Multi-project and Multi-profile joint Non-negative Matrix Factorization for cancer omic datasets.

MOTIVATION: The integration of multi-omic data using machine learning methods has been focused on solving relevant tasks such as predicting sensitivity to a drug or subtyping patients. Recent integration methods, such as joint Non-negative Matrix Factorization, have allowed researchers to exploit the information in the data to unravel the biological processes of multi-omic datasets. RESULTS: We present a novel method called Multi-project and Multi-profile joint Non-negative Matrix Factorization capable of integrating data from different sources, such as experimental and observational multi-omic data. The method can generate co-clusters between observations, predict profiles and relate latent variables. We applied the method to integrate low-grade glioma omic profiles from The Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia projects. The method allowed us to find gene clusters mainly enriched in cancer-associated terms. We identified groups of patients and cell lines similar to each other by comparing biological processes. We predicted the drug profile for patients, and we identified genetic signatures for resistant and sensitive tumors to a specific drug. AVAILABILITY AND IMPLEMENTATION: Source code repository is publicly available at https:/bitbucket.org/dsalazarb/mmjnmf/-Zenodo DOI: 10.5281/zenodo.5150920. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Acute Abdomen Secondary to a Spontaneous Perforation of the Biliary Tract, a Rare Complication of Choledocholithiasis.

INTRODUCTION: The spontaneous perforation of the biliary tract (SPBT) is an extremely rare cause of peritonitis, which was first described by Freeland in 1982, to date only around 70 cases have been reported. Here we present a case of spontaneous perforation of the biliary tract, in a patient with choledocholithiasis, which was treated with ultrasound-guided drainage and ERCP. CASE REPORT: A 51-year-old male was admitted to the emergency room for 15-day evolution jaundice, localized pain in the right flank and hypochondrium of 3days. He had a history of cholecystectomy 15 years ago and 4 episodes of cholangitis, the last one in 2015. A magnetic resonance imaging (MRI) was performed, that showed evidence of choledocholithiasis, in addition to a possible biliary leakage. The patient was treated with ultrasound-guided drainage and ERCP successfully. DISCUSSION: Spontaneous perforation of the biliary tract is a disease entity in which wall of the extrahepatic or intrahepatic duct is perforated without any traumatic or iatrogenic injury. The clinical presentation varies from nonspecific abdominal pain to biliary peritonitis, in most of the cases forming bilomas. Universal management involves decompression of the biliary tree and repair of the leak site. CONCLUSION: The spontaneous perforation of the biliary tract is a disease that represents a diagnostic challenge. The treatment in the patients with SPBT is not well established and has to be individualized for each case, depending on the history of the patient, the site of perforation, the time of evolution, the suspicion of infection, and the patient status.

A rare case of subacute appendicitis, actinomycosis as the final pathology reports: A case report and literature review.

INTRODUCTION: Acute appendicitis is the most common indication for an emergency abdominal surgery in the world, with a lifetime incidence of around 10%. Actinomycetes are the etiology of appendicitis in only 0.02%-0.06%, having as the final pathology report a chronic inflammatory response; less than 10% of the cases are diagnosed before surgery. Here, we present the case of a subacute appendicitis secondary to actinomycosis. CASE REPORT: A 39-year-old male presented with a twelve-day evolution of intermittent abdominal pain in the right lower quadrant, treated at the beginning with ciprofloxacin and urinary analgesic. The day of the admission he referred intense abdominal pain with nausea. An open appendectomy was preformed, finding a tumor-like edematous appendix with a diameter of approximately 2.5cm. DISCUSSION: Actinomyces are part of the typical flora of the oral cavity, gastrointestinal tract and vagina. The predominant form of human disease is A. Israelii, it requires an injury to the normal mucosa to penetrate and cause disease. Abdominal actinomycosis involves the appendix and caecum in 66% of the presentations, of these, perforated appendicitis is the stimulus in 75% of the cases. A combination of antibiotic therapy and operative treatment resolves actinomycosis in 90% of cases. CONCLUSION: Abdominal actinomycosis is an uncommon disease been the common presentation a perforated appendicitis, here we present a less common presentation of it with a non-perforated appendix.

Gallstone ileus: An overview of the literature. / El íleo biliar: una revisión de la literatura médica.

INTRODUCTION: Gallstone ileus represents 4% of the causes of bowel obstruction in the general population, but increases to 25% in patients above the age of 65 years. Gallstone ileus does not present with unique symptoms, making diagnosis difficult. Its management is surgical, but there is no consensus as to which of the different surgical techniques is the procedure of choice. At present, there is no recent review of this pathology. AIM: To conduct an up-to-date review of this disease. MATERIALS AND METHODS: Articles published within the time frame of 2000 to 2014 were found utilizing the PUBMED, EMBASE, and Cochrane Library search engines with the terms "gallstone ileus" plus "review" and the following filters: "review", "full text", and "humans". RESULTS: The results of this review showed that gallstone ileus etiology was due to intestinal obstruction from a gallstone that migrated into the intestinal lumen through a bilioenteric fistula. The presence of 2 of the 3 Rigler's triad signs was considered diagnostic. Abdominal tomography was the imaging study of choice for gallstone ileus diagnosis and the surgical procedures for management were enterolithotomy, one-stage surgery, and two-stage surgery. Enterolithotomy had lower morbidity and mortality than the other 2 procedures. CONCLUSIONS: The aim of gallstone ileus treatment is to release the obstruction, which is done through enterolithotomy. It is the recommended technique for gallstone ileus management because of its lower morbidity and mortality, compared with the other techniques.

