Risk assessment of recent Egyptian H5N1 influenza viruses.

Highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype are enzootic in poultry populations in different parts of the world, and have caused numerous human infections in recent years, particularly in Egypt. However, no sustained human-to-human transmission of these viruses has yet been reported. We tested nine naturally occurring Egyptian H5N1 viruses (isolated in 2014-2015) in ferrets and found that three of them transmitted via respiratory droplets, causing a fatal infection in one of the exposed animals. All isolates were sensitive to neuraminidase inhibitors. However, these viruses were not transmitted via respiratory droplets in three additional transmission experiments in ferrets. Currently, we do not know if the efficiency of transmission is very low or if subtle differences in experimental parameters contributed to these inconsistent results. Nonetheless, our findings heighten concern regarding the pandemic potential of recent Egyptian H5N1 influenza viruses.

Effect of corn bran and steep inclusion in finishing diets on diet digestibility, cattle performance, and nutrient mass balance.

One metabolism trial and 2 finishing trials were conducted to evaluate the effects of adding corn bran and steep liquor (steep) in replacement of dry-rolled corn (DRC) on diet digestibility, cattle performance, and nutrient mass balance in open feedlot pens. The metabolism trial (Exp. 1) used 8 ruminally cannulated heifers in a 4 × 4 Latin square design and the 2 finishing trials used 128 steer calves fed for 167 d (Exp. 2) and 256 yearling steers fed for 126 d (Exp. 3). Dietary treatments for all trials included a DRC-based control (CON), 30% corn bran (30/0), 30% corn bran plus 15% steep (30/15), and 45% corn bran plus 15% steep (45/15), in which by-products replaced DRC and molasses in the diet (DM basis). Diets were not isonitrogenous or isoenergetic. In the metabolism trial, feeding the by-product diets produced greater rumen pH (5.95) than CON (5.76; P < 0.01). Total tract DM and OM digestibility were greater for heifers fed CON than the by-product diets (P < 0.01). Dry matter and NDF ruminal disappearance (%/h) of corn bran were numerically less for cattle fed the CON diet than the by-product diets (2.36 vs. 2.84 and 0.72 vs. 1.66, respectively). In the performance trials, steers fed the by-product diets consumed more DM (P = 0.06) and G:F was either similar for all diets in Exp. 2 (P = 0.56) or less for cattle fed 30/0 than the other diets in Exp. 3 (P = 0.05). Percent N loss was reduced in Exp. 2 by including corn bran in diets compared with CON (P < 0.01). However, in Exp. 3, no differences in percent N loss were detected among treatments (P = 0.16), but more N was removed in the manure from pens where steers were fed by-products (P = 0.01). Although steep did not improve diet digestibility, it was beneficial in maintaining cattle performance in the feedlot studies. Feeding corn bran in combination with steep increased manure N removed and N in compost, but decreased percent N lost during the winter months only.

Phosphorus requirement and excretion of finishing beef cattle fed different concentrations of phosphorus.

Phosphorus is an expensive nutrient to supplement, and excess may lead to manure P challenges. Therefore, minimizing dietary P to meet requirements is important. Two experiments were conducted to determine the P requirement of finishing cattle (Exp. 1) and to evaluate the effects of feeding different P concentrations on the quantity and route of P excretion (Exp. 2). In Exp. 1, 60 heifers (BW = 278 kg +/- 17 kg) were individually fed 1 of 5 dietary P concentrations (0.10, 0.17, 0.24, 0.31, or 0.38% P). Cattle performance, plasma P concentration, bone characteristics, and bone P concentration were used to determine the P requirement. Intake and ADG increased quadratically (P < 0.01) as dietary P increased. Plasma P in heifers receiving the 0.10% treatment was less (P < 0.01) than the other treatments and suggested that these heifers were experiencing a P deficiency. Total ash weight of the phalanx bones increased linearly (P < 0.01) as dietary P increased. In Exp. 2 using a 5 x 5 Latin square design, 5 different diets varying in P concentration (0.12, 0.27, 0.42, 0.30, and 0.36% P) were fed to steers to evaluate route and quantity of P excreted. Steers excreted little (1.78 g/d on average) P in the urine as a percentage of total P excretion. Steers on the 0.12% P diet excreted very little P in urine (0.50 g/d). Excretion of P was less (P < 0.05) for the cattle fed 0.12% P compared with all other treatments. Results from cattle performance, plasma P concentrations, and bone characteristics indicate that the heifers fed 0.10% P were experiencing a deficiency and the P requirement of finishing heifers is between 0.10 and 0.17% P. Dietary P concentrations of 0.10 to 0.17% P resulted in decreased P excretion. Supplementation of mineral P is unnecessary in grain-based feedlot diets because dietary P will greatly exceed the requirements (<0.17%).

