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PubMed2005

Assisted hatching on assisted conception (IVF & ICSI).

BACKGROUND: Failure of implantation and conception may result from an inability of the blastocyst to escape from its outer coat, know as the zona pellucida. In vitro culture conditions and/or advancing maternal age may alter the architecture of the zona pellucida and result in hatching difficulties. Artificial disruption of this coat is known as assisted hatching (AH) has been proposed as a method of improving the success of assisted conception. OBJECTIVES: To determine whether assisted hatching (AH) of embryos facilitates live births and clinical pregnancy and whether it impacts on negative outcomes (such as multiple pregnancy and miscarriage). SEARCH STRATEGY: We searched the Cochrane Menstrual Disorders and Subfertility Group trials register (1 June 2005), the Cochrane Controlled Trials Register (Cochrane Library Issue 2, 2005), MEDLINE (1996 to June 2003), EMBASE (1980 to June 2005) and reference lists of articles. Authors were contacted for missing and/or unpublished data. SELECTION CRITERIA: Trials were identified and independently screened by two reviewers. Randomised controlled trials of AH (mechanical, chemical or laser disruption of the zona pellucida prior to embryo replacement) versus no AH that reported live birth, clinical pregnancy or implantation rates were included. DATA COLLECTION AND ANALYSIS: Qualitative assessments and data extraction were performed independently by two reviewers. Outcomes were extracted as rates and combined using random effects meta-analysis, sensitivity analysis, sub grouping and meta-regression where appropriate. MAIN RESULTS: Twenty-three randomised controlled trials consisting of 2668 women reported on 849 pregnancy outcomes. There was no significant difference in the odds of live births in the AH compared with control groups (6 RCTs; OR 1.19 95% CI 0.81 to 1.73; 163 births from 516 women). Women undergoing assisted hatching were significantly more likely to achieve clinical pregnancy (23 RCTs, OR 1.33, 95% CI 1.12 to 1.57). Miscarriage rates per woman were similar in both groups (12 RCTs OR 1.23 (95% CI 0.73 to 2.05). Multiple pregnancy rates per woman was increased in women who were randomised to AH compared with control women (9 RCTs OR 1.83 (95% CI 1.19 to 2.83). The improvement in clinical pregnancy rate means for a clinic with a success rate of 25% could anticipate improving the CPR to between 28 and 39%, all things being equal. The trials provided insufficient data to investigate the impact of assisted hatching on several important outcomes, including monozygotic twinning, embryo damage, congenital and chromosomal abnormalities, and in vitro blastocyst development. AUTHORS' CONCLUSIONS: Despite significantly improved odds of clinical pregnancy, there is insufficient evidence to determine any effect of AH on live birth rates. The increased multiple pregnancy rate is of concern although it likely that with a policy of single embryo transfer this may be lowered. Currently, there is insufficient evidence to recommend assisted hatching.

Embryo Implantation↗
PubMed2006

Assisted hatching on assisted conception (IVF & ICSI).

BACKGROUND: Failure of implantation and conception may result from an inability of the blastocyst to escape from its outer coat, know as the zona pellucida. In vitro culture conditions and/or advancing maternal age may alter the architecture of the zona pellucida and result in hatching difficulties. Artificial disruption of this coat is known as assisted hatching (AH) has been proposed as a method of improving the success of assisted conception. OBJECTIVES: To determine whether assisted hatching (AH) of embryos facilitates live births and clinical pregnancy and whether it impacts on negative outcomes (such as multiple pregnancy and miscarriage). SEARCH STRATEGY: We searched the Cochrane Menstrual Disorders and Subfertility Group trials register (1 June 2005), the Cochrane Controlled Trials Register (Cochrane Library Issue 2, 2005), MEDLINE (1996 to June 2003), EMBASE (1980 to June 2005) and reference lists of articles. Authors were contacted for missing and/or unpublished data. SELECTION CRITERIA: Trials were identified and independently screened by two reviewers. Randomised controlled trials of AH (mechanical, chemical or laser disruption of the zona pellucida prior to embryo replacement) versus no AH that reported live birth, clinical pregnancy or implantation rates were included. DATA COLLECTION AND ANALYSIS: Qualitative assessments and data extraction were performed independently by two reviewers. Outcomes were extracted as rates and combined using random effects meta-analysis, sensitivity analysis, sub grouping and meta-regression where appropriate. MAIN RESULTS: Twenty-three randomised controlled trials consisting of 2668 women reported on 849 pregnancy outcomes. There was no significant difference in the odds of live births in the AH compared with control groups (6 RCTs; OR 1.19 95% CI 0.81 to 1.73; 163 births from 516 women). Women undergoing assisted hatching were significantly more likely to achieve clinical pregnancy (23 RCTs, OR 1.33, 95% CI 1.12 to 1.57). Miscarriage rates per woman were similar in both groups (12 RCTs OR 1.23 (95% CI 0.73 to 2.05). Multiple pregnancy rates per woman was increased in women who were randomised to AH compared with control women (9 RCTs OR 1.83 (95% CI 1.19 to 2.83). The improvement in clinical pregnancy rate means for a clinic with a success rate of 25% could anticipate improving the CPR to between 28 and 39%, all things being equal. The trials provided insufficient data to investigate the impact of assisted hatching on several important outcomes, including monozygotic twinning, embryo damage, congenital and chromosomal abnormalities, and in vitro blastocyst development. AUTHORS' CONCLUSIONS: Despite significantly improved odds of clinical pregnancy, there is insufficient evidence to determine any effect of AH on live birth rates. The increased multiple pregnancy rate is of concern although it likely that with a policy of single embryo transfer this may be lowered. Currently, there is insufficient evidence to recommend assisted hatching.

