Time-cost analysis of a quantum key distribution system clocked at 100 MHz.

We describe the realization of a quantum key distribution (QKD) system clocked at 100 MHz. The system includes classical postprocessing implemented via software, and is operated over a 12 km standard telecommunication dark fiber in a real-world environment. A time-cost analysis of the sifted, error-corrected, and secret key rates relative to the raw key rate is presented, and the scalability of our implementation with respect to higher secret key rates is discussed.

Microgeographic population structure of green swordail fish: genetic differentiation despite abundant migration.

Swordtails (Xiphophorus; Poeciliidae) have figured prominently in research on fish mating behaviours, sexual selection, and carcinogenesis, but their population structures and dispersal patterns have been relatively neglected. Using nine microsatellite loci, we estimated genetic differentiation in Xiphophorus helleri within and between adjacent streams in Belize. The genetic data were complemented by a tagging study of movement within one stream. In the absence of physical dispersal barriers (waterfalls), population structure followed an isolation by distance (IBD) pattern. Genetic differentiation (F(ST) up to 0.07) was significant between and within creeks, despite high dispersal in the latter as judged by the tagging data. Such heterogeneity apparently was a result of genetic drift in local demes, due to small population sizes and highly skewed paternity. The IBD pattern was interrupted by waterfalls, boosting F(ST) above 0.30 between adjacent samples across these barriers. Overall, our results are helpful in understanding the interplay of evolutionary forces and population dynamics in a small fish living in a changeable habitat.

Improving the Glasgow Coma Scale score: motor score alone is a better predictor.

BACKGROUND: The Glasgow Coma Scale (GCS) has served as an assessment tool in head trauma and as a measure of physiologic derangement in outcome models (e.g., TRISS and Acute Physiology and Chronic Health Evaluation), but it has not been rigorously examined as a predictor of outcome. METHODS: Using a large trauma data set (National Trauma Data Bank, N = 204,181), we compared the predictive power (pseudo R2, receiver operating characteristic [ROC]) and calibration of the GCS to its components. RESULTS: The GCS is actually a collection of 120 different combinations of its 3 predictors grouped into 12 different scores by simple addition (motor [m] + verbal [v] + eye [e] = GCS score). Problematically, different combinations summing to a single GCS score may actually have very different mortalities. For example, the GCS score of 4 can represent any of three mve combinations: 2/1/1 (survival = 0.52), 1/2/1 (survival = 0.73), or 1/1/2 (survival = 0.81). In addition, the relationship between GCS score and survival is not linear, and furthermore, a logistic model based on GCS score is poorly calibrated even after fractional polynomial transformation. The m component of the GCS, by contrast, is not only linearly related to survival, but preserves almost all the predictive power of the GCS (ROC(GCS) = 0.89, ROC(m) = 0.87; pseudo R2(GCS) = 0.42, pseudo R2(m) = 0.40) and has a better calibrated logistic model. CONCLUSION: Because the motor component of the GCS contains virtually all the information of the GCS itself, can be measured in intubated patients, and is much better behaved statistically than the GCS, we believe that the motor component of the GCS should replace the GCS in outcome prediction models. Because the m component is nonlinear in the log odds of survival, however, it should be mathematically transformed before its inclusion in broader outcome prediction models.

Polymorphisms in CYP1A1 and smoking: no association with breast cancer risk.

Several studies have investigated polymorphisms in CYP1A1 and breast cancer risk with inconsistent results. We have carried out a population based case-control study of the Thr461Asn and Ile462Val polymorphisms in CYP1A1 to clarify their importance in determining breast cancer susceptibility. A total of 1873 cases and 712 controls were genotyped for Thr461Asn and 1948 cases and 1355 controls were genotyped for Ile462Val. We have also investigated a putative interaction between smoking and CYP1A1 genotype and breast cancer risk using a case only study design. The genotype distribution of Thr461Asp in controls was close to that expected under Hardy-Weinberg equilibrium (HWE). We detected no significant differences in genotype frequencies between breast cancer cases and controls (P = 0.68). Compared with the Thr/Thr homozygotes there was no significant risk for either the Thr/Asp heterozygote [OR = 1.1 (95% CI 0.8-1.4)] or the Asp/Asp homozygote [OR = 0.4 (0.02-6.1)]. The genotype distribution of Ile462Val in controls was also close to that expected under HWE with no significant differences between breast cancer cases and the controls (P = 0.44). No significant risk was found for either the Ile/Val heterozygote [OR = 0.8 (0.6-1.1)] or the Val/Val homozygote [OR = 2.7 (0.3-24)] compared with the Ile/Ile homozygotes. Furthermore, subgroup analyses revealed no effect of age or menopausal status on genotypic risks, and we found no evidence for an interaction between genotype and smoking habit or alcohol consumption and susceptibility to breast cancer. We combined our data for the Ile462Val polymorphism with those from four other published studies, but even with >5000 subjects, none of the genotype-associated risks achieved statistical significance, and there was no consistent pattern to the risks associated with increasing Val allele dosage [Ile/Val OR = 0.9 (0.7-1.1), Val/Val OR = 2.3 (0.4-12), and Val carrier OR = 1.0 (0.9-1.1)].