Effect of supplemental energy source and frequency on growing calf performance.

Crossbred heifers (n = 120; 265 kg, SD = 37) were fed individually (84 d) to determine the effect of supplement type, concentration, and frequency on intake and performance and to estimate the energy value of dry distillers grains plus solubles (DDGS) in a high-forage diet. Treatments were arranged in a 3 x 2 x 2 factorial, with 3 supplements, 2 concentrations, and 2 frequencies of supplementation. Supplements including dry-rolled corn (DRC), DRC with corn gluten meal (DRC + CGM), and DDGS were fed at 0.21% (LOW) or 0.81% (HIGH) of BW daily and were provided daily (DAILY) or 3 times weekly (ALT). Heifers were fed to consume grass hay (8.7% CP) ad libitum. Individual DMI, diet composition, BW, and ADG were used to calculate energy values for DDGS and DRC. Supplement type, concentration, frequency, and interactions were tested using the MIXED procedure of SAS, with BW included as a covariate. Supplement x concentration interactions for gain (P = 0.01) and G:F (P < 0.01) were detected. At the LOW concentration, heifers supplemented with DDGS gained more and were more efficient (P /= 0.22) between DDGS and DRC + CGM in HIGH treatments, although both improved (P

Influence of corn hybrid traits on digestibility and the efficiency of gain in feedlot cattle.

Two experiments were conducted to determine the influence of chemical and physical corn kernel traits on digestibility and feedlot cattle performance. Seven commercially available corn hybrids representing a range in kernel traits were evaluated for a variety of chemical and physical traits that included test weight, 1,000-grain weight, kernel size, starch, CP, amylose, Stenvert Hardness tests (kernel hardness traits), tangential abrasive dehulling device loss, 12-h in vitro starch disappearance, and rate and extent of in situ DM disappearance. Differences among hybrids existed for all physical kernel traits measured. In Exp. 1, 224 steers in 28 pens were fed the same hybrids for 167 d in a completely randomized design. All diets were formulated to have 12.5% CP and contained 66% dry-rolled corn (DM basis). There were no differences (P >0.20) among corn hybrids for DMI, ADG, or carcass characteristics. However, efficiency of gain (G:F) was influenced by hybrid (P < 0.01) with a difference of 9.5% from the least to the most efficient. In Exp. 2, 7 ruminally cannulated heifers were used in a 7 x 7 Latin square design to determine the effects of these hybrids on nutrient digestibility, VFA concentrations, and ruminal pH. Total-tract OM and starch digestibilities were not different (P >0.15) among hybrids and averaged 77.9 and 95.1%, respectively. Differences (P < 0.05) among hybrids existed for ruminal propionate concentration and the acetate to propionate ratio. Kernel hardness traits correlated (P < 0.05) with G:F were 1,000-grain weight (r = -0.81), Stenvert time to grind (r = -0.83), and the proportion of Stenvert soft to coarse particle height (r = 0.83). Propionate concentration was not correlated (r = 0.45) with G:F but was correlated (P = 0.02) to the Stenvert time to grind (r = -0.83). Cattle fed dry-rolled corn hybrids with greater proportions of soft endosperm had greater concentrations of propionate and gained more efficiently than cattle fed hybrids with a harder endosperm. Selecting for these softer kernel traits may improve the efficiency of gain in feedlot cattle.

Wet corn gluten feed and alfalfa hay levels in dry-rolled corn finishing diets: effects on finishing performance and feedlot nitrogen mass balance.