Embryo Implantation↗
PubMed2005

Development of a cDNA array for chicken gene expression analysis.

BACKGROUND: The application of microarray technology to functional genomic analysis in the chicken has been limited by the lack of arrays containing large numbers of genes. RESULTS: We have produced cDNA arrays using chicken EST collections generated by BBSRC, University of Delaware and the Fred Hutchinson Cancer Research Center. From a total of 363,838 chicken ESTs representing 24 different adult or embryonic tissues, a set of 11,447 non-redundant ESTs were selected and added to an existing collection of clones (4,162) from immune tissues and a chicken bursal cell line (DT40). Quality control analysis indicates there are 13,007 useable features on the array, including 160 control spots. The array provides broad coverage of mRNAs expressed in many tissues; in addition, clones with expression unique to various tissues can be detected. CONCLUSIONS: A chicken multi-tissue cDNA microarray with 13,007 features is now available to academic researchers from http://genomics@fhcrc.org. Sequence information for all features on the array is in GenBank, and clones can be readily obtained. Targeted users include researchers in comparative and developmental biology, immunology, vaccine and agricultural technology. These arrays will be an important resource for the entire research community using the chicken as a model.

Animals↗
PubMed2004

Laser prostatectomy for benign prostatic obstruction.

BACKGROUND: Symptomatic benign prostatic obstruction is a common problem for older men. The gold standard treatment, transurethral resection of the prostate (TURP), significantly improves urinary symptoms and urinary flow. However, TURP has up to a 20% morbidity. Currently, there are a number of minimally invasive procedures that may be safe, effective alternatives to TURP. One promising surgical technique is laser prostatectomy. OBJECTIVES: To assess the therapeutic efficacy and safety of laser prostatectomy techniques for treating men with symptomatic benign prostatic obstruction. SEARCH STRATEGY: Randomized controlled trials were identified from the Cochrane Collaboration Library, MEDLINE, EMBASE, bibliographies of retrieved articles and reviews, and contacting expert relevant trialists and laser manufacturers. SELECTION CRITERIA: All randomized controlled trials evaluating laser prostatectomy treatment for men with symptomatic BPH. Trials were eligible if they (1) were randomized comparisons of a laser technique with TURP, (2) included at least 10 men with BPO in each treatment arm, (3) provided at least 6-months follow-up, and (4) included clinical outcomes such as urologic symptom scales or urodynamic measurements. DATA COLLECTION AND ANALYSIS: Data extraction and assessment of methodologic quality was performed independently by two reviewers. Information on study design, subject and treatment characteristics, adverse events, urinary symptoms, and urinary flow were extracted using a standard form. MAIN RESULTS: 20 studies involving 1898 subjects were evaluated, including studies 4 with multiple comparisons. We found 8 comparisons of TURP with contact lasers, 8 with non-contact lasers, 4 with hybrid techniques, and one with interstitial laser coagulation (ILC). Two studies compared transurethral electrovaporization (TUVP) with contact lasers, one study compared interstitial laser coagulation with transurethral microwave thermotherapy (TUMT), and one study compared holmium contact lasers (HoLRP) with open prostatectomy. Among the studies comparing laser prostatectomy with TURP, follow-up duration ranged from 6 to 36 months. Mean age (67.2 yrs), mean baseline symptom score (20.2), and mean baseline peak urinary flow (9.2 ml/s) did not differ by treatment group. The pooled percentage improvements for mean urinary symptoms ranged from 59% to 68% with lasers and 63% to 77% with TURP. The improvements for mean peak urinary flow ranged from 56% to 119% with lasers and 96% to 127% with TURP. Overall, laser subjects were less likely to receive transfusions or develop strictures and their hospitalizations were shorter. Non-contact laser subjects were more likely to have dysuria, urinary tract infection, and retention. Re-operation occurred more often following laser procedures. REVIEWER'S CONCLUSIONS: Laser techniques are a useful alternative to TURP for treating BPO. Small sample sizes and differences in study design limit any definitive conclusions regarding the preferred type of laser technique. Data were insufficient to compare laser techniques with other minimally invasive procedures.

Aged↗
PubMed2001

Treatment for amphetamine psychosis.

