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Results for “Model explainability”

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PubMed2002

Thresholding rules for recovering a sparse signal from microarray experiments.

We consider array experiments that compare expression levels of a high number of genes in two cell lines with few repetitions and with no subject effect. We develop a statistical model that illustrates under which assumptions thresholding is optimal in the analysis of such microarray data. The results of our model explain the success of the empirical rule of two-fold change. We illustrate a thresholding procedure that is adaptive to the noise level of the experiment, the amount of genes analyzed, and the amount of genes that truly change expression level. This procedure, in a world of perfect knowledge on noise distribution, would allow reconstruction of a sparse signal, minimizing the false discovery rate. Given the amount of information actually available, the thresholding rule described provides a reasonable estimator for the change in expression of any gene in two compared cell lines.

Animals↗

PubMed2001

Reproducibility of peri-implant probing using a force-controlled probe.

The aim of the present study was to evaluate the reproducibility of probing depth (PD) and vertical attachment level (PAL-V) measurements at endosseous implants. Twenty partially edentulous patients who had received 44 Frialit-2 and 30 Astra implants between 1994 and 1996 were examined. At all teeth and implants, clinical parameters (GI, PlI, PD, PAL-V) were measured at 6 sites using the flexible plastic version of the universal explorer TPS probe. At the implants and at teeth that were in similar locations compared to the implants, PD and PAL-V measurements were repeated. For each of the 20 probes that had been used for clinical examination of the 20 patients, the probing force was assessed using a precision balance. As a measure of intraexaminer reproducibility, the following standard deviations of single PD and PAL-V measurements were calculated: Frialit-2: 0.71/0.74 mm; Astra: 0.72/0.75 mm; tooth: 0.59/0.57 mm (PD/PAL-V). Stepwise multiple regression analysis revealed implant/tooth position and GI to influence PD and PAL-V measurement error (P<0.001). At anterior teeth, a lower variability was observed than at posterior teeth (P<0.001). PD and PAL-V measurement error were higher at implants than at teeth and influenced by patients. The respective models explained 13% and 17% of the variability of the dependent variable (PD/PAL-V), respectively. Intraexaminer variability of PD and PAL-V measurements at implants tended to be higher than at teeth. Multivariate analysis of variance revealed probe and probe holder to statistically significantly (P<0.001) influence probing force. However, the differences in probing force between the various probe heads were very small. They reached a maximum of 0.054 N between probe 3 and 14 and may be looked upon as clinically irrelevant.

Adult↗

PubMed2005

Statistical modelling of formaldehyde occupational exposure levels in French industries, 1986-2003.

Occupational exposure databanks (OEDBs) have been cited as sources of exposure data for exposure surveillance and exposure assessment in epidemiology. In 2003, an extract was made from COLCHIC, the French national OEDB, of all concentrations of formaldehyde. The data were analysed with extended linear mixed-effects models in order to identify influent variables and elaborate a multi-sector picture of formaldehyde exposures. Respectively, 1401 and 1448 personal and area concentrations were available for the analysis. The fixed effects of the personal and area models explained, respectively, 57 and 53% of the total variance. Personal concentrations were related to the sampling duration (short-term higher than TWA levels), decreased with the year of sampling (-9% per year) and were higher when local exhaust ventilation was present. Personal levels taken during planned visits and for occupational illness notification purpose were consistently lower than those taken during ventilation modification programmes or because the hygienist suspected the presence of significant risk or exposure. Area concentrations were related to the sampling duration (short-term higher than TWA levels), and decreased with the year of sampling (-7% per year) and when the measurement sampling flow increased. Significant within-facility (correlation coefficient 0.4-0.5) and within-sampling campaign correlation (correlation coefficient 0.8) was found for both area and personal data. The industry/task classification appeared to have the greatest influence on exposure variability while the sample duration and the sampling flow were significant in some cases. Estimates made from the models for year 2002 showed elevated formaldehyde exposure in the fields of anatomopathological and biological analyses, operation of gluing machinery in the wood industry, operation and monitoring of mixers in the pharmaceutical industry, and garages and warehouses in urban transit authorities.

Air Pollutants, Occupational↗

PubMed2003

A conceptual model for empowerment of the female community health volunteers in Nepal.

