A semiparametric model for between-subject attributes: Applications to beta-diversity of microbiome data.

The human microbiome plays an important role in our health and identifying factors associated with microbiome composition provides insights into inherent disease mechanisms. By amplifying and sequencing the marker genes in high-throughput sequencing, with highly similar sequences binned together, we obtain operational taxonomic units (OTUs) profiles for each subject. Due to the high-dimensionality and nonnormality features of the OTUs, the measure of diversity is introduced as a summarization at the microbial community level, including the distance-based beta-diversity between individuals. Analyses of such between-subject attributes are not amenable to the predominant within-subject-based statistical paradigm, such as t-tests and linear regression. In this paper, we propose a new approach to model beta-diversity as a response within a regression setting by utilizing the functional response models (FRMs), a class of semiparametric models for between- as well as within-subject attributes. The new approach not only addresses limitations of current methods for beta-diversity with cross-sectional data, but also provides a premise for extending the approach to longitudinal and other clustered data in the future. The proposed approach is illustrated with both real and simulated data.

An Antiestrogenic Activity Score for tamoxifen and its metabolites is associated with breast cancer outcome.

PURPOSE: Endoxifen concentrations have been associated with breast cancer recurrence in tamoxifen-treated patients. However, tamoxifen itself and other metabolites also show antiestrogenic anti-tumor activity. Therefore, the aim of this study was to develop a comprehensive Antiestrogenic Activity Score (AAS), which accounts for concentration and antiestrogenic activity of tamoxifen and three metabolites. An association between the AAS and recurrence-free survival was investigated and compared to a previously published threshold for endoxifen concentrations of 5.97 ng/mL. PATIENTS AND METHODS: The antiestrogenic activities of tamoxifen, (Z)-endoxifen, (Z)-4-hydroxytamoxifen, and N-desmethyltamoxifen were determined in a cell proliferation assay. The AAS was determined by calculating the sum of each metabolite concentration multiplied by an IC50 ratio, relative to tamoxifen. The AAS was calculated for 1370 patients with estrogen receptor alpha (ERα)-positive breast cancer. An association between AAS and recurrence was investigated using Cox regression and compared with the 5.97 ng/mL endoxifen threshold using concordance indices. RESULTS: An AAS threshold of 1798 was associated with recurrence-free survival, hazard ratio (HR) 0.67 (95% confidence interval (CI) 0.47-0.96), bias corrected after bootstrap HR 0.69 (95% CI 0.48-0.99). The concordance indices for AAS and endoxifen did not significantly differ; however, using the AAS threshold instead of endoxifen led to different dose recommendations for 5.2% of the patients. CONCLUSIONS: Endoxifen concentrations can serve as a proxy for the antiestrogenic effect of tamoxifen and metabolites. However, for the aggregate effect of tamoxifen and three metabolites, defined by an integrative algorithm, a trend towards improving treatment is seen and moreover, is significantly associated with breast cancer recurrence.

Impact of breast cancer on anti-mullerian hormone levels in young women.

Young women with breast cancer face treatments that impair ovarian function, but it is not known if malignancy itself impacts ovarian reserve. As more breast cancer patients consider future fertility, it is important to determine if ovarian reserve is impacted by cancer, prior to any therapeutic intervention. A cross-sectional study was conducted comparing if ovarian reserve, as measured by anti-mullerian hormone (AMH), follicle stimulating hormone (FSH), and inhibin B (inhB), differed between 108 women with newly diagnosed breast cancer and 99 healthy women without breast cancer. Breast cancer participants were ages 28-44 and were recruited from two clinical breast programs. Healthy women ages 30-44 without a history of infertility were recruited from gynecology clinics and the community. The median age (interquartile range) was 40.2(5.5) years for breast cancer participants and 33.0(4.6) years for healthy controls. The unadjusted geometric mean AMH levels (SD) for breast cancer participants and controls were 0.66(3.6) and 1.1(2.9) ng/mL, respectively. Adjusting for age, body mass index, gravidity, race, menstrual pattern, and smoking, mean AMH levels were not significantly different between breast cancer participants and healthy controls (0.85 vs. 0.76 ng/mL, p = 0.60). FSH and inhB levels did not differ by breast cancer status. In exploratory analysis, the association between AMH and breast cancer status differed by age (p-interaction = 0.02). AMH may be lower with breast cancer status in women older than 37. In younger women, AMH levels did not differ significantly by breast cancer status. Among the youngest of breast cancer patients, ovarian reserve as measured by AMH, FSH, and inhibin B did not differ significantly from healthy women of similar age. In older breast cancer patients, ovarian reserve may be adversely impacted by cancer status. These findings support the potential success and need for fertility preservation strategies prior to institution of cancer treatment.