One-hundred ninety-two crossbred steers (initial BW = 351 +/- 11 kg) were used to determine the effects of removing alfalfa hay (AH) from dry-rolled corn-based diets containing wet corn gluten feed (WCGF) on animal performance and nutrient (N and OM) mass balance in open feedlot pens. Steers were stratified by weight and assigned randomly to 24 pens (2 x 3 factorial) and fed for 132 d from June to October 2002. Experimental diets contained either 0 or 35% WCGF and 0, 3.75, or 7.5% AH, and were formulated to be isonitrogenous. For efficiency of gain, an interaction occurred (P = 0.09) between AH and WCGF. Feed efficiencies of cattle fed 35% WCGF were improved 4.4% (P = 0.10) compared with efficiencies of cattle fed no WCGF at 0% AH; there was a marked improvement in ADG for cattle fed WCGF compared with no WCGF in diets with 0% AH. Within 35% WCGF diets, efficiency decreased as AH inclusion increased (P = 0.06). Efficiency was equal across AH levels when 0% WCGF was fed; however, ADG was decreased when AH was removed. Interactions between AH and WCGF were not detected for other performance or carcass criteria; therefore, main effects of AH and WCGF are discussed. Daily intake, ADG, and HCW increased linearly (P < 0.05) as dietary AH level increased. Feeding 35% WCGF also resulted in greater DMI (P < 0.01) and a tendency for greater ADG and HCW (P < or = 0.10) compared with steers fed no WCGF. Interactions between AH and WCGF were not observed for feedlot N mass balance. As level of AH increased across diets, N intake, N retention, and N excretion increased (P < 0.05). Steers fed 35% WCGF consumed and excreted more N (P < 0.01) than those fed no WCGF. More manure DM (P = 0.11), OM, and N (P < 0.01) were removed from pens housing steers fed 35% WCGF as well as greater OM and N recovery in finished compost. More N (kilogram/steer) was also lost to volatilization as a result of greater N excretion when WCGF was fed. Expressed as a percentage of N excretion, loss of N from pens housing steers fed 0 and 35% WCGF was not different, averaging nearly 80%. These data suggest that AH has less value when dry-rolled corn-based diets contain 35% WCGF and can be decreased from conventional levels. Furthermore, loss of N from open feedlot pens is high during the summer months, and feeding WCGF may not reduce N losses during these times of year.

Optimal wet corn gluten and protein levels in steam-flaked corn-based finishing diets for steer calves.

A feeding trial evaluated the hypothesis that wet corn gluten feed would improve growth performance of cattle fed steam-flaked corn-based finishing diets and supply required degradable intake protein (DIP). The trial used 360 steer calves (initial BW = 288 +/- 11 kg) housed in 36 pens for 166 d in an incomplete 4 x 3 factorial arrangement of treatments. Pens of steers were assigned to treatments according to a completely randomized design (four replicates per treatment combination). Treatments were wet corn gluten feed (0, 20, 30, or 40% of dietary DM) and CP (13.0, 13.7, or 14.4% of dietary DM) via supplemental urea as DIP. The 0% wet corn gluten feed treatment included only the 13.7% CP diet, and the 40% wet corn gluten feed treatment included only the 13.7 and 14.4% CP diets. Final dietary DIP concentration was 9.0% for 0% wet corn gluten feed; 8.7, 9.5, and 10.2% for 20% wet corn gluten feed; 9.0, 9.7, and 10.3% DIP for 30% wet corn gluten feed; and 10.0 and 10.6% for 40% wet corn gluten feed. Hot carcass weight, ADG, DMI, and G:F responded quadratically (P < or = 0.05) to wet corn gluten feed. The 20, 30, and 40% wet corn gluten feed treatments increased ADG by 7, 6, and 3% and increased DMI by 4, 5, and 5%, respectively, relative to the 0% wet corn gluten feed treatment. Feed efficiency was 102, 101, and 98% of the 0% wet corn gluten feed treatment for 20, 30, and 40% wet corn gluten feed, respectively. Hot carcass weight, ADG, and G:F increased linearly (P < or = 0.05) in response to increased DIP. Nonlinear analysis for DIP over the combined 20 and 30% wet corn gluten feed treatments indicated a DIP requirement of 9.6% of DM for ADG and 9.2% of DM for G:F, corresponding to 14.6 and 14.3% CP for 20% wet corn gluten feed and 14.8 and 14.5% CP for 30% wet corn gluten feed, respectively. Fat thickness, marbling, LM area, and USDA yield grade were not affected (P = 0.12 to 0.99) by wet corn gluten feed or CP. These results show that the inclusion rate of wet corn gluten feed for maximizing ADG and G:F in steam-flaked corn-based finishing diets is approximately 20% of DM. The DIP requirement determined in this trial averaged 9.4% of DM.