BACKGROUND: During the phase of chronic, high-dose consumption of amphetamines, many amphetamine users may have the experience of paranoia and hallucination. It has long been believed that dopamine antagonists, such as chlorpromazine, haloperidol, and thioridazine, are effective for the treatment of amphetamine psychosis. OBJECTIVES: To search and determine risks, benefits, and costs of a variety treatments for amphetamine psychosis. SEARCH STRATEGY: Electronic searches of MEDLINE (1966-2000), EMBASE (1980-2000), CINAHL (1982- January 2001) and Cochrane Controlled Trials Register (Cochrane Library 2000 issue 4) were undertaken. References to the articles obtained by any means were searched. SELECTION CRITERIA: All relevant randomised controlled trials (RCTs) and clinical trials (CCTs) were included. Participants were people with amphetamine psychosis, diagnosed by any set of criteria. Any kinds of biological and psychological treatments both alone and combined were examined. A variety of outcomes, for example, number of treatment responders, score changes, were considered. DATA COLLECTION AND ANALYSIS: Two reviewers evaluated and extracted the data independently. The dichotomous data were extracted on an intention-to-treat basis in which the dropouts were assigned as participants with the worst outcomes. The Relative Risk (RR) with the 95% confidence interval (95% CI) was used to assess the dichotomous data. The Weighted Mean Difference (WMD) with 95% CI was used to assess the continuous data. MAIN RESULTS: The comprehensive searches found no controlled trials of treatment for amphetamine psychosis meeting the criteria for considering studies. REVIEWER'S CONCLUSIONS: The evidence about the treatment for amphetamine psychosis is very limited. To our knowledge, no controlled trials of treatment for amphetamine psychosis have been carried out. The results of two studies in amphetamine users show that agitation and some psychotic symptoms may be abated within an hour after antipsychotic injection. Whether this limited evidence can be applied for amphetamine psychotic patients is not yet known. The risks and benefits of giving an antipsychotic injection should be further investigated in amphetamine psychotic patients. Medications that have been used for the treatment of acute exacerbation of schizophrenia should be studied in amphetamine psychotic patients. The medications that may be of interest are conventional antipsychotics, newer antipsychotics and benzodiazepines. However, naturalistic studies of amphetamine psychotic symptoms and course are also crucial for the development of study designs appropriate for further treatment studies of amphetamine psychosis.

Amphetamine-Related Disorders↗
PubMed2003

Ibuprofen for the prevention of patent ductus arteriosus in preterm and/or low birth weight infants.

BACKGROUND: A patent ductus arteriosus (PDA) often complicates the clinical course of preterm infants and increases the risk of intraventricular hemorrhage (IVH), necrotizing enterocolitis (NEC), chronic lung disease (CLD) and death. The standard treatment to close a PDA is indomethacin. Its use is associated with renal, gastrointestinal and cerebral side-effects. Ibuprofen has been shown to be effective in closing a PDA without reducing blood flow velocity to the brain, gut or kidneys. OBJECTIVES: To determine the effectiveness and safety of prophylactic ibuprofen compared to placebo/no intervention or other cyclo-oxygenase inhibitor drugs (indomethacin, mefenamic acid, etc) in the prevention of PDA in preterm infants. SEARCH STRATEGY: Randomized controlled trials comparing prophylactic ibuprofen use with placebo/no intervention/indomethacin were identified by searching the Cochrane Controlled Trial Register (The Cochrane Library, Issue 4, 2002), MEDLINE (1966-November 2002), CINAHL (1982-November 2002), EMBASE (1980-November 2002), reference lists of published trials and abstracts published in Pediatric Research (1990-2002). No language restrictions were applied. SELECTION CRITERIA: Randomized or quasi-randomized controlled trials comparing use of ibuprofen with placebo/no intervention or other cyclo-oxygenase inhibitor drugs (indomethacin, mefenamic acid, etc) for the prevention of PDA in preterm and/or low birth weight infants. DATA COLLECTION AND ANALYSIS: Data regarding the clinical outcomes including presence of PDA on day three and day seven, need for surgical ligation, need for rescue treatment with cyclo-oxygenase inhibitors, IVH, mortality, renal and gastrointestinal complications were extracted. Meta-analyses were performed using RevMan 4.1 and treatment estimates were reported as weighted mean difference (WMD), typical relative risk (RR), typical risk difference (RD) and, if statistically significant, number needed to treat (NNT) or number needed to harm (NNH), along with their 95% confidence intervals (CI). MAIN RESULTS: Four trials (n = 623) were included in the review. There was a statistically significant decrease in the incidence of PDA on day three in the ibuprofen group [typical RR 0.36 (95% CI 0.26, 0.49); typical RD -0.29 (95% CI -0.37, -0.21); NNT 3 (95% CI 3, 5); 3 trials, n = 488]. There was a significant increase in the serum creatinine levels in the ibuprofen group [WMD 0.11 mg/dl (95% CI 0.06, 0.17); 2 trials, n = 438]. There were no statistically significant differences in mortality, grade 3 or 4 IVH, CLD at 28 days or 36 weeks, need for surgical closure of PDA, NEC, GI hemorrhage, time to reach full feeds and urine output. One trial (Gournay 2002) (n = 135) reported on three infants in the ibuprofen group who developed pulmonary hypertension responsive to nitric oxide treatment. REVIEWER'S CONCLUSIONS: Prophylactic use of ibuprofen reduces the incidence of PDA. However, further trials, which address potential adverse effects including pulmonary hypertension, are needed. Such trials should include long-term neurodevelopmental outcomes. Trials comparing the effectiveness of prophylactic use of indomethacin versus ibuprofen may be warranted with particular reference to IVH, need for surgical ligation and neurodevelopmental outcome.

