Search PubMed⌕ Search

Biomedical subjects

J Herrero

Publications and source records attributed to J Herrero.

At least 19 recordsLinked to original sources
PubMed2006

Ensembl 2007.

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of chordate genome sequences. Over the past year the number of genomes available from Ensembl has increased from 15 to 33, with the addition of sites for the mammalian genomes of elephant, rabbit, armadillo, tenrec, platypus, pig, cat, bush baby, common shrew, microbat and european hedgehog; the fish genomes of stickleback and medaka and the second example of the genomes of the sea squirt (Ciona savignyi) and the mosquito (Aedes aegypti). Some of the major features added during the year include the first complete gene sets for genomes with low-sequence coverage, the introduction of new strain variation data and the introduction of new orthology/paralog annotations based on gene trees.

Animals↗
PubMed2006

Bifurcation analysis of multiple steady flow patterns for Rayleigh-Bénard convection in a cubical cavity at Pr = 130.

The bifurcation diagram of steady convective flow patterns inside a cubical cavity with adiabatic lateral walls heated from below and filled with silicone oil (Pr = 130) was determined for values of the Rayleigh number (Ra) up to 1.5 x 10(5). A continuation procedure based on the Galerkin spectral method was used to determine the steady convective solutions as a function of Ra. Bifurcations leading to either new steady or time-dependent solutions were identified and new steady solution branches were also continued. A total of fifteen steady solutions were tracked and the stability analysis predicted that six flow patterns were stable and that two, three, or even four of these patterns coexisted over certain ranges of Ra in the studied domain. Predicted flow patterns and transitions are in agreement with flow visualizations previously reported in the literature. The variation of the Nusselt number (Nu) as a function of Pr was investigated for three of the stable flow patterns identified: a x or y roll, a diagonal oriented roll and a pattern formed by four connected half rolls. It was found that whereas the Nusselt changes within the region 0.71 < or = Pr < or = 10 it tends to an asymptotic value with increasing Pr.

Journal Article↗
PubMed2006

Ensembl 2006.

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased from 4 to 19, with the addition of the mammalian genomes of Rhesus macaque and Opossum, the chordate genome of Ciona intestinalis and the import and integration of the yeast genome. The year has also seen extensive improvements to both data analysis and presentation, with the introduction of a redesigned website, the addition of RNA gene and regulatory annotation and substantial improvements to the integration of human genome variation data.

Animals↗
PubMed2005

Insulin-sensitizing agents: use in pregnancy and as therapy in polycystic ovary syndrome.

Treatment with insulin-sensitizing agents is a relatively recent therapeutic strategy in women with polycystic ovary syndrome (PCOS) and insulin resistance. The key areas addressed in this review include PCOS and the development of type 2 diabetes mellitus and gestational diabetes, as well as the use of insulin-sensitizing agents, particularly metformin, in the management of infertility in obese and non-obese PCOS women. Treatment with metformin in PCOS women undergoing IVF and the use of metformin during gestation will be discussed. The challenge for the health care professional should be the appropriate utilization of pharmacotherapies to improve insulin sensitivity and lower circulating insulin levels resulting in beneficial changes in PCOS phenotype. Further research into the potential role of other insulin-sensitizing agents, such as pioglitazone and rosiglitazone, in the treatment of infertile women with PCOS is needed.

Diabetes, Gestational↗
PubMed2005

Cervical squamous intraepithelial lesions of low-grade in HIV-infected women: recurrence, persistence, and progression, in treated and untreated women.