Effects of dry, wet, and rehydrated corn bran and corn processing method in beef finishing diets.

Two finishing trials were conducted to determine the effects of adding different types of corn bran, a component of corn gluten feed, on cattle performance. In Trial 1, 60 English crossbred yearling steers (283 +/- 6.7 kg) were used in a completely randomized design with four dietary treatments. Treatments were diets with no corn bran, dry corn bran (86% DM), wet corn bran (37% DM), and rehydrated dry bran (37% DM). Bran was fed at 40% of dietary DM. All finishing diets had (DM basis) 9% corn steep liquor with distillers solubles, 7.5% alfalfa hay, 3% tallow, and 5% supplement. Gain efficiency and ADG were greater (P < 0.01) for cattle fed no corn bran compared with all treatments containing corn bran; however, no differences were detected across corn bran types. In Trial 2, 340 English crossbred yearling steers (354 +/- 0.6 kg) were used in a randomized block design with treatments assigned based on a 2 x 4 + 2 factorial arrangement (four pens per treatment). One factor was the corn processing method used (dry-rolled corn, DRC; or steam-flaked corn, SFC). The other factor was corn bran type: dry (90% DM), wet (40% DM), or dry bran rehydrated to 40 or 60% DM. Bran was fed at 30% of dietary DM, replacing either DRC or SFC. Two control diets (DRC and SFC) were fed with no added bran. All finishing diets contained (DM basis) 10% corn steep liquor with distiller's solubles, 3.5% alfalfa hay, 3.5% sorghum silage, and 5% supplement. Corn bran type did not affect DMI (P = 0.61), ADG (P = 0.53), or G:F (P = 0.10). Dry matter intake was greater (P < 0.01) by steers fed bran compared with those fed no bran, and was greater by steers fed DRC than by steers fed SFC (P < 0.01). Interactions occurred (P < 0.01) between grain source and bran inclusion for ADG and G:F. The ADG by steers fed the SFC diet without bran was greater (P < 0.01) than by steers fed SFC diets with bran, whereas the ADG by steers fed DRC diets with or without bran was similar. Daily gain was 15.2% greater (P < 0.01) by steers fed SFC without bran than by steers fed DRC without bran. Gain efficiency was 16.9% greater (P < 0.01) for steers fed SFC without bran compared with steers fed DRC without bran. In DRC and SFC diets, feeding bran decreased (P < 0.01) G:F by 5.2 and 13.8%, respectively. The moisture content of corn bran had no effect on finishing steer performance, and drying corn bran did not affect its energy value in finishing cattle diets.

Effects of concentration and composition of wet corn gluten feed in steam-flaked corn-based finishing diets.

Two finishing experiments were conducted to determine the effects of concentration (Exp. 1) and composition of wet corn gluten feed (Exp. 2) in steam-flaked corn-based diets on feedlot steer performance. In Exp. 1, 192 English x Continental crossbred steer calves (299 +/- 0.6 kg) were used in a completely randomized design with six dietary treatments (four pens per treatment). Treatments were six concentrations of wet corn gluten feed (Sweet Bran, Cargill Inc., Blair, NE; 0, 10, 20, 25, 30, and 35%) replacing steam-flaked corn (DM basis). All diets contained 10% corn silage, 5% supplement, and 3.5% tallow (DM basis). Gain efficiency and ADG were similar (P > 0.25) among treatments. Dry matter intake was lower (P < 0.10) with 0% wet corn gluten feed than with concentrations of 20, 25, and 35% WCGF. Dry matter intake did not differ among treatments containing wet corn gluten feed. In Exp. 2, 160 English x Continental crossbred steer calves (315 +/- 0.6 kg) were used in a completely randomized design with five dietary treatments (four pens/treatment). Treatments were assigned based on four ratios of steep to corn bran/germ meal mix in wet corn gluten feed plus a negative control (CON). Wet corn gluten feed was fed at 25% of the dietary DM and was made by mixing steep and corn bran/germ meal into the diet. The four concentrations of steep in wet corn gluten feed that comprised the ratios were 37.5, 41.7, 45.8, and 50% (DM basis), with the remaining proportion being the bran/germ meal mix. Bran/germ meal mix was comprised of 60% dry corn bran, 24% germ meal, and 16% fine-cracked corn (DM basis). All diets contained 10% corn silage, 5% supplement, and 3.5% tallow (DM basis). Daily gain did not differ (P = 0.18) among treatments. Gain efficiency did not differ between CON and 50% steep; however, G:F was decreased (P < 0.05) for concentrations of 37.5, 41.7, and 45.8% steep compared with CON. A linear improvement (P < 0.05) was observed for G:F as concentration of steep increased as a proportion of wet corn gluten feed. These data suggest that wet corn gluten feed can be used at concentrations up to 35% of the dietary DM without adversely affecting performance, and that steep has more energy than bran/germ meal in steam-flaked corn-based diets.