A common variant in BRCA2 is associated with both breast cancer risk and prenatal viability.

Inherited mutations in the gene BRCA2 predispose carriers to early onset breast cancer, but such mutations account for fewer than 2% of all cases in East Anglia. It is likely that low penetrance alleles explain the greater part of inherited susceptibility to breast cancer; polymorphic variants in strongly predisposing genes, such as BRCA2, are candidates for this role. BRCA2 is thought to be involved in DNA double strand break-repair. Few mice in which Brca2 is truncated survive to birth; of those that do, most are male, smaller than their normal littermates and have high cancer incidence. Here we show that a common human polymorphism (N372H) in exon 10 of BRCA2 confers an increased risk of breast cancer: the HH homozygotes have a 1.31-fold (95% CI, 1.07-1.61) greater risk than the NN group. Moreover, in normal female controls of all ages there is a significant deficiency of homozygotes compared with that expected from Hardy-Weinberg equilibrium, whereas in males there is an excess of homozygotes: the HH group has an estimated fitness of 0.82 in females and 1.38 in males. Therefore, this variant of BRCA2 appears also to affect fetal survival in a sex-dependent manner.

The extent of linkage disequilibrium in four populations with distinct demographic histories.

The design and feasibility of whole-genome-association studies are critically dependent on the extent of linkage disequilibrium (LD) between markers. Although there has been extensive theoretical discussion of this, few empirical data exist. The authors have determined the extent of LD among 38 biallelic markers with minor allele frequencies >.1, since these are most comparable to the common disease-susceptibility polymorphisms that association studies aim to detect. The markers come from three chromosomal regions-1,335 kb on chromosome 13q12-13, 380 kb on chromosome 19q13.2, and 120 kb on chromosome 22q13.3-which have been extensively mapped. These markers were examined in approximately 1,600 individuals from four populations, all of European origin but with different demographic histories; Afrikaners, Ashkenazim, Finns, and East Anglian British. There are few differences, either in allele frequencies or in LD, among the populations studied. A similar inverse relationship was found between LD and distance in each genomic region and in each population. Mean D' is.68 for marker pairs <5 kb apart and is.24 for pairs separated by 10-20 kb, and the level of LD is not different from that seen in unlinked marker pairs separated by >500 kb. However, only 50% of marker pairs at distances <5 kb display sufficient LD (delta>.3) to be useful in association studies. Results of the present study, if representative of the whole genome, suggest that a whole-genome scan searching for common disease-susceptibility alleles would require markers spaced < or = 5 kb apart.

Polymorphisms in the human aromatase cytochrome P450 gene (CYP19) and breast cancer risk.

The aromatase enzyme catalyses the conversion of androgens to oestrogens in the oestrogen biosynthesis pathway. Because increased exposure to oestrogens is considered to be a risk factor for breast cancer, the human aromatase gene (CYP19) is a plausible candidate for low penetrance breast cancer susceptibility. Preliminary reports have suggested that specific alleles of a TTTA repeat may be associated with differences in breast cancer risk. We have identified two new polymorphisms in the CYP19 gene: a TCT insertion/deletion in intron 4 and a G-->T substitution in intron 6, which have rare allele frequencies of 0.35 and 0.45, respectively, in the British population. Comparison was made between the frequencies of these alleles and those of the TTTA repeat in up to 599 breast cancer cases and 433 normal controls from the East Anglian, British population. We found strong linkage disequilibrium between the alleles of these three loci, but no significant association of any alleles with breast cancer risk. The maximum odds ratios observed were: 1.03 (95% CI 0.68-1.55) for the intron 4 TCT insertion/deletion polymorphism [del/del versus ins/ins]; 1.56 (95% CI 0.63-3.83) for the intron 4 [TTTA](10) allele; 1.29 (95% CI 0. 75-2.21) for the intron 6 G-->T polymorphism [TT versus GG]. We conclude that the CYP19 gene has no major role in common breast cancer incidence in the British population.

