Sparse representation via ℓ1-minimization for underdetermined systems in classification of tumors with gene expression data

The development of cancer diagnosis models and cancer discovery from DNA microarray data are of great interest in bioinformatics and medicine. In pattern recognition and machine learning, a classification problem refers to finding an algorithm for assigning a given input data into one of several categories. Many natural signals are sparse or compressible in the sense that they have short representations when expressed in a suitable basis. Motivated by the recent successful algorithm developments for sparse signal recovery, we apply the selective nature of sparse representation to perform the above mentioned classification. In order to find such sparse representation we implement an ℓ(1)-minimization algorithm. This methodology overcomes the lack of robustness with respect to outliers. In contrast to other classification algorithms, no model selection dependency is involved. The minimization algorithm is a convex relaxation-like that has been proven to efficiently recover sparse signals. To study its performance, the proposed method is applied to six tumor gene expression datasets and numerically compared with various support vector machine methods (SVM). The numerical results show that the ℓ(1)-minimization algorithm proposed performs at least comparably and often better than SVMs.

Characterization of subcortical structures during deep brain stimulation utilizing support vector machines

In this paper we discuss an efficient methodology for the characterization of Microelectrode Recordings (MER) obtained during deep brain stimulation surgery for Parkinson's disease using Support Vector Machines and present the results of a preliminary study. The methodology is based in two algorithms: (1) an algorithm extracts multiple computational features from the microelectrode neurophysiology, and (2) integrates them in the support vector machines algorithm for classification. It has been applied to the problem of the recognition of subcortical structures: thalamus nucleus, zona incerta, subthalamic nucleus and substantia nigra. The SVM (support vector machines) algorithm performed quite well achieving 99.4% correct classification. In conclusion, the use of a computer-based system, like the one described in this paper, is intended to avoid human subjectivity in the localization of the subcortical structures and mainly the subthalamic nucleus (STN) for neurostimulation.

[Safety and efficacy of an early deambulation protocol after PTCA with an angio-seal device]

INTRODUCTION

In order to assess the efficacy and safety of an early deambulation (1-2 h) protocol after coronary angioplasty using the Angio-seal collagen plug, we analyzed a consecutive series of patients treated with this device versus a reference group treated with mechanical compression.

PATIENTS AND METHODS

Two hundred and seven coronary angioplasty patients were included from February to August 2000. Ninety-eight were treated with mechanical compression and one hundred and nine with the Angio-seal collagen plug. All patients were followed at discharge and fifteen days after surgery.

RESULTS

Eighty percent of the patients receiving the Angio-seal device achieved immediate hemostasis (< 1 min). In patients with mechanical compression hemostasis was achieved within 30 min in 68.3%, whereas 25.5% of patients required more than 40 min. First deambulation in the Angio-seal group was achieved within 2 h in 94.5% of the patients. The incidence of major complications was low in both groups (1 case in the Angio-seal group and 2 in the C-clamp group) without statistically significant differences. The Angio-seal group showed a lower incidence of overall vascular complications as compared to the C-clamp group (4.6% vs. 14.3%; p = 0.02).

CONCLUSION

Following our protocol, an early deambulation strategy after coronary angioplasty with the use of the Angio-seal collagen plug was feasible, safe and efficacious.

A novel NADPH-dependent aldehyde reductase gene from Vigna radiata confers resistance to the grapevine fungal toxin eutypine

Eutypine, 4-hydroxy-3-(3-methyl-3-butene-1-ynyl) benzyl aldehyde, is a toxin produced by Eutypa lata, the causal agent of eutypa dieback of grapevines. It has previously been demonstrated that tolerance of some cultivars to this disease was correlated with their capacity to convert eutypine to the corresponding alcohol, eutypinol, which lacks phytotoxicity. We have thus purified to homogeneity a protein from Vigna radiata that exhibited eutypine-reducing activity and have isolated the corresponding cDNA. This encodes an NADPH-dependent reductase of 36 kDa that we have named Vigna radiata eutypine-reducing enzyme (VR-ERE), based on the capacity of a recombinant form of the protein to reduce eutypine into eutypinol. The strongest homologies (86.8%) of VR-ERE at the amino acid level were found with CPRD14, a drought-inducible gene of unknown function, isolated from Vigna unguiculata and with an aromatic alcohol dehydrogenase (71.7%) from Eucalyptus gunnii. Biochemical characterization of VR-ERE revealed that a variety of compounds containing an aldehyde group can act as substrates. However, the highest affinity was observed with 3-substituted benzaldehydes. Expression of a VR-ERE transgene in Vitis vinifera cells cultured in vitro conferred resistance to the toxin. This discovery opens up new biotechnological approaches for the generation of grapevines resistant to eutypa dieback.