Tamoxifen metabolite concentrations, CYP2D6 genotype, and breast cancer outcomes.

We explored whether breast cancer outcomes are associated with endoxifen and other metabolites of tamoxifen and examined potential correlates of endoxifen concentration levels in serum including cytochrome P450 2D6 (CYP2D6) metabolizer phenotype and body mass index (BMI). Concentration levels of tamoxifen, endoxifen, 4-hydroxytamoxifen (4OH-tamoxifen), and N-desmethyltamoxifen (ND-tamoxifen) were measured from samples taken from 1,370 patients with estrogen receptor (ER)-positive breast cancer who were participating in the Women's Healthy Eating and Living (WHEL) Study. We tested these concentration levels for possible associations with breast cancer outcomes and found that breast cancer outcomes were not associated with the concentration levels of tamoxifen, 4-hydroxytamoxifen, and ND-tamoxifen. For endoxifen, a threshold was identified, with women in the upper four quintiles of endoxifen concentration appearing to have a 26% lower recurrence rate than women in the bottom quintile (hazard ratio (HR) = 0.74; 95% confidence interval (CI), (0.55-1.00)). The predictors of this higher-risk bottom quintile were poor/intermediate metabolizer genotype, higher BMI, and lower tamoxifen concentrations as compared with the mean for the cohort as a whole. This study suggests that there is a minimal concentration threshold above which endoxifen is effective against the recurrence of breast cancer and that ~80% of tamoxifen takers attain this threshold.

Droplet deformation and alignment for high-efficiency polarization-dependent holographic polymer-dispersed liquid-crystal reflection gratings.

Droplet deformation and alignment are achieved in holographic polymer-dispersed liquid-crystal reflection gratings by applying an in situ shear during recording. High diffraction efficiency (99%) is obtained for light polarized parallel to the shear, with nearly zero efficiency for perpendicular polarization, and no increase of incoherent scattering. Permanent polarization dependence is related to stress-induced morphology changes of liquid-crystal droplets that are frozen by polymerization. The system is studied by electron microscopy and modeled by anisotropic coupled-wave and scattering theory. The morphology is consistent with the theory of small deformations of liquid droplets in fluid flow. Diffraction efficiency measurements are in agreement with theory incorporating this morphology as well as concomitant orientation and alignment of liquid-crystal molecules.

Identification of evolutionarily conserved promoter elements and amino acids required for function of the C. elegans beta-catenin homolog BAR-1.

beta-catenins are conserved transcription factors regulated posttranslationally by Wnt signaling. bar-1 encodes a Caenorhabditis elegans beta-catenin acting in multiple Wnt-mediated processes, including cell fate specification by vulval precursor cells (VPCs) and migration of the Q(L) neuroblast progeny. We took two approaches to extend our knowledge of bar-1 function. First, we undertook a bar-1 promoter analysis using transcriptional GFP reporter fusions and found that bar-1 expression is regulated in specific cells at the transcriptional level. We identified promoter elements necessary for bar-1 expression in several cell types, including a 321-bp element sufficient for expression in ventral cord neurons (VCNs) and a 1.1-kb element sufficient for expression in the developing vulva and adult seam cells. Expression of bar-1 from the 321-bp element rescued the Uncoordinated (Unc) phenotype of bar-1 mutants, but not the vulval phenotype, suggesting that a Wnt pathway may act in ventral cord neurons to mediate proper locomotion. By comparison of the 1.1-kb element to homologous sequences from Caenorhabditis briggsae, we identified evolutionarily conserved sequences necessary for expression in vulval or seam cells. Second, we analyzed 24 mutations in bar-1 and identified several residues required for BAR-1 activity in C. elegans. By phylogenetic comparison, we found that most of these residues are conserved and may identify amino acids necessary for beta-catenin function in all species.