A rare case of a strangulated Littre's hernia with Meckel's diverticulum duplication. Case report and literature review.

INTRODUCTION: The Meckel's diverticulum (MD) is the most common congenital anomaly of the gastrointestinal tract present in approximately 1-4% of the population; the MD duplication is exceedingly rare with only a few reports of it. Here we present the firs case of a strangulated Littre's hernia with MD duplication. PRESENTATION OF CASE: A 30-year-old male presented to the emergency room with clinical signs of small bowel obstruction, at physical examination, a right incarcerated inguinal hernia with erythema was found. We did a laparotomy, and two MD were found, one in the sac with ischemia, and the other 90cm from the Bahuins valve. A diverticulectomy of the ischemic diverticulum was done, and the other MD was left in place; the inguinal region was repaired with a Lichtenstein technique. DISCUSSION: The complications of the MD are 3-4 times more frequent in men, been an intestinal obstruction, hemorrhage, diverticulitis, ulceration, and perforation. A Littrés hernia is when the MD is found in the sac; this is seen in the inguinal region in 50% of the cases. The management of a Littre's hernia is the resection of the MD; it could be done by an intestinal resection or by a diverticulectomy accordingly to the Park criteria. CONCLUSION: As to our knowledge, this is the first case of an incarcerated Littre's hernia with duplication of a Meckel's diverticulum.

Cervicovaginal agenesis treated with modified Yang-Monti technique in two steps: Case report and literature review.

INTRODUCTION: Müllerian duct anomalies are rare with less than 200 cases published in the literature. Recently, the implementation of the Yang-Monti principle for the creation of the neovagina has been used in 10 previous published cases. Here, we report the first case of cervicovaginal agenesis treated with the modified Yang-Monti technique in two steps in México. PRESENTATION OF CASE: A 14-year-old female presented to the pediatric consult with a history of primary amenorrhea and a chronic-cyclic pelvic pain. She had normal external genitalia and secondary sexual characteristics, with a small vaginal pouch. Pelvic ultrasonography and magnetic resonance showed the absence of cervix and proximal vagina. The surgical approach was carried out in two steps. In the first, a neovagina was created with the modified Yang-Monti technique. On a second step one year after, the neovaginal dome was anastomosed with the uterus in a diamond shape, using Gore-tex® in the cervicovaginal anastomosis, and a Foley catheter to prevent stenosis. After an 18-month follow-up, no complications have been observed. She has been taking Drospirenone and Ethinyl Estradiol with regular menstrual cycles. DISCUSSION: The surgical treatment of cervicovaginal agenesis has evolved. The advantages of the modified Yang-Monti technique lie in the possible diminution of the tension on the vascular pedicle, and the gained length of the neovagina. To perform this procedure in two steps, likely diminishes the risk of neovaginal ischemia and leakage of the anastomosis. CONCLUSION: The two-steps modified Yang-Monti technique represents a safe alternative for the management of cervicovaginal agenesis.

Grynfelt-Lesshaft hernia a case report and review of the literature.

INTRODUCTION: Lumbar hernia account for less than 2% of al abdominal hernias, been the Grynfelt-Lesshaft's hernia (GLH) more frequent than the others. With approximately 300 cases published in the literature, the general surgeon may have the chance of treat it ones in their professional life. CASE REPORT: A 42-years old male with human immunodeficiency virus and Diabetes Mellitus presented to the outpatient clinic with a GLH. Preoperative classified as a type "A" lumbar hernia an open approach was scheduled. We performed a Sandwich technique with a sublay and onlay ULTRAPRO(®) mesh fixed with PDS(®) II suture without complications and discharged the patient 24-h after. After six months, the patient denied any complication. DISCUSSION: Primary (spontaneous) lumbar hernias represent 50-60% of all GLH. The preoperative classification of a lumbar hernia is mandatory to propose the best surgical approach. According to the classification of Moreno-Egea A et al., the best technique for our patient was an open approach. The Sandwich technique has demonstrated good outcomes in the management of the GLH. CONCLUSION: The surgical approach should be according to the classification proposed and to the experience of the surgeon. The Sandwich technique has good outcomes.

Diagnostic value of serum fibrinogen as a predictive factor for complicated appendicitis (perforated). A cross-sectional study.

BACKGROUND: Acute appendicitis (AA) has a prevalence of 8% in the general population with a rate of complicated (perforated) appendicitis (CA) up to 40%. Serum fibrinogen may serve as an indicator for CA. PATIENTS AND METHODS: 115 patients were included from January 2012 to December 2012 using a positive pathology report for AA as a gold standard diagnostic method. We divided the patients into two groups accordingly to the pathology report: Complicated Appendicitis and Uncomplicated Appendicitis (UA). Our primary endpoint was to compare the levels of serum fibrinogen between the two groups and find if there is a relationship between fibrinogen level and CA. RESULTS: 68 patients were diagnosed with UA and 47 with CA. Using a fibrinogen value of 885 mg/dl we found to be the best cut-off for predicting complicated appendicitis with a sensitivity of 86.77% (76.87-93.71 IC 95%), a specificity of 91.49 (83.51-99.46 IC 95%), a positive predictive value of 93.65 (95% CI 86.81-99.64) and, a negative predictive value of 82.69 (95% CI 65.73-87.84). CONCLUSION: In the setting of a patient with a clinical diagnosis of AA, this study demonstrates fibrinogen as a good predictor factor for appendiceal perforation.