CONTEXT: The existing top-down approach of the training is not appropriate to empower the community health volunteers to produce a sustainable change in their performance. OBJECTIVE: To propose a conceptual model that relies on Freire's theory of empowerment education and the participatory action research methodology to empower the female community health volunteers (FCHVs) to increase their consciousness, competence and confidence in performing their job responsibilities. METHOD: The model explains the empowerment phenomenon as a process and outcome. As a process it occurs in the form of repeated reinforcement cycles with alternating activities of action and reflection and includes developing awareness, skills and confidence among FCHVs through small group activities. As an outcome, it results in the change in FCHVs' performance in increasing contraceptive acceptance among the rural women of reproductive age group. CONCLUSION: It is hoped that empowerment of FCHVs will bring sustainable change in their performance and will consequently produce notable improvement in the health of women and children in particular and in the community in general.

Community Health Workers↗

PubMed1999

Adolescent sibling bereavement as a catalyst for spiritual development: a model for understanding.

While our understanding of adolescent bereavement has greatly expanded in recent years, one area yet to be clarified is the relationship between grief following a significant loss and spirituality. This article strengthens our understanding of this connection in two ways. First, the authors present a conceptual model explaining how developmental changes in cognitive capacity during the adolescent life stage make it possible to challenge one's beliefs and search for new meaning. The crisis of experiencing the death of a sibling during this period has the potential, then, of serving as a catalyst for enhanced spirituality--defined as a quest for new meaning. Secondly, interviews with four adolescents following the death of a sibling add more detailed understanding of that quest for meaning. Quotations drawn from these interviews illustrate these young persons' shifting perspective of self, others, the sibling relationship, a higher power, death, and life.

Adolescent↗

PubMed2007

Age at growth hormone therapy start and first-year responsiveness to growth hormone are major determinants of height outcome in idiopathic short stature.

AIM: To develop methods to identify factors associated with a favorable outcome in GH-treated children with idiopathic short stature (ISS). METHODS: From 4,685 children listed as having ISS within KIGS (Pfizer International Growth Database), we studied (a) the prediction model group (n = 657) to develop the first-year prediction model, and (b) the near adult height group (NAH; n = 256) which received GH for >4 years to develop descriptive models for adult height and overall height gain. RESULTS: NAH group at GH start: age was 10.0 years, height -2.5 SD score (SDS), weight -2.3 SDS, height minus mid-parental height (MPH) -1.5 SDS; GH dose 0.19 mg/kg/week. Height gain was 1.1 SDS at a median age of 17.2 years. Growth response correlated positively with GH dose and weight at the start of GH treatment, and negatively with age and height SDS minus MPH SDS. The model explains 39% (error SD 1.2 cm) of the variability. Adult height correlated (R(2) = 0.64) positively with height at GH start, MPH and the first-year responsiveness to GH, and negatively with age. CONCLUSIONS: Prepubertal children with ISS who show an appropriate first-year response to GH are likely to benefit from long-term treatment, even on low GH dosages.

Adolescent↗

PubMed2005

Stochastic-based descriptors studying biopolymers biological properties: extended MARCH-INSIDE methodology describing antibacterial activity of lactoferricin derivatives.

Lactoferricin are a number of related peptides derived from the enzymatic cleavage of lactoferrin, an iron-binding protein. These peptides, and other peptides derived from them by simple amino acid substitutions, have shown interesting antibacterial activity. In this paper we applied the MARCH-INSIDE methodology extended to peptide and proteins, to a QSAR study related to antibacterial activity of 31 derivatives of lactoffericin against E. Coli and S. Aureus by means of Linear Discriminant (LDA) and Multiple Linear Regression Analysis (MLR). In the case of LDA we obtained models that classify correctly more than 80% of all cases (85.7% for E. Coli antibacterial activity and 83.9 for S. Aureus). With the application of a Leave-One-Out Cross Validation Procedure, the percentage of good classification of both classification models remained near the above reported values (87.1% for E. Coli antibacterial activity and 83.9 for S. Aureus). We obtained several linear regression models taking into account total and local descriptors. The inclusion of those local descriptors improved the correlation parameters, the statistical quality, and the predictive power of the former model obtained only with total descriptors. The best models explained more than 80% of the experimental variance in the antimicrobial activity of those compounds. These results are comparable with those reported previously by Strom (Strom, M. B.; Rekdal, O.; Svendesen, J. S. J Peptide Res 2001, 57, 127-139.) and Tore-Lejon (Lejon, T.; Strom, M.; Svendsen, S. J Protein Sci 2001, 7, 74-78.; Lejon, T.; Svendsen J. S.; Haug, B. E. J Peptide Sci 2002, 8, 302-306.) in a smaller dataset applying Z-scales and volume-based descriptors and PLS as statistical techniques.

Amino Acid Sequence↗

PubMed1993

Condom use: a self-efficacy model.

