with a 3 days evolution, with an episode of hematemesis 2 h before admission. His abdomen was bloated and tender at the epigastric region. The laboratory exams revealed mild leucocytosis and CRP elevation with normal pancreatic tests. The abdominal CT scan revealed an intestinal occlusion. An exploratory laparotomy was performed, disclosing an incarcerated Petersen space hernia of the common limb, with obstruction and dilatation of the biliary limb.

CONCLUSION

The knowledge of this anatomic post-operative defect and a low threshold for diagnosis are crucial to its management, since its nonspecific clinical and laboratory findings. Early operative intervention is warranted in order to avoid the severe complications of bowel necrosis.

Early gastric cancer: The importance of early diagnosis on prognosis of gastric carcinoma

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Background: The aim of this study was to evaluate the characteristics of early gastric cancer (EGC) in comparison to advanced tumors and its role in patient's prognosis.

Methods: This study was related to 1,272 patients admitted with gastric or gastroesophageal junction carcinoma in our department, between January 1988 and December 2008. During this period the incidence of EGC was 12.68% (3.62% T0, 42.75% T1a and 53.62% T1b). Several clinical, pathological and staging parameters were evaluated according to classification in EGC and advanced tumors.

Results: Significant differences were observed in location (p<0.001); type of resection surgery (p<0.001) and of lymphadenectomy (p=0.008 for Siewert and p<0.001 for Japanese classifications) with less radical surgery in EGC patients. This type of tumors presented characteristics associated with a better prognosis in the following pathological parameters: tumor dimensions (p<0.001), macroscopic form (p<0.001), Ming's classification (p<0.001), venous invasion (p<0.001) and lymphatic permeation (p<0.001). The 5-year survival rate of this series was 33.7%. There were significant differences in survival curves according to classification in EGC and advanced tumors (73% at 5 years and 26% at 5 years, respectively). Cox-regression analysis identified age, T and lymph node ratio as independent prognostic factors. There was no significant differences in age (cut-off 45 years), but there was significant differences in lymph node metastasis (p<0.001). In 23.87% of EGC there was lymph node involvement, with significant differences (p=0.002) according to the depth wall invasion [T0 (100% N0), T1a (91.5% N0, 8.5% N1), T1b (60.8% N0, 21.6% N1, 13.5% N2, 4.1% N3a)].

Conclusions: The EGC percentage in our series was lower in comparison with other countries with high incidence of gastric cancer. The prognosis of the patients with gastric carcinoma continues to be gloomy mainly due to the late diagnosis and, given that the surgical treatment doesn't seem plausible of achieving a margin of significant additional progression, the need for an early diagnosis emerges if an improvement in patient survival is desired.

No significant financial relationships to disclose.

Early-onset gastric cancer: A distinct clinical entity with a different prognosis?

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Background: This study aimed to evaluate the early onset gastric cancer (EOGC), considered as gastric cancer in a patient younger than 45 years, as a distinct entity with a different prognosis.

Methods: This study is related to 1,256 patients admitted with gastric or gastroesophageal junction carcinoma in our department between January 1988 and December 2008. There were 10.59% (133 cases) of EOGC in our series. The following clinical, pathological and staging parameters were studied: age, gender, tumor location, ressecability, type of resection surgery, type of resection, type of lymphadenectomy (Siewert and Japanese classifications), number of lymph nodes studied, tumor dimensions, macroscopic form, histological classification (Lauren and Ming), venous invasion, lymphatic permeation, perineural invasion, depth wall invasion (T), lymph node metastases (N) – TNM and Japanese classification and lymph node ratio – distance metastases (M) and stage.

Results: Significant differences were observed in the type of resection surgery (p<0.001) and type of lymphadenectomy (p=0.008), with more radical surgery performed in EOGC patients. Some tumor characteristics also showed significant differences: tumor dimensions (p=0.004), with EOGC usually smaller; diffuse type according to Lauren's classification (p<0.001); infiltrative type according to Ming's classification (p=0.001); less venous invasion (p=0.005); less lymphatic permeation (p=0.029). There were no significant differences in the staging parameters. There were significant differences in the survival rate (p<0.001), with 5-year survival rate of 44% in patients with EOGC compared with 31% in older patients. Cox-regression analysis revealed that age was an independent prognostic factor (HR 2,166, 1,133-4,139 CI 95%, p = 0.019), as well as depth wall invasion (T) and lymph node ratio.

Conclusions: In this study, EOGC revealed to be a distinct clinical entity that presented differences in various clinico-pathological parameters. Despite EOGC presented more aggressive pathological characteristics, there was a better survival in this group, probably because the physical status of younger patients which allowed a more aggressive treatment.

No significant financial relationships to disclose.

Malnutrition among hospitalized patients. A problem of physician awareness

Between 25% and 50% of patients admitted to an acute medical service are malnourished. Physicians are often unaware which patients are admitted at nutritional risk and make no attempt to arrest further nutritional decline until a dramatic deterioration has occurred. We studied all patients admitted to an acute medical ward service before and after their physicians were taught to recognize nutritional deficiency early and to intervene appropriately. During the initial period, the house staff correctly identified two (12.5%) of 16 patients as being malnourished. During the posteducation period, physicians correctly identified all 14 patients admitted at nutritional risk (100%), using a simple screening device that required only routine admission data. In all cases, the appropriate nutritional intervention was subsequently made. Results were further validated using a pretest and posttest, showing a significant improvement in nutritional knowledge. We conclude that physicians are not presently being taught to recognize malnutrition, that such malnutrition is latrogenically worsened in the hospital, and that physician education can effectively correct this problem.