BACKGROUND: Human immunodeficiency virus (HIV)-infected patients are more predisposed than HIV-negative women to develop squamous intraepithelial lesions (SIL) of the uterine cervix, and cervical dysplasia may be of higher grade in HIV-positive women than in HIV-negative subjects, with more extensive and multi-centric involvement of the lower genital tract by human papillomavirus (HPV)-associated lesions. Moreover, recurrence and progression rate of cervical intraepithelial neoplasia (CIN) is particularly higher in immunocompromised women. DESIGN: Retrospective case-control study of HIV-positive women and HIV-negative controls, all affected by low-grade SIL of the uterine cervix, treated by loop excision or followed-up without treatment. Correlation of progression and recurrence of SIL with HIV status and CD4+ count. PATIENTS: From September 1990 to October 1997, 75 HIV-positive low-grade-SIL patients, 47 treated and 28 followed-up without treatment, and 75 HIV-negative low-grade-SIL controls, 45 treated and 30 followed-up. RESULTS: Among treated patients, 17/47 (36.2%) HIV-positive and 5/45 (11.1%) controls had recurrence (P < 0.0101, O.R. = 4.53, 95% CI = 1.5-13.7), progression of untreated lesion was seen in 15/28 (53.6%) HIV-positive and 7/30 (23%) controls (P < 0.05, O.R. = 3.79, 95% CI = 1.23-11.69). The risk of recurrence or progression of low-grade SIL linked to HIV seropositivity is about 4-5 times higher in comparison with seronegative counterpart, matched for age, risk factors and lesion size. More significantly, considering the cut-off of 200 CD4+/mm(3) in HIV-positive women, 13/17 cases of recurrence (P < 0.05, O.R. = 4.88, 95% CI = 1.28-18.58) and 10/15 cases with progression (P < 0.05, O.R. = 6.67, 95% CI = 1.24-35.73) were immunocompromised (<200 CD4+/mm3), with a significant higher risk of recurrence or progression linked to immunodeficiency status. Considering time of progression or recurrence, during follow-up, Kaplan-Meier curves shows that HIV-positive status and immunodeficiency are correlated with more rapid evolution of cervical dysplasia and HPV-related lesions: comparison of recurrence in treated patients report P < 0.005 and progression in untreated P<0.05 (Mantel-Haenszel log-rank test). CONCLUSIONS: Immunological status seems to be a determinant factor in prognosis of cervical SIL, HIV-positive women affected by this lesion, even if low-grade, need more aggressive management than the immunocompetent counterpart. Strict cytologic and colposcopic screening is recommended and CD4+ count and HPV-DNA testing may be useful risk indicators. Excisional procedures are preferred, while ablative treatments or wait and see policy may expose to some risk this type of population with poor compliance to follow-up.

Case-Control Studies↗
PubMed2005

Ensembl 2005.

The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution.

Animals↗
PubMed2004

Treatment of stage I and II Hodgkin's lymphoma with ABVD chemotherapy: results after 7 years of a prospective study.

BACKGROUND: Chemotherapy with ABVD (doxorubicin, bleomycin, vinblastine and darcarbacine) schedule is the standard treatment for advanced Hodgkin's lymphoma. Certain facts, including a low toxicity compared with MOPP/ABV (mechlorethamine, vincristine, procarbazine, prednisone, doxorubicin, bleomycin and vinblastine) and minimal potential for inducing second neoplasias or patient sterility, support the use of ABVD to treat early disease stages. In the present study, we prospectively evaluated the long-term efficacy and toxicity of six cycles of ABVD as treatment for early-stage Hodgkin's lymphoma. PATIENTS AND METHODS: From January 1990 to June 2002, 95 patients with stage I and II Hodgkin's lymphoma were treated with six ABVD cycles. Fifteen patients who met the criteria for mediastinal bulky disease also received further radiotherapy on the mediastinum. RESULTS: After six cycles, 89 patients (94%) showed a complete response (CR) and six patients (6%) showed a partial response (PR). These PRs became CRs after radiotherapy. After a median follow-up of 78 months, 14 patients had relapsed and three had died. Overall survival and progression-free survival rates at 7 years were 96% and 84%, respectively. For patients with stage IA and IIA without mediastinal bulky disease, the survival rates were 97% and 88%, respectively. CONCLUSIONS: The administration of six ABVD cycles is an effective and safe treatment in patients with stage I and II Hodgkin's lymphoma.

Adolescent↗
PubMed2003

Gene expression data preprocessing.

We present an interactive web tool for preprocessing microarray gene expression data. It analyses the data, suggests the most appropriate transformations and proceeds with them after user agreement. The normal preprocessing steps include scale transformations, management of missing values, replicate handling, flat pattern filtering and pattern standardization and they are required before performing any pattern analysis. The processed data set can be sent to other pattern analysis tools.

Database Management Systems↗
PubMed2003

Management of N0 neck in laryngeal carcinoma. Impact on patient's survival.

Management of patients with carcinoma of the larynx should systematically include an appropriate treatment of lymph nodes according to the TNM stage. One of the most controversial points of the treatment in these patients is the management of the clinically negative neck (N(0)). A retrospective study of 295 patients with laryngeal carcinoma and N(0) neck undergoing treatment in our centre between 1983 and 1993 is presented. We observed a significant decrease in the survival of clinically N(0) patients with histologically affected lymph nodes. Lymphadenopathy was more frequently detected in patients with supraglottic tumours (38 per cent) when compared to glottic tumours (16 per cent). In our experience, routine bilateral and unilateral dissection of N(0) necks in all supraglottic tumours and in T3-T4 glottic tumours, respectively, is the most beneficial approach for patients in terms of survival.