A survey of heterosexually active college students gathered information about condom use, self-efficacy (SE), outcome expectancies, sexual attitudes, peer group influences, acquired immunodeficiency syndrome (AIDS) knowledge, and perceived vulnerability to AIDS. On the basis of A. Bandura's (1986) social-cognitive theory, a structural model with SE as the central mediator was formulated and evaluated with LISREL. This model explained 46% of the variance in condom use from judgments of SE and effects attributable to peers and 53% of the variance in SE from outcome expectancies and peer group influences. Sexual attitudes, AIDS knowledge, and perceived vulnerability did not predict condom use. Most students were well-informed about human immunodeficiency virus (HIV) transmission but reported not feeling at risk, even though many engaged in risky sexual behavior.

Acquired Immunodeficiency Syndrome↗

PubMed2006

Validation of the VRN-H2/VRN-H1 epistatic model in barley reveals that intron length variation in VRN-H1 may account for a continuum of vernalization sensitivity.

The epistatic interaction of alleles at the VRN-H1 and VRN-H2 loci determines vernalization sensitivity in barley. To validate the current molecular model for the two-locus epistasis, we crossed homozygous vernalization-insensitive plants harboring a predicted "winter type" allele at either VRN-H1 (Dicktoo) or VRN-H2 (Oregon Wolfe Barley Dominant), or at both VRN-H (Calicuchima-sib) loci and measured the flowering time of unvernalized F(2) progeny under long-day photoperiod. We assessed whether the spring growth habit of Calicuchima-sib is an exception to the two-locus epistatic model or contains novel "spring" alleles at VRN-H1 (HvBM5A) and/or VRN-H2 (ZCCT-H) by determining allele sequence variants at these loci and their effects relative to growth habit. We found that (a) progeny with predicted "winter type" alleles at both VRN-H1 and VRN-H2 alleles exhibited an extremely delayed flowering (i.e. vernalization-sensitive) phenotype in two out of the three F(2) populations, (b) sequence flanking the vernalization critical region of HvBM5A intron 1 likely influences degree of vernalization sensitivity, (c) a winter habit is retained when ZCCT-Ha has been deleted, and (d) the ZCCT-H genes have higher levels of allelic polymorphism than other winterhardiness regulatory genes. Our results validate the model explaining the epistatic interaction of VRN-H2 and VRN-H1 under long-day conditions, demonstrate recovery of vernalization-sensitive progeny from crosses of vernalization-insensitive genotypes, show that intron length variation in VRN-H1 may account for a continuum of vernalization sensitivity, and provide molecular markers that are accurate predictors of "winter vs spring type" alleles at the VRN-H loci.

Acclimatization↗

PubMed2005

Cyclic silicate active site and stereochemical match for apatite nucleation on pseudowollastonite bioceramic-bone interfaces.

Hydroxyapatite (Ca5(PO4)3(OH)) forms on pseudowollastonite (psW) (alpha-CaSiO3) in vitro in simulated body fluid, human parotid saliva and cell-culture medium, and in vivo in implanted rat tibias. We used crystallographic constraints with ab initio molecular orbital calculations to identify the active site and reaction mechanism for heterogeneous nucleation of the earliest calcium phosphate oligomer/phase. The active site is the planar, cyclic, silicate trimer (Si3O9) on the (001) face of psW. The trimer has three silanol groups (>SiOH) arranged at 60 degrees from each other, providing a stereochemical match for O atoms bonded to Ca2+ on the (001) face of hydroxyapatite. Calcium phosphate nucleation is modeled in steps as hydrolysis of surface Ca-O bonds with leaching of Ca2+ into solution, protonation of the surface Si-O groups to form silanols, calcium sorption as an inner-sphere surface complex and, attachment of HPO4(2-). Our model explains the experimental solution and high resolution transmission electron microscopy data for epitaxial hydroxyapatite growth on psW in vitro and in vivo. We propose that the cyclic silicate trimer is the universal active site for heterogeneous, stereochemically promoted nucleation on silicate-based bioactive ceramics. A critical active site-density and a point of zero charge of the bioceramic less than physiological pH are required for bioactivity.

Aluminum↗

PubMed2004

The structure of a yeast RNA-editing deaminase provides insight into the fold and function of activation-induced deaminase and APOBEC-1.