Cyclooxygenase Inhibitors↗
PubMed2001

Treatment for amphetamine withdrawal.

BACKGROUND: Amphetamine withdrawal has been less studied although it is a common problem with a prevalent rate of 87% among amphetamine users. Its symptoms, in particular intense craving, may be a critical factor leading to relapse of amphetamine use. In clinical practice, treatment for cocaine withdrawal has been recommended for the management of amphetamine withdrawal although the pharmacodynamic and pharmacokinetic properties of these two substances are not the same. OBJECTIVES: To search and determine risks, benefits, and costs of a variety of treatments for the management of amphetamine withdrawal. SEARCH STRATEGY: Electronic searches of MEDLINE (1966 - December 2000), EMBASE (1980 - February 2001), CINAHL (1982 - January 2001) and Cochrane Controlled Trials Register (Cochrane Library 2000 issue 4) were undertaken. References to the articles obtained by any means were searched. SELECTION CRITERIA: All relevant randomised controlled trials (RCTs) and controlled clinical trials (CCTs) were included. Participants were people with amphetamine withdrawal, diagnosed by any set of criteria. Any kinds of biological and psychological treatments both alone and combined were examined. A variety of outcomes, for example, number of treatment responders, score changes, were considered. DATA COLLECTION AND ANALYSIS: Two reviewers evaluated and extracted the data independently. The dichotomous data were extracted on an intention-to-treat basis in which the dropouts were assigned as participants with the worst outcomes. The Relative Risk (RR) with the 95% confidence interval (95% CI) was used to assess the dichotomous data. The Weighted Mean Difference (WMD) with 95% CI was used to assessed the continuous data. MAIN RESULTS: The results of two studies have shown some benefits of amineptine in the treatment of amphetamine withdrawal. Those benefits can be seen in the respects of discontinuation rate and global state, as measured by Clinical Global Impression Scale. However, no direct benefit of amineptine on amphetamine withdrawal symptoms or craving was shown. REVIEWER'S CONCLUSIONS: The evidence about the treatment for amphetamine withdrawal is very limited. Amineptine has limited benefits on some amphetamine withdrawal symptoms. Due to a number of reports of amineptine abuse, it has been withdrawn from the market for a few years. At present, no available treatment has been demonstrated to be effective in the treatment of amphetamine withdrawal. The medications that should be considered for further treatment studies may be those with the propensities to increase dopamine, norepinephrine and/or serotonin activities of the brain. Naturalistic studies of amphetamine withdrawal symptoms and course are also crucial for the development of study designs appropriate for further treatment studies of amphetamine withdrawal.

Amphetamine↗
PubMed2002

Haloperidol dose for the acute phase of schizophrenia.

BACKGROUND: Haloperidol is a benchmark, accessible antipsychotic against which the effects of newer treatments are gauged. OBJECTIVES: The primary goal of this review is to determine the best range of doses for haloperidol for the treatment of people acutely ill with schizophrenia. SEARCH STRATEGY: The reviewers searched Biological Abstracts (1980-1999), CINAHL (1982-1999), The Cochrane Library (1999, Issue 2), The Cochrane Schizophrenia Group's Register (December 1999), EMBASE (1980-1999), MEDLINE (1966-1999) and PsycLIT (1887-1999). They also inspected all references of all identified trials and included studies sought as a citation on SCISEARCH database (1980-1999). Authors of identified studies and pharmaceutical companies were also contacted. SELECTION CRITERIA: Studies were selected if they involved people being treated for acute schizophrenia, randomised to two or more dose ranges of non-depot haloperidol, and if they reported clinically meaningful outcomes. DATA COLLECTION AND ANALYSIS: The reviewers independently and blindly inspected citations (10% reliability check), they ordered papers, and reliably re-inspected and quality assessed the full reports. The reviewers, again working independently, also extracted data. For homogeneous dichotomous data the relative risk (RR), 95% confidence intervals (CI) were calculated on an intention-to-treat basis. Reviewers assumed that people who left the study early or were lost to follow-up had a negative outcome. Weighted mean differences (WMD) were calculated for continuous outcomes that reported intention to treat (ITT), last observation carried forward (LOCF) data. Data was excluded if loss to follow-up was greater than 50%. MAIN RESULTS: Sixteen trials with nineteen different randomised dose comparisons were included. No studies reported data on relapse rates, quality of life and none compared >1.5-3.0 mg/day haloperidol to higher dose ranges. Using low doses (>3-7.5mg/day) did not clearly result in loss of efficacy (no clinically important improvement in global state, versus >7.5-15mg/day n=48, 1 RCT, RR 1.09 CI 0.7 to 1.8; versus >15-35mg/day n=81, 2 RCTs, 0.95 CI 0.8 to 1.2). Doses of haloperidol in the range of >3-7.5 mg/day had a lower rate of development of clinically significant extrapyramidal adverse effects than higher doses (clinically significant extrapyramidal adverse effects, versus >7.5-15mg/day n=64, 2 RCTs, RR 0.12 CI 0.01 to 2.1; versus >15-35mg/day n=144, 3 RCTs RR 0.59 CI 0.5 to 0.8, NNH 3 CI 2 to 6; versus >35mg/day n=86, 2 RCTs, RR 0.70 CI 0.5 to 1.1). All other comparisons between dose ranges did not yield statistically significant differences, but several, particularly with lower dose ranges, were underpowered to detect clinically meaningful differences. REVIEWER'S CONCLUSIONS: No results are conclusive and all are based on small, short, studies. It would be understandable, however, if clinicians were cautious in prescribing doses in excess of 7.5 mg/day of haloperidol to a person with uncomplicated acute schizophrenia, and if people with schizophrenia were equally reticent to take greater doses. Further research is needed regarding the efficacy and tolerability of the >1.5-3.0 mg/day dose range.