No association between androgen or vitamin D receptor gene polymorphisms and risk of breast cancer.

Endogenous hormone exposure is known to alter breast cancer susceptibility and genes responsive to such hormones are plausible candidates for predisposition genes. We have examined polymorphisms in genes for two members of the nuclear receptor superfamily which are expressed in breast tissue and known to moderate rates of cell proliferation in a case-control association study: the androgen receptor (AR) and the vitamin D receptor (VDR). We have used two series of Caucasian female breast cancer cases, one incident and one prevalent, and compared both with two sets of matched controls from the East Anglian region of Britain. Since the results are similar in the two series we have combined them. The AR poly[Gly](n) and poly[Gln](n) tracts were genotyped in a total of 508 female breast cancer cases and 426 controls. The VDR TaqI polymorphism was analysed in 951 cases and 627 controls drawn from the same population series. There were no significant differences between cases and controls for either the AR or VDR polymorphisms. Compared with individuals with two short alleles (<22 repeats) of the AR poly[Gln](n) tract, the odds ratios and 95% confidence intervals (95% CI) for individuals with one or two long alleles were 0.82 (95% CI 0.62-1.09) and 1.31 (95% CI 0.87-1.97), respectively. Heterozygotes and homozygotes for the VDR TaqI cutting site had odds ratios of 1.01 (95% CI 0.81-1.27) and 0.97 (95% CI 0.71-1.32), respectively. None of the AR or VDR polymorphisms investigated has a major effect on risk of breast cancer in the British population.

A systematic review of genetic polymorphisms and breast cancer risk.

Studies investigating the relationship between common genetic variants and cancer risk are being reported with rapidly increasing frequency. We have identified 46 published case-control studies that have examined the effect of common alleles of 18 different genes on breast cancer risk. Of these, 12 report statistically significant associations, none of which were reported by more than one study. However, many of the studies were small: 10 of the 46 had 80% power or greater to detect a rare allele homozygote relative risk <2.5. We therefore combined the results of individual studies to obtain more precise estimates of risk. Statistically significant differences in genotype frequencies were found in three case-control comparisons of unselected cases. These were for CYP19 (TTTA)n polymorphism [(TTTA)10 carrier odds ratio (OR) = 2.33; P = 0.002], the GSTP1 Ile105Val polymorphism (Val carrier OR = 1.60; P = 0.02), and the TP53 Arg72Pro polymorphism (Pro carrier OR = 1.27; P = 0.03). In addition, the GSTM1 gene deletion was found to be significantly associated with postmenopausal breast cancer (null homozygote OR = 1.33; P = 0.04). There was also some evidence that homozygotes for the PR PROGINS allele are protected against breast cancer, although this result was of borderline statistical significance. For polymorphisms in BRCA1, COMT, CYP17, CYP1A1, NAT1, and NAT2, the best estimate of risk either from the individual studies or the meta-analyses was sufficiently precise to exclude a relative risk of 1.5 or greater. For the polymorphisms in EDH17B2, ER, CYP2D6, CYP2E1, GSTT1, HSP70, and TNFalpha, the risk estimates, although nonsignificant, were insufficiently precise to exclude a moderate risk (>1.5). Precise estimation of the risks associated with these and other as yet untested genes, as well as investigation of more complex risks arising from gene-gene and gene-environment interactions, will require much larger studies.

Semicontinuous cardiac output monitoring using a neural network.

OBJECTIVES: This study compared 2-mL bolus thermodilution cardiac output measurements with standard 10-mL bolus measurements. DESIGN: Cardiac output was measured with the new 2-mL bolus technique and the 10-mL standard thermodilution technique in a perspective series. We describe a system that automatically cools and injects 2-mL boluses of saline into a standard pulmonary artery catheter. It uses a Peltier effect solid-state cooler and pneumatically driven syringe injector to measure cardiac output once per minute. SETTING: Animal laboratory. ANIMALS: Eight adult Duroc swine weighing between 38.0 and 57.5 kg. INTERVENTIONS: Once each minute, 2 mL of cooled 5% dextrose was injected through the pulmonary catheter. Once every 8 mins, four sequential measurements of cardiac output were made using 10-mL injections. MEASUREMENTS AND MAIN RESULTS: A total of 1249 paired waveforms were processed with both a conventional algorithm and with a neural network. For the conventional algorithm, the correlation coefficient was r2 = .92 and the SD of the difference was 1.30 L/min. For the neural network, the correlation coefficient was r2 = .94 and the SD of the difference was 0.88 L/min. Output filtering improved the results in both cases. CONCLUSION: Neural networks accurately derive cardiac output from 2-mL bolus thermodilution injections, allowing cardiac output to be monitored automatically once per minute in many patients. The technique is convenient and uses standard low-cost catheters.