Activation-induced deaminase (AID) uses base deamination for class-switch recombination and somatic hypermutation and is related to the mammalian RNA-editing enzyme apolipoprotein B editing catalytic subunit 1 (APOBEC-1). CDD1 is a yeast ortholog of APOBEC-1 that exhibits cytidine deaminase and RNA-editing activity. Here, we present the crystal structure of CDD1 at 2.0-A resolution and its use in comparative modeling of APOBEC-1 and AID. The models explain dimerization and the need for trans-acting loops that contribute to active site formation. Substrate selectivity appears to be regulated by a central active site "flap" whose size and flexibility accommodate large substrates in contrast to deaminases of pyrimidine metabolism that bind only small nucleosides or free bases. Most importantly, the results suggested both AID and APOBEC-1 are equally likely to bind single-stranded DNA or RNA, which has implications for the identification of natural AID targets.

APOBEC-1 Deaminase↗

PubMed1983

Involvement of reverse transcription in the replication of cauliflower mosaic virus: a detailed model and test of some aspects.

A model is presented according to which cauliflower mosaic virus (CaMV) DNA is replicated via an RNA intermediate. The model explains the typical S1 nuclease-sensitive sites in mature CaMV DNA, the occurrence of the large, terminally redundant transcript, the local separation of CaMV transcription and CaMV assembly, the abundance of knotted CaMV DNA forms, and the high recombination frequency. A site of perfect homology to plant tRNA was detected. Extracts from a mixture of nuclei and inclusion bodies can be separated into fast-sedimenting complexes elongating endogenous CaMV RNA, and slow-sedimenting ones elongating endogenous CaMV DNA. The CaMV DNA synthesis can be partly inhibited both by RNAase and actinomycin D, suggesting the presence of a mixture of RNA- and DNA-templates.

DNA Replication↗

PubMed1998

Psychological distress and use of ambulatory medical services in the Quebec Medicare system.

OBJECTIVE: To document the impact of psychological distress symptoms on the use of ambulatory medical services in a universal insurance coverage context. DATA SOURCES: Data from the Quebec Health Survey (1987) linked with billing data from the Quebec Medicare system. The time frame for the utilization variables is one year before and one year after the QHS survey. STUDY DESIGN: LISREL was used to test a model introducing perceived health need as an explanatory factor of the relationship between psychological distress and the number of visits to a physician. Two samples were formed from the matched file. Sample A (n = 2,000) was used in an exploratory phase to adequately specify the model. Sample B (n = 2,000) was used to confirm the results obtained with Sample A. PRINCIPAL FINDINGS: The proposed model explained 35 percent of the number of visits to a physician in Sample A and 24 percent in Sample B. The effect of psychological distress symptoms on the respondent's perceived health need was as important as the effect of physical health status. The effect of the respondent's previous health services utilization on the number of visits to a physician was also significant. CONCLUSIONS: These results may be interpreted to indicate that in a universal insurance coverage context, psychological distress is a significant predictor of perceived health need.

Adolescent↗

PubMed2001

Determinants of fasting glucose in young Guatemalan adults.

OBJECTIVE: To examine correlates of fasting glucose, a precursor for type 2 diabetes mellitus, in young adults in Guatemala, a country undergoing an epidemiologic transition. DESIGN: Cross-sectional. METHODS: Anthropometric, lifestyle, dietary, serum lipid, and socioeconomic characteristic data were collected on 189 men and 201 women (mean age 24.4 years) born in four villages in Eastern Guatemala. We used linear regression to identify parsimonious predictive models, including 2-way interactions. RESULTS: In men, mean fasting glucose was 87.3 mg/dL (SD 10.2); our model explained 30% of variance. Body mass index (BMI), abdomen-to-hip ratio (AHR), and total cholesterol showed graded positive effects. BMI and AHR interacted (P<.001); men with high BMI and high AHR had the highest fasting glucose levels. No dietary factors independently predicted fasting glucose. In women, mean fasting glucose was 83.9 mg/dL (SD 8.5); 22% of variance was explained by BMI, energy-adjusted fat intake, physical activity, birth village, and current residence (rural/urban). BMI and fasting glucose were positively related. Urban residence interacted with birth village (P=.06) and physical activity (P=.13). CONCLUSIONS: The major conclusion drawn from this study is that increased adiposity, even among lean individuals, is the largest environmental predictor of fasting glucose. Prevention and control of obesity in young adults in transitioning countries are key strategies for the prevention of diabetes.

Adult↗

PubMed2005

Evaluation of a level of response to alcohol-based structural equation model in adolescents.