Predictive factors of oxygen desaturation during upper gastrointestinal endoscopy in nonsedated patients

BACKGROUND

Hypoxemia can occur during upper gastrointestinal endoscopy with or without pharmacologic sedation. We investigated possible predictive factors of severe oxygen desaturation (SaO2 < 90%) in nonsedated patients undergoing endoscopy.

METHODS

A total of 481 patients who underwent upper gastrointestinal endoscopy without sedation were monitored with continuous pulse oximetry. Multivariate logistic regression analysis was used to identify factors related to the patient, the examination, and the monitoring data that would predict severe desaturation.

RESULTS

Mild desaturation (SaO2 between 90% and 94%) was found in 23.7% of the patients, and severe desaturation (SaO2 < 90%) was found in 6.4%. The variables found to predict severe desaturation were basal SaO2 < 95% (odds ratio 67.7), respiratory disease (odds ratio 30.5), more than one attempt needed for intubation (odds ratio 39.4), emergency procedure (odds ratio 14.9), and American Society of Anesthesiologists score of III or IV (odds ratio 3.9).

CONCLUSIONS

The predictive variables analyzed in this study can be used to identify patients who are at increased risk for desaturation. Such patients require very close monitoring (pulse oximetry at a minimum). Endoscopists and assistants should be especially alert to the possibility of respiratory depression in these patients.

[Small intestine adenocarcinoma with Crohn's disease]

We report a 57-year-old male with a 11-years history of Crohn's disease who developed small bowel adenocarcinoma. The patient was admitted with intestinal partial obstruction and he underwent a laparotomy because an abscess in right lower quadrant was suspected. He was successfully treated with resection and adjuvant chemotherapy, without evidence of recurrence after a 2-year follow-up. A review of the literature reveals that about 100 cases have been reported. We describe the distinguishing features of small bowel adenocarcinoma arising in Crohn's disease and we emphasize the difficulty in making an early diagnosis.

[Value of laparoscopy in ascites of undetermined origin]

OBJECTIVE

To assess the diagnostic accuracy of laparoscopy in the study of patients with ascites of unknown cause, and the frequency of laparoscopy use for that indication after the advent of ultrasonography and computed tomography.

DESIGN

A retrospective study of 4.536 laparoscopies performed in 16 years, in two periods of 8 years, and the correlation with the pathologic diagnosis.

PATIENTS

137 patients in whom laparoscopy was indicated for the study of ascites of unknown cause.

RESULTS

63.5% of laparoscopies were performed over the first 8-year period, and 36.5% in the second (p = 0.0001), and for the study of ascites 2.6 and 3.8% respectively. Laparoscopy and biopsy were diagnostic in 98.5% of cases; 51% carcinomatosis, 17.5% liver cirrhosis, 11.7% hepatic neoplasm and others. Two of five cases of peritoneal tuberculosis were considered carcinomatosis at laparoscopy. There were no serious complications.

CONCLUSIONS

The advent of new imaging method has reduced the use of laparoscopy, although it is still employed frequently for the study of ascites. Laparoscopy with biopsy when necessary has an excellent effectiveness and accuracy for the diagnosis of ascites of unknown cause.

[Juvenile polyposis in 2 patients of the same family]

Two cases of juvenile familiar polyposis (one 40-year-old male and his 14-year-old daughter) are presented. The girl presented intermittent rectal bleeding since the age of 10 with growth retardation and chronic anemia. The child was treated by colectomy with more than 100 juvenile polyps without adenomatous alterations being observed in the surgical specimen. Juvenile gastric polyps were also endoscopically observed. The father underwent sigmoidectomy for a adenomatous polyp of this localization. Later review of the surgical specimen demonstrated a juvenile polyp with zones of adenomatous alterations. The diagnostic difficulties of this rare entity and the therapeutic options available are discussed.