Adult↗
PubMed2001

Serum erythropoietin levels in ovarian cancer patients receiving chemotherapy.

OBJECTIVE: To investigate the effects of repeated cis-dichlorodiamine-platinum (CDDP) exposure on serum erythropoietin (Epo) levels. STUDY DESIGN: In seven patients with ovarian cancer, Epo and haemoglobin concentration (c(Hb)) were measured before, 24h and 7 days after administration of the first three courses of chemotherapy. In seven control patients undergoing gynaecological surgery for non-malignant reasons, Epo and c(Hb) were measured before, 24h and 7 days after the operation. RESULTS: Following Epo increased, independent of concomitant anaemia, especially after the third course: 51mU/ml (S.D. 46) versus 122mU/ml (S.D. 83) (P=0.02). In the control patients, Epo was lower although the decrease of c(Hb) was significantly higher. CONCLUSION: Cis-platinum chemotherapy induces an increase in erythropoietin levels independent of anaemia. The underlying mechanism remains to be investigated.

Aged↗
PubMed2001

Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate.

The public availability of numerous microbial genomes is enabling the analysis of bacterial biology in great detail and with an unprecedented, organism-wide and taxon-wide, broad scope. Streptococcus pneumoniae is one of the most important bacterial pathogens throughout the world. We present here sequences and functional annotations for 2.1-Mbp of pneumococcal DNA, covering more than 90% of the total estimated size of the genome. The sequenced strain is a clinical isolate resistant to macrolides and tetracycline. It carries a type 19F capsular locus, but multilocus sequence typing for several conserved genetic loci suggests that the strain sequenced belongs to a pneumococcal lineage that most often expresses a serotype 15 capsular polysaccharide. A total of 2,046 putative open reading frames (ORFs) longer than 100 amino acids were identified (average of 1,009 bp per ORF), including all described two-component systems and aminoacyl tRNA synthetases. Comparisons to other complete, or nearly complete, bacterial genomes were made and are presented in a graphical form for all the predicted proteins.

DNA, Bacterial↗
PubMed2001

A hierarchical unsupervised growing neural network for clustering gene expression patterns.

MOTIVATION: We describe a new approach to the analysis of gene expression data coming from DNA array experiments, using an unsupervised neural network. DNA array technologies allow monitoring thousands of genes rapidly and efficiently. One of the interests of these studies is the search for correlated gene expression patterns, and this is usually achieved by clustering them. The Self-Organising Tree Algorithm, (SOTA) (Dopazo,J. and Carazo,J.M. (1997) J. Mol. Evol., 44, 226-233), is a neural network that grows adopting the topology of a binary tree. The result of the algorithm is a hierarchical cluster obtained with the accuracy and robustness of a neural network. RESULTS: SOTA clustering confers several advantages over classical hierarchical clustering methods. SOTA is a divisive method: the clustering process is performed from top to bottom, i.e. the highest hierarchical levels are resolved before going to the details of the lowest levels. The growing can be stopped at the desired hierarchical level. Moreover, a criterion to stop the growing of the tree, based on the approximate distribution of probability obtained by randomisation of the original data set, is provided. By means of this criterion, a statistical support for the definition of clusters is proposed. In addition, obtaining average gene expression patterns is a built-in feature of the algorithm. Different neurons defining the different hierarchical levels represent the averages of the gene expression patterns contained in the clusters. Since SOTA runtimes are approximately linear with the number of items to be classified, it is especially suitable for dealing with huge amounts of data. The method proposed is very general and applies to any data providing that they can be coded as a series of numbers and that a computable measure of similarity between data items can be used. AVAILABILITY: A server running the program can be found at: http://bioinfo.cnio.es/sotarray.

Algorithms↗
PubMed2000

Land Evaluation in a Salt-Affected Irrigated District Using an Index of Productive Potential.

/ The indiscriminate allocation of funds supporting agricultural policies can lead to land misuse, with undesirable effects either on the shorter to mid-term productivity or on the environment. This article proposes a methodology, based on land rating, that can be useful to land-use planning or to decide about environmental protection measures. The methodology is applied to the land evaluation of a 260-km(2) semiarid irrigated area with salt-affected soils. The available soil map is at 1:100,000 scale and its mapping units are used for the land evaluation with the FAO framework. These data are then elaborated using the index value method. This procedure gives a map of land evaluation units and a table that rates the productive potential of these units for six crops: alfalfa, barley, maize, rice, sunflower, and wheat.