Acute Disease↗
PubMed2003

Metalloporphyrins for treatment of unconjugated hyperbilirubinemia in neonates.

BACKGROUND: Metalloporphyrins are heme analogues that inhibit heme oxygenase, the rate-limiting enzyme in the catabolism of heme to bilirubin. By preventing the formation of bilirubin, they have the potential to reduce the level of unconjugated bilirubin in neonates and thereby reduce the risk of neonatal encephalopathy and long term neurodevelopmental impairment from bilirubin toxicity to the nervous system. OBJECTIVES: 1. To determine the efficacy of metalloporphyrins in reducing bilirubin levels, reducing the need for phototherapy or exchange transfusion and reducing the incidence of bilirubin encephalopathy in neonates with unconjugated hyperbilirubinemia when compared to placebo, phototherapy or exchange transfusion. 2. To determine the nature and frequency of side effects of metalloporphyrins when used to treat unconjugated hyperbilirubinemia in neonates. SEARCH STRATEGY: We searched Medline (1966 - January 2003) and the Cochrane Controlled Trials Register (CCTR) from the Cochrane Library (2003, issue 1). We hand-searched the articles cited in each publication obtained. We hand searched the abstracts of the Society for Pediatric Research (USA) (published in Pediatric Research) for the years 1985 - 2002. SELECTION CRITERIA: We included only randomized controlled studies, in which preterm or term neonates (age 28 days of life or less) with unconjugated hyperbilirubinemia due to any cause were randomly allocated to receive a metalloporphyrin in the treatment arm(s), and to receive a placebo or a conventional treatment (phototherapy or exchange transfusion) or no treatment for hyperbilirubinemia in the comparison arm(s). Any preparation of metalloporphyrin could be used, in any form, by any route, at any dose. DATA COLLECTION AND ANALYSIS: Two authors extracted data independently. Data were entered into Revman by one author and checked by a second author. Prespecified subgroup analyses were planned in term versus preterm infants, hemolytic versus non-hemolytic causes of jaundice and according to the type of metalloporphyrin used. MAIN RESULTS: Three small studies, enrolling a total of 170 infants, were eligible for inclusion in this review. None blinded intervention or outcome assessment. In all three studies some patients were excluded after randomization. Metalloporphyrin-treated infants appeared to have short-term benefits compared to controls, including a lower maximum plasma bilirubin level in one study, a lower frequency of severe hyperbilirubinemia in one study, a decreased need for phototherapy, fewer plasma bilirubin measurements and a shorter duration of hospitalization. None of the enrolled infants required an exchange transfusion in the two studies that described this outcome. None of the studies reported on neonatal kernicterus, death, long-term neurodevelopmental outcomes or iron deficiency anemia. Though a small number of metalloporphyrin-treated as well as control infants developed a photosensitivity rash, the trials were too small to rule out an increase in the risk of photosensitivity or other adverse effects from metalloporphyrin treatment. No subgroup analyses were possible due to the small number of included trials. REVIEWER'S CONCLUSIONS: Treatment of neonatal unconjugated hyperbilirubinemia with metalloporphyrins may reduce neonatal bilirubin levels and decrease the need for phototherapy and hospitalization. There is no evidence to support or refute the possibility that treatment with a metalloporphyrin decreases the risk of neonatal kernicterus or of long-term neurodevelopmental impairment due to bilirubin encephalopathy. There is no evidence to support or refute the possibility that cutaneous photosensitivity is increased with metalloporphyrin treatment. Routine treatment of neonatal unconjugated hyperbilirubinemia with a metalloporphyrin cannot be recommended at present.

Humans↗
PubMed2006

GEDA: new knowledge base of gene expression in drug addiction.