Correlates of obesity in postmenopausal women with breast cancer: comparison of genetic, demographic, disease-related, life history and dietary factors.

BACKGROUND: Obesity in women has been associated with a variety of factors, including genetic predisposition, social class, early age at menarche, exercise, alcohol consumption and diet. Obesity is a risk factor for the occurrence and the recurrence of breast cancer in postmenopausal women, perhaps because of increased exposure to estrogen, insulin and insulin-like growth factors (IGFs). The progesterone receptor (PR) and the steroid hormone receptor coactivator pCIP/ACTR/AIB1/TRAM1/RAC3 (AIB1) are hypothesized to mediate signaling crosstalk between these hormonal pathways. Polymorphisms in both genes have been described and their association with breast cancer risk reported. If genetic factors contribute to obesity, and the PR and AIB1 genes influence estrogenic, insulin and IGF pathways, then genetic patterns resulting from PR and AIB1 polymorphisms may be associated with obesity in postmenopausal women. OBJECTIVE: We compared the PR and AIB1 genotypes of postmenopausal women with breast cancer with demographic, disease-related, reproductive, lifestyle and dietary variables in terms of the strength of their relationship with obesity (BMI> or =30 kg/m2). SUBJECTS: A total of 301 postmenopausal women previously diagnosed with Stage I, II or IIIA breast cancer, who are enrolled in the Women's Healthy Eating and Living (WHEL) study (age: 34.5-70.8 y, BMI: 17.8-54.6 kg/m2). MEASUREMENTS: The PR polymorphism PROGINS was identified by PCR. The length of the AIB1 polyglutamine repeat was determined by PCR and nondenaturing gel electrophoresis or DNA sequencing. BMI was obtained at the baseline clinic visit upon entry into the WHEL study. Information about date of diagnosis, stage of disease, tumor hormone receptor status and adjuvant treatment received were obtained from medical records. Reproductive, menstrual history, demographic, family history of cancer, smoking history and exercise frequency and intensity information were obtained from questionnaires. Dietary and alcohol intake data came from four 24-h telephone recalls of food intake obtained at the study entry. RESULTS: The combined inheritance of PROGINS A1/A1 and AIB1 28/29, 28/30, 28/31, 29/29 or 29/30 (AIB1 LG) genotypes (adjusted odds ratio (OR)=2.22 (95% confidence interval 1.25-3.93)) and early age at menarche (<12 y) (adjusted OR=2.34 (1.12-4.86)) were each associated with the risk for obesity. Current use of tamoxifen (adjusted OR=0.49 (0.28-0.87)) and an alcohol intake > or =10 g/day (adjusted OR=0.28 (0.11-0.77)) were inversely associated with BMI > or =30 kg/m2. CONCLUSION: Early age at menarche and a PROGINS A1/A1+AIB1 LG genetic pattern had comparable levels of association with obesity in this cross-sectional sample of postmenopausal women with breast cancer. Since this was a cross-sectional rather than a case-control design, the association between PROGINS and AIB1 genotype and obesity found in this sample should be considered preliminary, and must be re-evaluated with a new and larger sample.

Switchable orthorhombic F photonic crystals formed by holographic polymerization-induced phase separation of liquid crystal.

Electrically switchable photonic crystals are simply and rapidly formed by holographic polymerization-induced phase separation of liquid crystal from a monomer-liquid crystal mixture. We report the fabrication and electro-optical properties of liquid-crystal-filled polymer photonic crystals of orthorhombic F symmetry. Inverse opal and fcc structures can also be obtained. The crystals exhibit electrically switchable Bragg diffraction at ~8-10 V/microm with crystal structure in good agreement with theoretical expectations. These photonic crystals compare favorably with liquid-crystal-imbibed colloidal crystal arrays.