Journal Article↗
PubMed2000

[Tubal involvement in nasopharyngeal carcinoma].

Nasopharyngeal carcinomas are frequently diagnosed in advanced stages in patients who present with secretory otitis or neck mass. However, survival after treatment is directly related to early diagnosis. The present study analyzed Eustachian tube involvement in nasopharyngeal carcinoma as a pathogenic mechanism in secretory otitis. The presence of otologic symptoms was correlated with the morphological description of the tumor and clinical manifestations in 198 patients with nasopharyngeal carcicoma.

Carcinoma↗
PubMed2000

Expression profiles and biological function.

Expression arrays facilitate the monitoring of changes in expression patterns of large collections of genes. It is generally expected that genes with similar expression patterns would correspond to proteins of common biological function. We assess this common assumption by comparing levels of similarity of expression patterns and statistical significance of biological terms that describe the corresponding protein functions. Terms are automatically obtained by mining large collections of Medline abstracts. We propose that the combined use of the tools for expression profiles clustering and automatic function retrieval, can be useful tools for the detection of biologically relevant associations between genes in complex gene expression experiments. The results obtained using publicly available experimental data show how, in general, an increase in the similarity of the expression patterns is accompanied by an enhancement of the amount of specific functional information or, in other words, how the selected terms became more specific following an increase in the specificity of the expression patterns. Particularly interesting are the discrepancies from this general trend, i.e. groups of genes with similar expression patterns but very little in common at the functional level. In these cases the similarity of their expression profiles becomes the first link between previously unrelated genes.

Cluster Analysis↗
PubMed1999

Different cumulative pregnancy rates in patients with repeated IVF- or ICSI cycles: possible influence of a male factor.

The low rate of ongoing pregnancies in IVF cycles leads to a high number of repeated cycles in couples with previously failed attempts. Therefore it would be helpful to have a prediction about the chance of becoming pregnant in a repeated cycle. In a retrospective study the data of about 4246 cycles were analysed. Because the pregnancy rates in IVF- and ICSI cycles are generally different, these two groups were distinguished between and the outcome in patients with one, two or more attempts was analysed. The rate of ongoing pregnancies per patient was lower after IVF (24.9%) than after ICSI (32.9%), but was similar or even slightly increased in patients with more than one attempt. On the other hand, there was a high pregnancy rate with ICSI in the first two cycles (35.9%), but patients with more than two ICSI cycles had a significantly lower chance of becoming pregnant (20.7%). Factors that are known to influence the pregnancy rate, such as stimulation protocol, oocyte quality or number of transferred embryos, were similar in all groups. However, significantly reduced embryo quality with successive cycles was only observed in ICSI patients. There might be a negative selection of patients with poor embryo quality and previously failed attempts after ICSI, possibly due to an andrological factor. The differences between IVF- and ICSI patients are based on treatment indications, and andrological diseases are the predominant indication for ICSI. Although no correlation was found between changes in conventional sperm parameters and number of treated cycles, there might be a subgroup of andrological patients selected by repeatedly failed ICSI cycles. Chromosomal or genetic disturbances in spermatozoa of this subgroup could be the reason for failure.

Adult↗
PubMed1998

Leiomyomatosis peritonealis disseminata associated with endometriosis: a case report and literature review.

Leiomyomatosis peritonealis disseminata (LPD) is a rare disease characterised by the presence of multiple smooth muscle tumour nodules throughout the peritoneal cavity. Approximately 50 cases of LPD have been reported to date in the world literature. There is a very high association with excess exogenous and endogenous female gonadal steroids, specifically oestrogen and progesterone. LPD has been described almost only in premenopausal women and is mostly asymptomatic. Four cases of malignant transformation of this disease have been reported. We report a case of a patient with prolonged exposure to oral contraceptives, operated because of hypermenorrhea and 'myoma in statu nascendi'. A metastasing myomatous tumour was suspected during the operation. LPD was diagnosed by intraoperative histological examination. Abdominal hysterectomy was performed. Five months later a second laparotomy had to be done because of an ovarian endometriosis tumour of about 10 cm size. A bilateral salpingo-oophorectomy and omentectomy were performed.

Adult↗