Effect of organic matter addition to the pen surface and pen cleaning frequency on nitrogen mass balance in open feedlots.

Three finishing trials were conducted to determine the effects of dietary manipulation and management on N losses from open feedlots. In each experiment, 96 steers were assigned randomly to 12 nutrient balance pens. In Trial 1, calves were fed for 180 d during the winter/spring months; in Trial 2, yearlings were fed for 132 d in the summer. In Trials 1 and 2, N losses from pens were compared directly by adding OM to the pen surface or indirectly by feeding digestible ingredients designed to increase OM excretion. The dietary treatment (BRAN) included 30% corn bran (DM basis) replacing dry-rolled corn. Pens where OM was directly added received sawdust applications (SAWDUST) at a rate to match OM excretion from the BRAN diet. These two treatments were compared with a conventional, 75% dry-rolled corn diet (CON). Because CON and SAWDUST diets were identical, performance for both treatments was similar during Trials 1 and 2. The BRAN diet decreased (P < 0.10) gain efficiency during Trials 1 and 2 by 9.5% relative to CON. Fecal N excretion was greater (P < 0.01) for calves and yearlings when BRAN was fed compared with CON. Adding OM to the pen surface increased (P < 0.01) the amount of N in manure removed from pens and reduced (P < 0.10) N losses in Trial 1. Nitrogen losses were not significantly different among treatments in Trial 2. In Trial 3, calves were fed for 166 d during the winter/spring months. A 2 x 2 factorial design was used to evaluate pen cleaning frequency and diets similar to CON and BRAN. Pens were either cleaned monthly or once at the end of the feeding period. Daily DMI was greater (P = 0.01) and ADG was lower (P < 0.01) when cattle were fed BRAN compared with CON. Responses from all three trials indicate a negative effect of BRAN on gain efficiency. Dietary treatment and cleaning frequency interacted for N balance in the feedlot. Nitrogen losses decreased and manure N increased (P < 0.10) for cattle fed BRAN compared with CON when pens were cleaned monthly. Feeding BRAN did not affect total manure N, but resulted in higher N losses when pens were cleaned only once. For all trials, BRAN increased the amount of N remaining in composted manure. Adding OM to pen surfaces and/or cleaning pens more frequently may decrease N losses from open feedlot pens and from compost, although responses seem influenced by ambient temperature or season.

The Effects of Radiofrequency Electromagnetic Radiation on the Adhesion Behavior of Aqueous Suspensions.

The effect of radiofrequency treatment on the adhesion behavior of amidine and carboxylated polystyrene latexes was investigated. The isoelectric points pH(IEP) of copper and zinc were initially measured as 9.4 and 9.5, respectively, using a technique proposed by N. Kallay, Z. Torbic, M. Golic, and E. Matijevic [J. Phys. Chem. 95, 7028 (1991)] based on the attachment of charged colloids to metallic surfaces in an aqueous medium. Statistical analysis showed that the technique was repeatable with a coefficient of variation less than 6% and an accuracy greater than 95%. The effect of a radiofrequency signal (27 MHz) on adhesion behavior was evaluated and it was found that there was reduced attachment at pH values when the colloid and metallic surface were oppositely charged and enhanced attachment between similarly charged particles. It is proposed that this is due to a reduction in the surface potential of the charged particles due to thickening of the adsorbed layer by hydrogen and hydroxyl ions. Copyright 2000 Academic Press.