A prospective study of stress among women undergoing in vitro fertilization or gamete intrafallopian transfer.

OBJECTIVE: To evaluate whether baseline or procedural stress during in vitro fertilization (IVF) or gamete intrafallopian transfer (GIFT) affects pregnancy or live birth delivery rates. DESIGN: Prospective study. SETTING: Seven clinics in Southern California between 1993 and 1998. PATIENT(S): One hundred and fifty-one women completed two questionnaires. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): The number of oocytes aspirated and fertilized, the number of embryos transferred, the achievement of a pregnancy, live birth delivery, and infant outcomes. RESULT(S): Positive-affect negative-affect score at baseline negatively influenced the number of oocytes retrieved and embryos transferred. A higher expectation of pregnancy was associated with greater numbers of oocytes fertilized and embryos transferred. At baseline, the risk of no live birth was 93% lower for women who had the highest positive-affect score compared to those with the lowest score. Furthermore, the score on the Infertility Reaction Scale was related to negative outcomes in live birth delivery, infant birth weight, and multiple births. During the time of the procedure, the PANAS and Bipolar Profile of Moods States results were related to the number of oocytes fertilized and embryos transferred; stress did not affect pregnancy or delivery. CONCLUSION(S): Baseline (acute and chronic) stress affected biologic end points (i.e., number of oocytes retrieved and fertilized), as well as pregnancy, live birth delivery, birth weight, and multiple gestations, whereas (procedural) stress only influenced biologic end points.

The divergent Caenorhabditis elegans beta-catenin proteins BAR-1, WRM-1 and HMP-2 make distinct protein interactions but retain functional redundancy in vivo.

beta-Catenins function both in cell adhesion as part of the cadherin/catenin complex and in Wnt signal transduction as transcription factors. Vertebrates express two related proteins, beta-catenin and plakoglobin, while Drosophila has a single family member, Armadillo. Caenorhabditis elegans expresses three beta-catenin-related proteins, BAR-1, HMP-2, and WRM-1, which are quite diverged in sequence from each other and other beta-catenins. While BAR-1 and WRM-1 are known to act in Wnt-mediated processes, and HMP-2 acts in a complex with cadherin/alpha-catenin homologs, it is unclear whether all three proteins retain the other functions of beta-catenin. Here we show that BAR-1, like vertebrate beta-catenin, has redundant transcription activation domains in its amino- and carboxyl-terminal regions but that HMP-2 and WRM-1 also possess the ability to activate transcription. We show via yeast two-hybrid analysis that these three proteins display distinct patterns of protein interactions. Surprisingly, we find that both WRM-1 and HMP-2 can substitute for BAR-1 in C. elegans when expressed from the bar-1 promoter. Therefore, although their mutant phenotypes and protein interaction patterns strongly suggest that the functions of beta-catenin in other species have been segregated among three diverged proteins in C. elegans, these proteins still retain sufficient similarity to display functional redundancy in vivo.

Effects of female and male smoking on success rates of IVF and gamete intra-Fallopian transfer.

BACKGROUND: Smoking by both male and female partners may play a significant role in the success rates of assisted reproductive technologies. The objective of this 5-year prospective study was to investigate the influence of cigarette smoking by the wife, husband, and couple at various time points (e.g. lifetime, week prior, or during the procedures) on different biological parameters of IVF and gamete intra-Fallopian transfer (GIFT). METHODS AND RESULTS: A total of 221 couples, aged >20 years, of Caucasian, Black, Asian or Hispanic descent were recruited from seven infertility clinics located in Southern California. Couples (i.e. either female or male or both) who ever smoked compared with non-smokers, had adjusted relative risks (RR) of 2.41 (95% CI 1.07-5.45, P = 0.03) of not achieving a pregnancy, and 3.76 (95% CI 1.40-10.03, P < 0.01) of not having a live birth delivery, while adjusting for potential confounders. For couples who smoked for >5 years, there was an adjusted RR = 4.27 of not achieving a pregnancy (95% CI l.53-11.97, P = 0.01). The number of oocytes retrieved decreased by 40% for couples (smokers, n = 6) and by 46% for men who smoked during the week of the visit for IVF or GIFT. Women who smoked in their lifetime had adjusted risks of 2.71 of not achieving a pregnancy (95% CI 1.37-5.35, P < 0.01), and 2.51 (95% CI 1.11-5.67, P < 0.03) of not having a live birth delivery. CONCLUSIONS: There is compelling evidence that couples should be made aware that smoking years before undergoing IVF and GIFT can impact treatment outcome. This study may also provide insight into the timing and effects of male and female smoking on natural reproduction.