Abuse of drugs can elicit compulsive drug seeking behaviors upon repeated administration, and ultimately leads to the phenomenon of addiction. We developed a procedure for the standardization of microarray gene expression data of rat brain in drug addiction and stored them in a single integrated database system, focusing on more effective data processing and interpretation. Another characteristic of the present database is that it has a systematic flexibility for statistical analysis and linking with other databases. Basically, we adopt an intelligent SQL querying system, as the foundation of our DB, in order to set up an interactive module which can automatically read the raw gene expression data in the standardized format. We maximize the usability of this DB, helping users study significant gene expression and identify biological function of the genes through integrated up-to-date gene information such as GO annotation and metabolic pathway. For collecting the latest information of selected gene from the database, we also set up the local BLAST search engine and nonredundant sequence database updated by NCBI server on a daily basis. We find that the present database is a useful query interface and data-mining tool, specifically for finding out the genes related to drug addiction. We apply this system to the identification and characterization of methamphetamine-induced genes' behavior in rat brain.

Animals↗
PubMed2004

The primate embryo gene expression resource: a novel resource to facilitate rapid analysis of gene expression patterns in non-human primate oocytes and preimplantation stage embryos.

Detailed molecular studies of preimplantation stage development in a suitable nonhuman primate model organism have been inhibited due to the cost and scarcity of embryos. To circumvent these limitations, we have created a new resource for the research community, designated as the Primate Embryo Gene Expression Resource (PREGER). The PREGER sample collection currently contains over 160 informative samples of oocytes, obtained from various sized antral follicles, and embryos obtained through a variety of different protocols. The PREGER makes it possible to undertake quantitative gene-expression studies in rhesus monkey oocytes and embryos through simple and cost-effective hybridization-based methods. The PREGER also makes available other molecular tools to facilitate nonhuman primate embryology. We used PREGER here to compare the temporal expression patterns of five housekeeping mRNAs and three transcription factor mRNAs between mouse and rhesus monkey. We observed noticeable differences in temporal expression patterns between species for some mRNAs, but clear similarities for others. Our results also provide new information related to genome activation and the effects of embryo culture conditions on gene expression in primate embryos. These results provide one illustration of how the PREGER can be employed to obtain novel insight into primate embryogenesis.

Animals↗
PubMed2006

Identification of markers for Helicobacter pylori strains isolated from children with peptic ulcer disease by suppressive subtractive hybridization.

Peptic ulcer disease (PUD) occurs after a long-term Helicobacter pylori infection. However, the disease can develop earlier, and rare cases have been observed in children, suggesting that these H. pylori strains may be more virulent. We used suppressive subtractive hybridization for comparative genomics between H. pylori strains isolated from a 5-year-old child with duodenal ulcer and from a sex- and age-matched child with gastritis only. The prevalence of the 30 tester-specific subtracted sequences was determined on a collection of H. pylori strains from children (15 ulcers and 30 gastritis) and from adults (46 ulcers and 44 gastritis). Two of these sequences, jhp0562 (80.0% versus 33.3%, P = 0.008) and jhp0870 (80.0% versus 36.7%, P = 0.015), were highly associated with PUD in children and a third sequence, jhp0828, was less associated (40.0% versus 10.0%, P = 0.048). Among adult strains, none of the 30 sequences was associated with PUD. However, both jhp0562 and jhp0870 were less prevalent in adenocarcinoma strains than in PUD strains from children and adults, the difference being statistically significant for jhp0870. In conclusion, two H. pylori genes were identified as being strongly associated with PUD in children, and their putative roles as an outer membrane protein for jhp0870 and in lipopolysaccharide biosynthesis for jhp0562, suggest that they may be novel virulence factors of H. pylori.

Adult↗
PubMed2004

Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome.

BACKGROUND: The genus Arachis is native to a region that includes Central Brazil and neighboring countries. Little is known about the genetic variability of the Brazilian cultivated peanut (Arachis hypogaea, genome AABB) germplasm collection at the DNA level. The understanding of the genetic diversity of cultivated and wild species of peanut (Arachis spp.) is essential to develop strategies of collection, conservation and use of the germplasm in variety development. The identity of the ancestor progenitor species of cultivated peanut has also been of great interest. Several species have been suggested as putative AA and BB genome donors to allotetraploid A. hypogaea. Microsatellite or SSR (Simple Sequence Repeat) markers are co-dominant, multiallelic, and highly polymorphic genetic markers, appropriate for genetic diversity studies. Microsatellite markers may also, to some extent, support phylogenetic inferences. Here we report the use of a set of microsatellite markers, including newly developed ones, for phylogenetic inferences and the analysis of genetic variation of accessions of A. hypogea and its wild relatives. RESULTS: A total of 67 new microsatellite markers (mainly TTG motif) were developed for Arachis. Only three of these markers, however, were polymorphic in cultivated peanut. These three new markers plus five other markers characterized previously were evaluated for number of alleles per locus and gene diversity using 60 accessions of A. hypogaea. Genetic relationships among these 60 accessions and a sample of 36 wild accessions representative of section Arachis were estimated using allelic variation observed in a selected set of 12 SSR markers. Results showed that the Brazilian peanut germplasm collection has considerable levels of genetic diversity detected by SSR markers. Similarity groups for A. hypogaea accessions were established, which is a useful criteria for selecting parental plants for crop improvement. Microsatellite marker transferability was up to 76% for species of the section Arachis, but only 45% for species from the other eight Arachis sections tested. A new marker (Ah-041) presented a 100% transferability and could be used to classify the peanut accessions in AA and non-AA genome carriers. CONCLUSION: The level of polymorphism observed among accessions of A. hypogaea analyzed with newly developed microsatellite markers was low, corroborating the accumulated data which show that cultivated peanut presents a relatively reduced variation at the DNA level. A selected panel of SSR markers allowed the classification of A. hypogaea accessions into two major groups. The identification of similarity groups will be useful for the selection of parental plants to be used in breeding programs. Marker transferability is relatively high between accessions of section Arachis. The possibility of using microsatellite markers developed for one species in genetic evaluation of other species greatly reduces the cost of the analysis, since the development of microsatellite markers is still expensive and time consuming. The SSR markers developed in this study could be very useful for genetic analysis of wild species of Arachis, including comparative genome mapping, population genetic structure and phylogenetic inferences among species.