The decay of the latent reservoir of replication-competent HIV-1 is inversely correlated with the extent of residual viral replication during prolonged anti-retroviral therapy.

Replication-competent HIV-1 can be isolated from infected patients despite prolonged plasma virus suppression by anti-retroviral treatment. Recent studies have identified resting, memory CD4+ T lymphocytes as a long-lived latent reservoir of HIV-1 (refs. 4,5). Cross-sectional analyses indicate that the reservoir is rather small, between 103 and 107 cells per patient. In individuals whose plasma viremia levels are well suppressed by anti-retroviral therapy, peripheral blood mononuclear cells containing replication-competent HIV-1 were found to decay with a mean half-life of approximately 6 months, close to the decay characteristics of memory lymphocytes in humans and monkeys. In contrast, little decay was found in a less-selective patient population. We undertook this study to address this apparent discrepancy. Using a quantitative micro-culture assay, we demonstrate here that the latent reservoir decays with a mean half-life of 6.3 months in patients who consistently maintain plasma HIV-1 RNA levels of fewer than 50 copies/ml. Slower decay rates occur in individuals who experience intermittent episodes of plasma viremia. Our findings indicate that the persistence of the latent reservoir of HIV-1 despite prolonged treatment is due not only to its slow intrinsic decay characteristics but also to the inability of current drug regimens to completely block HIV-1 replication.

Persistence of HIV-1 transcription in peripheral-blood mononuclear cells in patients receiving potent antiretroviral therapy.

BACKGROUND AND METHODS: Although potent antiretroviral therapy can control infection with human immunodeficiency virus type 1 (HIV-1), a long-lived reservoir of infectious virus persists in CD4+ T cells. We investigated this viral reservoir by measuring the levels of cell-associated viral DNA and messenger RNA (mRNA) that are essential for HIV-1 replication. Approximately every 6 months, we obtained samples of peripheral-blood mononuclear cells from five men with long-standing HIV-1 infection who had had undetectable levels of plasma HIV-1 RNA for 20 months or more during treatment with potent antiretroviral drugs. RESULTS: Before treatment, plasma levels of HIV-1 RNA correlated with the levels of cell-associated unintegrated HIV-1 DNA and unspliced viral mRNA. After treatment, plasma levels of HIV-1 RNA fell by more than 2.7 log to undetectable levels. The decrease in cell-associated integrated and unintegrated HIV-1 DNA and mRNA occurred in two phases. The first phase occurred during the initial 500 days of treatment and was characterized by substantial decreases in the levels of DNA and mRNA, but not to undetectable levels. The concentrations of cell-associated unintegrated viral DNA, integrated proviral DNA, and unspliced viral mRNA decreased by 1.25 to 1.46 log. The second phase occurred during the subsequent 300 days or more of treatment and was characterized by a plateau in the levels of HIV-1 DNA and unspliced mRNA. After an initial rapid decline, the ratio of unspliced to multiply spliced viral mRNA (a measure of active viral transcription) stabilized and remained greater than zero at each measurement. CONCLUSIONS: Despite treatment with potent antiretroviral drugs and the suppression of plasma HIV-1 RNA to undetectable levels for 20 months or more, HIV-1 transcription persists in peripheral-blood mononuclear cells. Unless the quasi-steady state levels of HIV DNA and mRNA eventually disappear with longer periods of therapy, these findings suggest that HIV-1 infection cannot be eradicated with current treatments.

Design and analysis of serial limiting dilution assays with small sample sizes.

We study the design of serial limiting dilution assays (SLDAs) for estimation of effector cell frequency in settings that restrict severely the amount of material available for assay, and for which the assumption of a single-hit Poisson model is reasonable. For different designs (that is, dilution factor, number of dilution levels, and number of replicates at each level), we evaluate maximum likelihood and minimum chi-square estimators, using four quantitative criteria: probability of a non-informative assay (PNI), bias, coefficient of variation (CV), and mean squared error (MSE). Our results are exact, not simulation-based, nor approximations. We found that differences between these two estimators were insubstantial by comparison with the effect on the estimators of the experimental design. Bias was severe in small assays, and could lead, in extremely small designs, to overestimation of effector frequency by as much as 100%. These four criteria provide a rigorous basis for determining the most effective apportionment of total effort among replicates and dilution levels. By increasing the dilution factor and favoring the number of replicates over the number of dilution levels, the PNI is reduced while bias, CV and MSE are increased; and vice versa. Our study is easily extended to estimation of the density of biologically active particles per volume. It can also be extended to alternatives to the single-hit Poisson model for a serial limiting dilution assay.