OBJECTIVE: A low level of response (LR) to alcohol relates to a family history of alcoholism and predicts future heavier drinking and alcohol-related problems. The current analyses evaluate how LR functions within the context of a Social Information Processing Model, using 238 subjects aged 13 to 19 years from the Collaborative Study on the Genetics of Alcoholism (COGA). METHOD: A structural equation model (SEM) was used to evaluate the relationship among (1) a family history (FH) of alcoholism, (2) the LR to alcohol, (3) expectations as measured by the Alcohol Expectancy Questionnaire and (4) the recent pattern of drinking among parents in the home as predictors of the maximum recent quantity of drinking, the maximum number of drinks ever consumed in 24 hours and the number of alcohol problems in the teenage subjects. RESULTS: When tested in the SEM, LR functioned as a mediator of the relationship between an FH of alcoholism and alcoholic outcome, and expectancy functioned as a partial mediator of the relationship between LR and outcome. Invariance testing revealed that the SEM performed similarly in light and heavy drinkers, the two sexes, and older versus young subjects. Both the measurement model and SEM had good characteristics of fit, and direct paths within the model explained 49% of the variance of outcome. CONCLUSIONS: Consistent with results from the San Diego Prospective Study, when tested in the more heterogeneous COGA population, LR functioned as a mediator of the relationship between the FH and alcoholic outcome. In these adolescents, LR not only had a direct relationship to alcoholic outcome but, in contrast to prior results in adults, also appeared to operate through expectations of the effects of alcohol in predicting heavier drinking and a higher rate of alcohol-related problems among teenagers.

Adolescent↗

PubMed1999

Complementary therapies and cancer care: an overview.

The use of complementary therapies by patients with cancer is increasingly common, despite limited evidence for their efficacy and safety. The widespread use of complementary therapies has major implications for research and practice. In this paper, we provide an overview of the current state of knowledge regarding issues related to the use of complementary therapies by patients with cancer. So far, complementary therapies have not been defined very well, which makes it difficult to assess the precise extent of their use. The difference in philosophy underlying conventional and complementary treatments appears to contribute to the attractiveness of complementary therapies. Conventional medical practitioners are beginning to recognize the importance of many of the elements of this philosophy, which is evidenced in the patient-centered model. Explaining how patients with cancer make the decision to use complementary therapies has been the subject of many studies. However, as yet, no formal theory of decision making has been developed. Communication between patients and physicians about complementary therapies is an important part of the patients' decision-making process. Many gaps can be identified in knowledge of complementary therapy use by patients with cancer. Not only is there a need to increase knowledge by conducting more research and improving the research infrastructure, but attention should also be paid to information dissemination, education, and planning and development of health policies.

Communication↗

PubMed1998

The consequences of universalizing health services: children's use of health services in Catalonia.

The purpose of this study was to assess the role of needs and social factors in the use of health services among children under age 15 in Catalonia, Spain, where health care reform was explicitly designed to facilitate universal access to primary care according to health needs. Data from the Catalan Health Interview Survey of 1994, a multistage probability sample (2,433 children under 15 years old), were analyzed. Multiple regression examined the relationship between health needs and number of visits in the last year, controlling for the effect of sociodemographic characteristics. Two logistic regression equations were selected to predict heavy (more than seven visits per year) and light (less than two visits) utilization of services. The multiple regression model explained 14.3 percent of the variance in number of visits, with health status perception, disability, reported chronic condition, restriction of activities, and having had a recent accident by far the most important determinants. No familial socioeconomic characteristics, including social class, education, or family size, influenced the extent of use. In contrast to health systems not designed to achieve either universal access according to need or strong primary care, universal access to health services in Catalonia appears to enhance the use of services among children with health needs, regardless of socioeconomic characteristics.

Adolescent↗

PubMed1990

[Longitudinal analysis of the development of pulmonary function in childhood].

In order to evaluate, longitudinally, the development of pulmonary function in childhood, maximal expiratory flow volume (MEFV) curves, height, and weight of 441 fourth grade school children were measured in 1980, and again two and four years later. The same instruments were used to measure pulmonary function, height, and weight in all three surveys. In addition, pulmonary function tests were performed by the same examiner in all three surveys. Three hundred and twenty five children had acceptable results for MEFV curves at all of three surveys. Two simple linear models were fitted to the distribution of pulmonary function measurements. One has age, height, functional level of the individual child, and the interaction of age and height as explanatory variables. In the other model, the natural logarithm of pulmonary function measurements was considered as a dependent variable, and age, height, and functional level of the individual child were employed as explanatory variables. The models explained the distribution of forced vital capacity (FVC), forced expiratory volume in one second (FEV1), and maximal expiratory flows (MEFs) quite well both in males and in females. These results suggest that the development of FVC and FEV1 against height was not linear, and that age was an independent contributor to the development even after adjusting for height. Tracking in the development of MEFs as well as FVC and FEV1 was observed, suggesting that functional development of MEFs for an individual child could be evaluated accurately utilizing percentile curves as in the case of FVC and FEV1.

Adolescent↗