Factor V Leiden, prothrombin 20210G-->A and the MTHFR C677T mutations in childhood stroke.

Ischaemic stroke is a rare occurrence in children and in a proportion of cases the aetiology remains unknown. We have investigated the role of thrombophilia in the aetiology of this condition. Of 50 cases identified at two centres, 37 were available for detailed haematological analysis. No cases were identified with deficiencies of antithrombin, protein C or protein S. One case had elevated IgG anticardiolipin antibodies at low titre. The prevalence of the prothrombin 20210 G-->A mutation, factor V Leiden (FVL) mutation and the C677T mutation in the MTHFR gene was compared in cases to that observed in random unselected cord blood controls. The odds ratio for stroke was not significantly increased in carriers of the prothrombin mutation (OR 1.2; 95% CI 0.1-10.7), FVL (OR 2.5; 95% CI 0.5-13.5), or the C677T mutation (OR 1.7; 95% CI 0.6-4.5). Our findings suggest that thrombophilia may not play a significant role in the aetiology of stroke in children, although a large prospective study is required to investigate this area further.

Mutation of the RET proto-oncogene is correlated with RET immunostaining in subpopulations of cells in sporadic medullary thyroid carcinoma.

Mutations in the RET proto-oncogene, which encodes a receptor tyrosine kinase, are associated with the pathogenesis of medullary thyroid carcinoma (MTC). Somatic mutations in RET, predominantly at codon 918, and very rarely at codon 883, have been found in a proportion of sporadic MTC. We have previously shown that approximately 80% of sporadic MTCs had at least one subpopulation with a somatic RET mutation. Uneven distribution of somatic mutation within a single tumor or among metastases from a single individual was notable. In the present study, we sought to correlate RET expression, as demonstrated by RET immunohistochemistry, with mutation status in sporadic MTC for each tumor. Seventy evaluable subpopulations, belonging to 28 unrelated sporadic cases, comprising primary MTC and metastases, were immunostained with two different polyclonal antibodies raised against the C-terminus of RET. The regional presence of codon 918 or 883 seemed to coincide with increased RET immunopositivity in at least 62 of 70 (89%, P < 0.000001) tumor subpopulations. The reasons for this concordance are not entirely clear but could be related to either RNA or protein stability. Preliminary studies have suggested that the presence of somatic codon 918 mutation in MTC has a prognostic significance. If these preliminary results prove true, then given our data, we can further explore the feasibility of RET immunocytochemistry as a rapid assessment for the presence of somatic codon 918 for molecular diagnostic and prognostic purposes.

No association between a polymorphism in the steroid metabolism gene CYP17 and risk of breast cancer.

A recent study showed an association between a single base substitution, T-->C, in the promotor region of the CYP17 gene, the risk of breast cancer and age at menarche in Asian, African-American and Latino women from California and Hawaii. The C allele was associated with increased risk of breast cancer, significantly so for patients presenting with advanced disease, whereas the TT genotype was associated with later age at menarche in control subjects. We attempted to confirm these findings in a large case-control study in East Anglia, England (835 cases and 591 control subjects). We found no evidence of an increased risk of breast cancer [odds ratio (OR) 1.10, confidence interval (CI) 0.89-1.37] or advanced breast cancer (OR 0.88, CI 0.38-2.01) in C allele carriers, nor any association between age at menarche and genotype. We conclude that these alleles do not significantly alter breast cancer risk in the English population.

Detection of the hepatitis C virus by rt-PCR.

The hepatitis C virus (HCV) is an orgainsm of the age of molecular biology, for its discovery and much of the research into the infection have relied heavily on molecular techniques. The development of molecular cloning enabled a successful strategy that finally identified HCV (1)as the cause of 90% of posttransfusion (2)and > 50% of sporadic non-A, non-B hepatitis (3) after the failure by immunological techniques to discover the responsible agent. It is an important infection as most infected patients developed chronic hepatitis (> 50%) that can progress to cirrhosis and hepatocellular carcinoma (4-6) . Following the identification of the viral genome, antibody tests were developed which could detect exposure to the virus (7). The presence of antibodies to HCV, however, does not distinguish between those with chronic infection and those who had cleared the virus. Chronic HCV infection can be difficult to diagnose as patients may be asymptomatic and have normal liver biochemistry (8),(9) despite abnormal liver histology. Therefore, demonstration of virus RNA (usually from serum samples) is often necessary to confirm Infection. Detection of HCV RNA requires the sensitivity of nucleic acid amplification (e.g., the polymerase chain reaction) as circulating levels of vnus RNA can be very low (10),(11). Such tests are now widely used to confirm infection, monitor the response to anti-viral therapy, and in epidemiological studies of HCV infection.