Alleles↗
PubMed2004

Evaluation of partial 16S ribosomal DNA sequencing for identification of nocardia species by using the MicroSeq 500 system with an expanded database.

Identification of clinically significant nocardiae to the species level is important in patient diagnosis and treatment. A study was performed to evaluate Nocardia species identification obtained by partial 16S ribosomal DNA (rDNA) sequencing by the MicroSeq 500 system with an expanded database. The expanded portion of the database was developed from partial 5' 16S rDNA sequences derived from 28 reference strains (from the American Type Culture Collection and the Japanese Collection of Microorganisms). The expanded MicroSeq 500 system was compared to (i). conventional identification obtained from a combination of growth characteristics with biochemical and drug susceptibility tests; (ii). molecular techniques involving restriction enzyme analysis (REA) of portions of the 16S rRNA and 65-kDa heat shock protein genes; and (iii). when necessary, sequencing of a 999-bp fragment of the 16S rRNA gene. An unknown isolate was identified as a particular species if the sequence obtained by partial 16S rDNA sequencing by the expanded MicroSeq 500 system was 99.0% similar to that of the reference strain. Ninety-four nocardiae representing 10 separate species were isolated from patient specimens and examined by using the three different methods. Sequencing of partial 16S rDNA by the expanded MicroSeq 500 system resulted in only 72% agreement with conventional methods for species identification and 90% agreement with the alternative molecular methods. Molecular methods for identification of Nocardia species provide more accurate and rapid results than the conventional methods using biochemical and susceptibility testing. With an expanded database, the MicroSeq 500 system for partial 16S rDNA was able to correctly identify the human pathogens N. brasiliensis, N. cyriacigeorgica, N. farcinica, N. nova, N. otitidiscaviarum, and N. veterana.

DNA, Ribosomal↗
PubMed2001

Strategies for integrating primary health services in middle- and low-income countries: effects on performance, costs and patient outcomes.

BACKGROUND: Integration of primary health care is change to bring together inputs, organisation, management and delivery of particular service functions. Integration has been promoted in the health sector to improve the efficiency of health care delivery. The need for integration arose from perceptions that services were fragmented when delivered through separate vertical programmes. Integration is relevant to the health system at various levels, and this review is concerned with integration at the point of delivery. OBJECTIVES: To assess the effects of strategies to integrate primary health care services on producing a more coherent product and improving health care delivery and health status, in relation to service cost, outputs, impact and user acceptability. SEARCH STRATEGY: We searched the Cochrane Effective Practice and Organisation of Care Group specialised register (August 2000), MEDLINE (1966 to September 2000), EMBASE (1988 to September 2000), Socio Files (1974 to September 2000), Popline (1970 to September 2000), HealthStar (1975 to September 2000), Cinahl (1982 to September 2000); Cab Health (1972 to 1999), International Bibliography of the Social Sciences (1970 to 1999), and reference lists of articles. We also searched the Internet and World Health Organization (WHO) library database, hand searched relevant WHO publications and contacted experts in the field. SELECTION CRITERIA: Randomised trials, controlled before and after studies, and interrupted time series analyses of integration strategies in primary health care services. Health services in high-income countries were excluded. The primary outcomes were service outputs: productivity and coverage, impact, user acceptability and unit cost. DATA COLLECTION AND ANALYSIS: Two reviewers independently extracted data and assessed study quality. MAIN RESULTS: Four studies were included. There was no consistent pattern of benefit. Integration had a clear positive effect on the outputs in only one study; in another it had similar effects to vertical programme delivery but greater effect than the control group. In the other two studies integration resulted in negative outputs in comparison with vertical programmes, although in one of these integration performed better than the control group. REVIEWER'S CONCLUSIONS: Few studies of good quality, large and with rigorous study design have been carried out to investigate the evidence to support integration as a style of service delivery. In fact, some studies found greater effects for vertical health care delivery. Policy makers and planners considering integration could introduce strategies, using rigorous study design, to allow further evaluation and increase the base of studies from which to draw evidence.

Clinical Trials as Topic↗
PubMed2006

Low level of genetic diversity in cultivated Pigeonpea compared to its wild relatives is revealed by diversity arrays technology.