Investigation of light-induced conformation changes in spiropyran-modified succinylated poly(L-lysine).

To determine the maximum range of coupling between side-chain photochromism and polypeptide conformation change, we modified the carboxylate side chains of succinylated poly(L-lysine) with a spiropyran to form polypeptide I. The extent of modification was determined to be 35.5%. The spacer group length between the polypeptide alpha-carbon and the dye was 12 atoms, providing minimum polypeptide-dye interaction. Conformation changes were monitored by circular dichroism as a function of light adaptation and solvent composition (hexafluoroisopropanol [HFIP] vs trifluoroethanol [TFE]). Under all solvent compositions, the dark-adapted dye was in the merocyanine form. Light adaptation by visible light converted the dye to the spiropyran form. When dissolved in TFE, I adopted a helical conformation insensitive to light adaptation. With increasing percentage HFIP, a solvent-induced helix-to-coil transition was observed around 80% (vol/vol) HFIP. At 100% HFIP, both light- and dark-adapted forms of I were in the coil state. Near the midpoint of the solvent-induced helix-to-coil transition, light adaptation caused conformation changes. Applying helix-to-coil transition theory, we measured a statistically significant difference in coil segment-HFIP binding constant for light- vs dark-adapted solutions (6.38 +/- 0.03 M-1 vs 6.56 +/- 0.03 M-1), but not for the nucleation parameter sigma (1.2 +/- 0.4 10(-3) vs 1.3 +/- 0.3 x 10(-3). The small binding constant difference translated to a light-induced binding energy difference of 17 cal/mol/monomer. Near the midpoint of the helix-to-coil transition, collective interactions between monomer units made possible the translation of a small energy difference (less than RT) into large macromolecular conformation changes.(ABSTRACT TRUNCATED AT 250 WORDS)

Volume holographic image storage and electro-optical readout in a polymer-dispersed liquid-crystal film.

We report storage and electrical switching of holographic image data in an economical polymer-dispersed liquidcrystal material. The hologram is recorded in a fast, single-step process and can be reversibly erased and restored repeatedly by the application of fields of approximately 10-15 V/ microm, with a response time of 22 micros and a relaxation time of 42 micros. Simple (quasi-sinusoidal) holographic transmission gratings also are studied with switching fields of <5 V/ microm and with response and relaxation times of 25 and 44 micros, respectively.

Holographic grating formation in poly(spiropyran I-glutamate).

An argon-ion laser interferometer (0.3638 or 0.488 microm) wrote photoreversible holographic grating (fringe spacing 0.39-100 microm) on spin-cast thin films (5 microm thick) of poly(spiropyran l-glutamate).

Kinetic study of the helix to coil dark reaction of poly(spiropyran-L-glutamate).

An investigation of kinetics of the helix to coil dark reaction of light adapted poly(spiropyran-L-glutamic acid) (PSLG) dissolved in hexafluoroisopropanol was performed. The reaction was associated with the spiropyran (SP) to merocyanine (MC) ring opening. The ring opening reaction monitored with UV/VIS spectroscopy showed first order kinetics. Chromophore and polypeptide backbone circular dichroism data fit to an expression consistent with a single intermediate series mechanism. By FTIR, we monitored the polypeptide alpha-helix amide I, the MC chromophore--C = C--stretch and the protonated unmodified carboxylate C = O stretch bands. During the first step of the series mechanism, changes in the hydrogen bonding of the unmodified carboxylate groups occurred, suggesting breakup of polypeptide aggregates. The second step of the proposed series mechanism was dominated by the helix to coil transition and the ring opening of SP to MC. The CD spectrum of MC in the dark adapted PSLG was red shifted and had a narrower bandwidth than the UV/VIS spectrum. The kinetic and spectroscopic data suggested that a fraction (population I) of the MC chromophores experienced optical activity induced by the chiral polypeptide environment, while the remainder of the MC chromophores (population II) were solvated and enantiomeric.