Clinical outcome of hypogammaglobulinaemic patients following outbreak of acute hepatitis C: 2 year follow up.

In 1994, an outbreak of hepatitis C virus (HCV) infection, genotype 1a, occurred in 30 hypogammaglobulinaemic patients in the UK from one batch of contaminated anti-HCV screened intravenous immunoglobulin. This study aimed to study prospectively the outcome of HCV in hypogammaglobulinaemic patients, and to assess the response to early treatment with interferon-alpha, 6 million units three times weekly for 6 months. Data were collected using standardized questionnaires. Five patients with secondary hypogammaglobulinaemia due to lymphoid malignancy were not treated and all have died of their primary malignancy. Of 25 patients with primary hypogammaglobulinaemia, one resolved HCV infection before treatment, 17 commenced on treatment, and seven declined or treatment was contra-indicated. Thirteen of 17 patients completed therapy and seven (54%) have a sustained response (normal transaminases, negative serum HCV RNA) at 6 and 12 months after treatment. Two of the 12 patients with primary hypogammaglobulinaemia, who were not treated or failed to complete treatment, have cleared the virus. Liver biopsy was performed in patients not clearing HCV and was abnormal in all. Four patients developed liver failure within 2 years, of whom three have died and one has been successfully transplanted. In conclusion, HCV can cause rapid severe liver disease in hypogammaglobulinaemic patients. Early treatment with high-dose interferon-alpha results in a high clearance of HCV.

Perinatal mortality in northern Benin.

PIP: The perinatal mortality rate (PMR) at the Hopital Evangelique in the Borgon region of Benin was 224/1000 in 1984 compared to 164/1000 in 1994. Despite the decrease, the rate was still high. Perinatal deaths for 1994 were reviewed retrospectively from case notes and data routinely recorded (presentation, distance traveled, and prenatal care). The probable causes of death were determined. A total of 511 babies were delivered by 484 women in 1994 at the hospital. There were 62 stillbirths (26 cases of birth asphyxia, 14 cases of antepartum hemorrhage, 7 cases of ruptured uterus, and 6 cases of intrauterine death before labor) and 22 neonatal deaths (7 cases of birth asphyxia and 11 cases of prematurity). Maternal errors accounted for 14 stillbirths and 4 neonatal deaths; logistical difficulties accounted for 8 stillbirths and 4 neonatal deaths; and the errors of management/referring maternity accounted for 4 stillbirths and 1 neonatal death. Some examples of maternal errors included a patient (gravida 6, para 5) who had not received prenatal care and presented with antepartum hemorrhage after being in labor for 72 hours. She had a ruptured uterus and required hysterectomy. Another patient (gravida 6, para 5) who had not received prenatal care presented to a maternity unit in labor with a shoulder presentation. On arrival, and after referral, intrauterine death was diagnosed and the fetus was delivered. Examples of logistical problems included a primigravida referred from a maternity unit more than 50 km away for delay in the second stage of labor. She delivered normally after arrival; however, the baby was asphyxiated and died. A patient who was gravida 2, para 1 was referred from a maternity unit with a cord prolapse. The fetal heart beat was present on leaving the maternity unit but was absent on arrival at the hospital. Bad management cases related to prolonged labor or attempts at a traumatic vaginal delivery. Maternal errors were the main source of deaths; thus, prenatal and intrapartum care should be more accessible to reduce the PMR.^ieng

Mutation analysis of the c-mos proto-oncogene and the endothelin-B receptor gene in medullary thyroid carcinoma and phaeochromocytoma.

The characteristic tumours of MEN 2 are medullary thyroid carcinoma (MTC) and phaeochromocytoma. Somatic RET mutations have been found in only 23-40% of sporadic MTC and 10% of sporadic phaeochromocytomas. Thus, we sought other genes which may play a role in the pathogenesis of these tumours. We carried out direct sequence analysis of human c-mos and human ENRB in a series of sporadic MTC and phaeochromocytomas to determine if somatic mutations in these two genes could account for some of the sporadic MEN 2-related tumours in which no RET mutations are detected. No somatic mutations were found.