Understanding the distribution of genetic diversity among individuals, populations and gene pools is crucial for the efficient management of germplasm collections and breeding programs. Diversity analysis is routinely carried out using sequencing of selected gene(s) or molecular marker technologies. Here we report on the development of Diversity Arrays Technology (DArT) for pigeonpea (Cajanus cajan) and its wild relatives. DArT tests thousands of genomic loci for polymorphism and provides the binary scores for hundreds of markers in a single hybridization-based assay. We tested eight complexity reduction methods using various combinations of restriction enzymes and selected PstI/HaeIII genomic representation with the largest frequency of polymorphic clones (19.8%) to produce genotyping arrays. The performance of the PstI/HaeIII array was evaluated by typing 96 accessions representing nearly 20 species of Cajanus. A total of nearly 700 markers were identified with the average call rate of 96.0% and the scoring reproducibility of 99.7%. DArT markers revealed genetic relationships among the accessions consistent with the available information and systematic classification. Most of the diversity was among the wild relatives of pigeonpea or between the wild species and the cultivated C. cajan. Only 64 markers were polymorphic among the cultivated accessions. Such narrow genetic base is likely to represent a serious impediment to breeding progress in pigeonpea. Our study shows that DArT can be effectively applied in molecular systematics and biodiversity studies.

Biodiversity↗
PubMed2003

Functional genomics reveals relationships between the retrovirus-like Ty1 element and its host Saccharomyces cerevisiae.

Retroviruses and their relatives, the long terminal repeat (LTR) retrotransposons, carry out complex life cycles within the cells of their hosts. We have exploited a collection of gene deletion mutants developed by the Saccharomyces Genome Deletion Project to perform a functional genomics screen for host factors that influence the retrovirus-like Ty1 element in yeast. A total of 101 genes that presumably influence many different aspects of the Ty1 retrotransposition cycle were identified from our analysis of 4483 homozygous diploid deletion strains. Of the 101 identified mutants, 46 had significantly altered levels of Ty1 cDNA, whereas the remaining 55 mutants had normal levels of Ty1 cDNA. Thus, approximately half of the mutants apparently affected the early stages of retrotransposition leading up to the assembly of virus-like particles and cDNA replication, whereas the remaining half affected steps that occur after cDNA replication. Although most of the mutants retained the ability to target Ty1 integration to tRNA genes, 2 mutants had reduced levels of tRNA gene targeting. Over 25% of the gene products identified in this study were conserved in other organisms, suggesting that this collection of host factors can serve as a starting point for identifying host factors that influence LTR retroelements and retroviruses in other organisms. Overall, our data indicate that Ty1 requires a large number of cellular host factors to complete its retrotransposition cycle efficiently.

Blotting, Southern↗
PubMed2005

Antibiotic regimens for suspected late onset sepsis in newborn infants.

BACKGROUND: Late onset neonatal sepsis (systemic infection after 48 hours of age) continues to be a significant cause of morbidity and mortality. Early treatment with antibiotics is essential as infants can deteriorate rapidly. It is not clear which antibiotic regimen is most suitable for initial treatment of suspected late onset sepsis. OBJECTIVES: To compare the effectiveness and adverse effects of different antibiotic regimens for treatment of suspected late onset sepsis in newborn infants. SEARCH STRATEGY: The standard search strategy of the Cochrane Neonatal Review Group was used. This includes electronic searches of the Cochrane Central Register of Controlled Trials (CENTRAL, The Cochrane Library, Issue 4, 2004), MEDLINE (1966 - Dec 2004), EMBASE (1980 - Dec 2004) and CINAHL (1982 - Dec 2004), electronic abstracts of Pediatric Academic Society meetings (1996 - Dec 2004) and previous reviews including cross references (all articles referenced). SELECTION CRITERIA: Randomised and quasi randomised controlled trials comparing different initial antibiotic regimens in neonates with suspected late onset sepsis were evaluated. DATA COLLECTION AND ANALYSIS: Both reviewer authors screened abstracts and papers against the inclusion criteria, appraised the quality of and extracted data from papers. For dichotomous outcomes, treatment effect was expressed as relative risk and risk difference with 95% confidence intervals. NNT was calculated for outcomes for which there was a statistically significant reduction in risk difference. MAIN RESULTS: Thirteen studies were identified as possibly eligible for inclusion. The majority of studies were excluded as they did not separate data for early and late onset infection. Two studies are still awaiting assessment. Only one small study, in 24 neonates, was included in this review. It compared beta-lactam therapy with a combination of beta lactam plus aminoglycoside. The study did not meet our prespecified criteria for good methodological quality. In babies with suspected infection there was no significant difference in mortality (RR 0.17, 95% CI 0.01 to 3.23) or treatment failure (RR 0.17, 95% CI 0.01 to 3.23). Antibiotic resistance was assessed and there were no cases in either group. AUTHORS' CONCLUSIONS: There is inadequate evidence from randomised trials in favour of any particular antibiotic regimen for the treatment of suspected late onset neonatal sepsis. The available evidence is not of high quality. Although suspected sepsis and antibiotic use is common, quality research is required to specifically address both narrow and broad spectrum antibiotic use for late onset neonatal sepsis. Future research also needs to assess cost effectiveness and the impact of antibiotics in different settings such as developed or developing countries and lower gestational age groups.

Aminoglycosides↗