Diagnosis of endometrial carcinoma: predictive value of transvaginal color Doppler

The objective of this study was to determine whether transvaginal ultrasound plus color Doppler flow improve the ability to diagnose endometrial carcinoma and allow better discrimination between benign and malignant endometrial lesions. One hundred thirty women with abnormal uterine bleeding were evaluated with transvaginal color Doppler before fractional dilatation and curettage (D&C). The endometrial line thickness and endometrial characteristics were evaluated by endosonography. The resistive and pulsatile indices of the uterine arteries and of the endometrium were evaluated with transvaginal color Doppler. Following D&C and tissue diagnosis, women were divided into two groups, 62 with a histologic diagnosis of endometrial adenocarcinoma and 68 with benign endometrial tissue. All women with endometrial carcinoma underwent TAH and BSO. A complete histopathologic study was done an all surgical specimens. The International Federation of Gynecology and Obstetrics (FIGO) stage and tissue grading were determined in all cases. The histopathologic findings were correlated with ultrasound and transvaginal color Doppler results. Patients with adenocarcinoma had an average endometrial thickness of 26.13 mm (range 8-87 mm). The average thickness for functional endometrium (proliferative) was 10.5 mm (range 6-23 mm). There was no case of carcinoma where the endometrial thickness was less than 8 mm. Intraendometrial neovascularization was not observed in any case with functional or atrophic endometrium. The flow indices in patients with endometrial adenocarcinomas are significantly different from the flow indices of patients with benign endometrial tissue. Transvaginal color Doppler increases the sensitivity of endometrial malignancy diagnosis. The method is capable of detecting important differences in flow indices and endometrial line characteristics between benign and malignant endometrial tissue.

Narrow A/T-rich zones present at the distal 5'-flanking sequences of the zein genes Zc1 and Zc2 bind a unique 30 kDa HMG-like protein

Nuclear extracts from maize endosperm were used to investigate protein-DNA interactions in the 5'-upstream region of the Zc1 and Zc2 genes. These genes encode for zeins of apparent molecular mass (MWapp) 16 and 28 kDa, respectively, which accumulate in the endosperm during seed maturation. Binding assays revealed specific binding of a nuclear protein to three A/T-rich elements, 0.9-1.0 kbp upstream from the initiation codon. One of these elements (41 bp, 88% A/T), present in Zc1, contained a 13 nucleotide duplication. The other two (28 bp, 86% A/T; 42 bp alternating A-T) are consecutive elements in Zc2. Competition experiments strongly suggest that the three elements bind to the same protein. Protein-DNA interaction was detected in endosperm nuclear extracts of 8 to 21 days after pollination (DAP), as well as in 25 DAP embryos and in different tissues from plantlets. The protein factor has an MWapp of ca. 30 kDa. This factor has properties suggesting it is an HMG-like protein. These results are consistent with a growing accumulation of data for a number of genes indicating that A/T-rich elements, located at distal and proximal zones of the 5'-flanking sequences, interact with HMG-like proteins.

[Primary segmental sclerosing cholangitis associated with Sjögren's syndrome]

We report the case of a patient with primary sclerosing cholangitis associated with Sjögren's syndrome and Raynaud's phenomenon, an uncommon association. The presence of periportal lymph nodes with features similar to those described in autoimmune diseases suggests an immune pathogenesis of the disease. The localized and segmentary involvement of the common duct is also an uncommon finding. The pathogenetic and therapeutic aspects are discussed.

[Evaluation of compliance with appointments and the control of blood pressure in a group of hypertensive patients]

The social and public health relevance of hypertension (HT) is well know. In the present study, 308 hypertensive patients were evaluated in two six month periods. An organized variation was carried out, consisting of the suppression of the scheduled visit with subsequent attention of the patient by visit on demand. The evaluated variables were the degree of compliance with the appointment and the control of the blood pressure levels in the two periods, depending on sex, age, and degree of hypertension. Better results were achieved during the first period (with scheduled visit), both regarding compliance and control. Therefore, it seems preferable to keep scheduled visits for the HT protocols.

[Double esophageal membrane in a patient with Plummer-Vinson syndrome]

A case is presented of a 27-year-old patient with Plummer-Vinson syndrome. Radiological and endoscopic study detected a double membrane in the cervical esophagus. After esophageal dilation, dysphagia remitted and the patient remains asymptomatic.

[Malabsorption syndrome caused by Giardia lamblia in gastrectomized patients]

We report three adult patients with gastrectomy who had malabsorption caused by Giardia lamblia. Type II gastrectomy had been carried out in the three patients several years before, and the clinical presentation was similar: chronic diarrhea with malabsorption. A remarkable fact was that the search for parasites in feces was repeatedly negative in two patients, the protozoon being identified in the intestinal biopsy samples. In the third case, the diagnosis was made by the visualization of Giardia cysts in the feces.