Effects of two-photon absorption on degenerate four-wave mixing in solutions of diphenyl polyenes.

We have observed double-peaked phase-conjugate pulses in the degenerate four-wave mixing of nanosecond laser pulses in solutions of diphenyl polyenes. We attribute this to the superposition of fast and slow gratings, where the slow grating is due to two-photon absorption. This is supported by the results of time delay and polarization experiments as well as evidence of a second spatial harmonic grating.

Optical limiting in solutions of diphenyl polyenes.

The optical-limiting behavior of a series of trans-alpha, omega-diphenyl polyene compounds was observed in solutions of chloroform. The influence of planarity, the substitution of donor and acceptor groups, and the extent of pi-electron delocalization on the nonlinear thresholds of the diphenyl polyenes in an optical-limiting geometry were examined. A saturation effect of optical-limiting nonlinear thresholds, consistent with the theoretical work, was observed at 10-11 pi-electron bonds. The temporal profiles of the transmitted laser pulses and the power dependence of the nonlinear thresholds as a function of spot size and wavelength were examined. These examinations led to the conclusion that the predominant nonlinear mechanism was quasi-steady-state self-focusing. Nonlinear thresholds an order of magnitude lower, and thus effective n(2) and X(3) values an order of magnitude higher, than the well-known self-focusing medium CS(2) were observed. Our studies demonstrate that this series of polyenes consists of efficient broadband nonresonant optical-limiting materials.

Induction, prevention and mechanisms of contrast media-induced acute renal failure.

This study describes the development of an experimental model of reversible acute renal failure following infusion of contrast media radiographic dye. Experiments were also performed to investigate possible methods of prevention as well as examine single nephron mechanisms involved in the pathogenesis of the renal failure. Acute renal failure was consistently produced by indomethacin treatment (18 mg/kg) and an intravenous infusion of contrast media (7 ml/kg) into New Zealand rabbits that had been on a low sodium diet for one week. Glomerular filtration rate (GFR), measured by daily creatinine clearance in unanesthetized animals, was significantly decreased (P less than 0.001) 24, 48, and 72 hours following infusion of the contrast dye. Two weeks after induction of acute renal failure, GFR had returned to control. GFR was unchanged during the same time period when the sodium deprived rabbits were given either indomethacin or contrast media alone. Chronic administration of DOCA (1 mg/kg s.c.) and saline drinking water which increased sodium and solute excretions and decreased plasma renin activity also prevented the decrease in GFR. However, acute infusion of either saline or mannitol, which transiently increased sodium and solute excretions and decreased plasma renin activity, did not protect against the development of acute renal failure. Light microscopy revealed no glomerular or tubular changes and no visible obstruction. Micropuncture experiments were performed on three additional groups of anesthetized rabbits: control, acute renal failure, and recovery. Recovery rabbits were allowed a two week period after renal failure before they were micropunctured.(ABSTRACT TRUNCATED AT 250 WORDS)

Evaluation of gentamicin pharmacokinetics during peritoneal dialysis.

The pharmacokinetics of gentamicin were examined in two functionally anephric patients undergoing peritoneal dialysis (PD). Peritoneal dialysis effectively decreased the gentamicin half-life (t1/2 beta) by 73 and 78% while increasing total body clearance [QB(ml/min/kg] of gentamicin 4.3- and 3.4-fold. The appreciable variability in gentamicin pharmacokinetics among renal failure patients being peritoneally dialyzed may necessitate dosage adjustments based on rapid and accurate measurement of serum gentamicin concentrations.