The Ariel Project: A prospective cohort study of maternal-child transmission of human immunodeficiency virus type 1 in the era of maternal antiretroviral therapy.

In a prospective cohort study, clinical and biologic factors that contribute to maternal-child transmission of human immunodeficiency virus type 1 (HIV-1) were studied. HIV-infected pregnant women and their infants were evaluated prospectively according to a standardized protocol. Of 204 evaluable women, 81% received zidovudine during their pregnancy. The infection rate among the 209 evaluable infants was 9.1%. By univariate analysis, histologic chorioamnionitis, prolonged rupture of membranes, and a history of genital warts were significantly associated with transmission. Additional factors associated with transmission that approached significance included a higher maternal virus load at delivery and the presence of cocaine in the urine. In a logistic regression model, histologic chorioamnionitis was the only independent predictor of transmission. Despite a significantly higher transmission rate at one site, no unique viral genotype was found at any site. Thus, chorioamnionitis was found to be the major risk factor for transmission among women receiving zidovudine.

Maternal HIV-1 viral load and vertical transmission of infection: the Ariel Project for the prevention of HIV transmission from mother to infant.

Most HIV-1 infections of children result from mother-to-infant transmission, which may occur perinatally or postnatally, as a consequence of breast feeding. In this study, the influence of maternal viral load on transmission of infection to infants from non-breast-feeding mothers was examined using samples of plasma and peripheral blood mononuclear cells (PBMCs) collected at several time points during pregnancy and the 6-month period after delivery. These samples were analyzed by several quantitative methods, including virus cultures of PBMCs and polymerase chain reaction (PCR) assays for HIV-1 RNA in plasma and DNA in PBMCs. The risk of transmission increased slightly with a higher viral load, but transmission and nontransmission occurred over the entire range of values for each assay. No threshold value of virus load was identified which discriminated between transmitters and nontransmitters. We also noted a significant rise in viral load and a decline in CD4+ lymphocytes in the six months after delivery. These findings suggest that a high maternal viral load is insufficient to fully explain vertical transmission of HIV-1. Additional studies are needed to examine the post-partum increase in viremia.

Protein evolution on partially correlated landscapes.

We extend an earlier model of protein evolution on a rugged landscape to the case in which the landscape exhibits a variable degree of correlation (i.e., smoothness). Correlation is introduced by assuming that a protein is composed of a set of independent blocks or domains and that mutation in one block affects the contribution of that block alone to the overall fitness of the protein. We study the statistical structure of such landscapes and apply our theory to the evolution by somatic hypermutation of antibody molecules composed of framework and complementarity-determining regions. We predict the expected number of replacement mutations in each region.

Assessment of inhomogeneities in an E. coli physical map.

A statistical method based on r-fragments, sums of distances between (r + 1) consecutive restriction enzyme sites, is introduced for detecting nonrandomness in the distribution or too markers in sequence data. The technique is applicable whenever large numbers of markers are available and will detect clumping, excessive dispersion or too much evenness of spacing of the markers. It is particularly adapted to varying the scale on which inhomogeneities can be detected, from nearest neighbor interactions to more distant interactions. The r-fragment procedure is applied primarily to the Kohara et al. (1) physical map of E. coli. Other applications to DAM methylation sites in E. coli and NotI sites in human chromosome 21 are presented. Restriction sites for the eight enzymes used in (1) appear to be randomly distributed, although at widely differing densities. These conclusions are substantially in agreement with the analysis of Churchill et al. (3). Extreme variability in the density of the eight restriction enzyme sites cannot be explained by variability in mono-, di- or trinucleotide frequencies.

Protein evolution on rugged landscapes.

We analyze a mathematical model of protein evolution in which the evolutionary process is viewed as hill-climbing on a random fitness landscape. In studying the structure of such landscapes, we note that a large number of local optima exist, and we calculate the time and number of mutational changes until a protein gets trapped at a local optimum. Such a hill-climbing process may underlie the evolution of antibody molecules by somatic hypermutation.